Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/staden/staden_2.0.0+b11-4+b1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/staden-2.0.0+b11-4+b13tb_3szx/staden_2.0.0+b11-4+b1_amd64.buildinfo Get source package info: staden=2.0.0+b11-4 Source URL: http://snapshot.notset.fr/mr/package/staden/2.0.0+b11-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-1 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-6 binutils=2.34-8 binutils-common=2.34-8 binutils-x86-64-linux-gnu=2.34-8 bsdmainutils=11.1.2+b1 bsdutils=1:2.35.1-5 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.3.0-13 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.1 debianutils=4.9.1 dh-autoreconf=19 dh-strip-nondeterminism=1.8.0-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0-1 fontconfig-config=2.13.1-4.2 fonts-dejavu-core=2.37-1 g++=4:9.2.1-3.1 g++-9=9.3.0-13 gcc=4:9.2.1-3.1 gcc-10-base=10.1.0-2 gcc-9=9.3.0-13 gcc-9-base=9.3.0-13 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.4-1 groff-base=1.22.4-5 gzip=1.10-2 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 itcl3=3.4.3-3+b1 itcl3-dev=3.4.3-3+b1 itk3=3.4.2-3+b1 itk3-dev=3.4.2-3+b1 iwidgets4=4.1.1-2 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan5=9.3.0-13 libatomic1=10.1.0-2 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3 libaudit1=1:2.8.5-3+b1 libbinutils=2.34-8 libblkid1=2.35.1-5 libbrotli1=1.0.7-6.1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libbz2-dev=1.0.8-2 libc-bin=2.30-8 libc-dev-bin=2.30-8 libc6=2.30-8 libc6-dev=2.30-8 libcap-ng0=0.7.9-2.1+b2 libcc1-0=10.1.0-2 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.16-1 libcrypt1=1:4.4.16-1 libctf-nobfd0=2.34-8 libctf0=2.34-8 libcurl3-gnutls=7.68.0-1 libcurl4-gnutls-dev=7.68.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.252 libdebhelper-perl=13.1 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libexpat1=2.2.9-1 libexpat1-dev=2.2.9-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.8.0-1 libfontconfig-dev=2.13.1-4.2 libfontconfig1=2.13.1-4.2 libfontconfig1-dev=2.13.1-4.2 libfreetype-dev=2.10.1-2 libfreetype6=2.10.1-2 libfreetype6-dev=2.10.1-2 libgcc-9-dev=9.3.0-13 libgcc-s1=10.1.0-2 libgcrypt20=1.8.5-5 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.64.2-1 libgmp10=2:6.2.0+dfsg-4 libgnutls30=3.6.13-2 libgomp1=10.1.0-2 libgpg-error0=1.37-1 libgssapi-krb5-2=1.17-7 libhogweed5=3.5.1+really3.5.1-2 libhtscodecs-dev=0.5-3 libhtscodecs2=0.5-3 libice-dev=2:1.0.9-2 libice6=2:1.0.9-2 libicu63=63.2-3 libidn2-0=2.3.0-1 libisl22=0.22.1-1 libitm1=10.1.0-2 libk5crypto3=1.17-7 libkeyutils1=1.6.1-2 libkrb5-3=1.17-7 libkrb5support0=1.17-7 libldap-2.4-2=2.4.50+dfsg-1 libldap-common=2.4.50+dfsg-1 liblsan0=10.1.0-2 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.35.1-5 libmpc3=1.1.0-1 libmpfr6=4.0.2-1 libncurses-dev=6.2-1 libncurses5-dev=6.2-1 libncurses6=6.2-1 libncursesw6=6.2-1 libnettle7=3.5.1+really3.5.1-2 libnghttp2-14=1.40.0-1 libp11-kit0=0.23.20-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-12+b1 libperl5.30=5.30.2-1 libpipeline1=1.5.2-2 libpng-dev=1.6.37-2 libpng16-16=1.6.37-2 libpsl5=0.21.0-1 libpthread-stubs0-dev=0.4-1 libquadmath0=10.1.0-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.4.3-1+b1 libselinux1=3.0-1+b3 libsigsegv2=2.12-2 libsm-dev=2:1.2.3-1 libsm6=2:1.2.3-1 libsmartcols1=2.35.1-5 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1g-1 libstaden-read-dev=1.14.12-2 libstaden-read14=1.14.12-2 libstdc++-9-dev=9.3.0-13 libstdc++6=10.1.0-2 libsub-override-perl=0.09-2 libsystemd0=245.5-3 libtasn1-6=4.16.0-2 libtcl8.6=8.6.10+dfsg-1 libtinfo6=6.2-1 libtk8.6=8.6.10-1 libtool=2.4.6-14 libtsan0=10.1.0-2 libubsan1=10.1.0-2 libuchardet0=0.0.6-3 libudev1=245.5-3 libunistring2=0.9.10-2 libuuid1=2.35.2-1 libx11-6=2:1.6.9-2+b1 libx11-data=2:1.6.9-2 libx11-dev=2:1.6.9-2+b1 libxau-dev=1:1.0.8-1+b2 libxau6=1:1.0.8-1+b2 libxcb1=1.14-2 libxcb1-dev=1.14-2 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext-dev=2:1.3.3-1+b2 libxext6=2:1.3.3-1+b2 libxft-dev=2.3.2-2 libxft2=2.3.2-2 libxml2=2.9.10+dfsg-5 libxrender-dev=1:0.9.10-1 libxrender1=1:0.9.10-1 libxss-dev=1:1.2.3-1 libxss1=1:1.2.3-1 libxt-dev=1:1.1.5-1+b3 libxt6=1:1.1.5-1+b3 linux-libc-dev=5.6.7-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-2+b1 man-db=2.9.1-1 mawk=1.3.4.20200120-2 ncurses-base=6.2-1 ncurses-bin=6.2-1 patch=2.7.6-6 perl=5.30.2-1 perl-base=5.30.2-1 perl-modules-5.30=5.30.2-1 pkg-config=0.29.2-1 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-3 tar=1.30+dfsg-7 tcl=8.6.9+1+b1 tcl-dev=8.6.9+1+b1 tcl8.6=8.6.10+dfsg-1 tcl8.6-dev=8.6.10+dfsg-1 tk=8.6.9+1+b1 tk-dev=8.6.9+1+b1 tk8.6=8.6.10-1 tk8.6-dev=8.6.10-1 tklib=0.7-2 tzdata=2020a-1 ucf=3.0041 util-linux=2.35.1-5 uuid-dev=2.35.2-1 x11-common=1:7.7+20 x11proto-core-dev=2020.1-1 x11proto-dev=2020.1-1 x11proto-scrnsaver-dev=2020.1-1 x11proto-xext-dev=2020.1-1 xorg-sgml-doctools=1:1.11-1 xtrans-dev=1.4.0-1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200522T084859Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200520T205149Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d staden=2.0.0+b11-4 && mkdir -p /build/staden-5my1Zk && dpkg-source --no-check -x /*.dsc /build/staden-5my1Zk/staden-2.0.0+b11 && cd /build/staden-5my1Zk/staden-2.0.0+b11 && { printf '%s' 'staden (2.0.0+b11-4+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libstaden-read14 -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 21 May 2020 16:12:04 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/staden-5my1Zk" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/staden-5my1Zk/staden-2.0.0+b11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1590077524" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/staden-5my1Zk /tmp/staden-2.0.0+b11-4+b13tb_3szx bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200520T205149Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.a0vGgZY_vO as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.a0vGgZY_vO Reading package lists... Building dependency tree... util-linux is already the newest version (2.35.1-5). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20200520T205149Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200520T205149Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (820 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4482 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.30-8) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20200522T084859Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200520T205149Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.a0vGgZY_vO Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200522T084859Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20200520T205149Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20200522T084859Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200522T084859Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200522T084859Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20200522T084859Z unstable/main amd64 Packages [11.2 MB] Fetched 33.9 MB in 29s (1172 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.a0vGgZY_vO I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d staden=2.0.0+b11-4 && mkdir -p /build/staden-5my1Zk && dpkg-source --no-check -x /*.dsc /build/staden-5my1Zk/staden-2.0.0+b11 && cd /build/staden-5my1Zk/staden-2.0.0+b11 && { printf '%s' 'staden (2.0.0+b11-4+b1) sid; urgency=low, binary-only=yes * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild against libstaden-read14 -- amd64 / i386 Build Daemon (x86-ubc-01) Thu, 21 May 2020 16:12:04 +0000 '; cat debian/changelog; } > debian/changelog.debrebuild && mv debian/changelog.debrebuild debian/changelog && chown -R builduser:builduser /build/staden-5my1Zk"' exec /tmp/mmdebstrap.a0vGgZY_vO Reading package lists... NOTICE: 'staden' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/staden.git Please use: git clone https://salsa.debian.org/med-team/staden.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 4773 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main staden 2.0.0+b11-4 (dsc) [2218 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main staden 2.0.0+b11-4 (tar) [4755 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main staden 2.0.0+b11-4 (diff) [16.3 kB] Fetched 4773 kB in 4s (1175 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'staden_2.0.0+b11-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting staden in /build/staden-5my1Zk/staden-2.0.0+b11 dpkg-source: info: unpacking staden_2.0.0+b11.orig.tar.gz dpkg-source: info: unpacking staden_2.0.0+b11-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying make_help_menus_work.patch dpkg-source: info: applying fix_tcl_path.patch dpkg-source: info: applying fix_awk.patch dpkg-source: info: applying enable_setting_stadenroot.patch dpkg-source: info: applying include_xalloc.patch dpkg-source: info: applying use_mkstemp_instead_of_tmpnam.patch dpkg-source: info: applying fix_implicit_declaration.patch dpkg-source: info: applying autoconfig.patch dpkg-source: info: applying spelling.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/staden-5my1Zk/staden-2.0.0+b11 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1590077524" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.a0vGgZY_vO dpkg-buildpackage: info: source package staden dpkg-buildpackage: info: source version 2.0.0+b11-4+b1 dpkg-buildpackage: info: source distribution sid dpkg-buildpackage: info: source changed by amd64 / i386 Build Daemon (x86-ubc-01) dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11' make spotless || true make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11' make[2]: *** No rule to make target 'spotless'. Stop. make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11' rm -f config.log config.status rm -f Makefile shlib.conf staden_config.h system.mk find -name debian -prune -o -name .dir -exec rm '{}' ';' make[1]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_auto_configure -- \ --with-itcl=/usr/lib/tcltk/x86_64-linux-gnu \ --with-itk=/usr/lib/tcltk/x86_64-linux-gnu ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-itcl=/usr/lib/tcltk/x86_64-linux-gnu --with-itk=/usr/lib/tcltk/x86_64-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for gawk... no checking for mawk... mawk checking for curl-config... /usr/bin/curl-config checking for the version of libcurl... 7.68.0 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking lzma.h usability... yes checking lzma.h presence... yes checking for lzma.h... yes checking for png_create_write_struct in -lpng... yes checking png.h usability... yes checking png.h presence... yes checking for png.h... yes checking for staden-io_lib-config... no checking for io_lib-config... /usr/bin/io_lib-config checking if io_lib version >= 1.12.5... yes checking io_lib/Read.h usability... yes checking io_lib/Read.h presence... yes checking for io_lib/Read.h... yes checking for mvwprintw in -lncurses... yes checking ncurses.h usability... yes checking ncurses.h presence... yes checking for ncurses.h... yes checking for ANSI C header files... (cached) yes checking for sys/wait.h that is POSIX.1 compatible... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for zlib.h... (cached) yes checking pwd.h usability... yes checking pwd.h presence... yes checking for pwd.h... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for library containing cos... -lm checking for popen... yes checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking whether byte ordering is bigendian... no checking for inline... inline checking for correct TEA configuration... ok (TEA 3.9) configure: configuring staden 2.0.0b11-2016 checking for Tcl configuration... found /usr/lib/tclConfig.sh checking for existence of /usr/lib/tclConfig.sh... loading checking platform... unix checking for Tk configuration... found /usr/lib/tkConfig.sh checking for existence of /usr/lib/tkConfig.sh... loading checking for ranlib... ranlib checking if 64bit support is requested... no checking if 64bit Sparc VIS support is requested... no checking if compiler supports visibility "hidden"... yes checking if rpath support is requested... yes checking system version... Linux-5.10.0-8-amd64 checking for ar... ar checking for SEH support in compiler... no checking for EXCEPTION_DISPOSITION support in include files... no checking for winnt.h that ignores VOID define... no checking for cast to union support... yes checking for required early compiler flags... none checking for 64-bit integer type... using long checking for tclsh... /usr/bin/tclsh8.6 checking for Tcl public headers... /usr/include/tcl8.6 checking for Tcl private include files... Using srcdir found in tclConfig.sh: /usr/include/tcl8.6/tcl-private checking for Tk public headers... /usr/include/tcl8.6 checking for Tk private include files... Using srcdir found in tkConfig.sh: /usr/include/tcl8.6/tk-private checking tklib directory... yes (/usr/share/tcltk/tklib0.7) checking iwidgets directory... yes (/usr/share/tcltk/iwidgets4.1.0) checking itcl directory... vers=/3004000/ yes (/usr/lib/tcltk/x86_64-linux-gnu/itcl3.4) checking itk directory... yes (/usr/lib/tcltk/x86_64-linux-gnu/itk3.4) configure: creating ./config.status config.status: creating Makefile config.status: creating system.mk config.status: creating shlib.conf config.status: creating gap5/gap5 config.status: creating gap5/tg_view config.status: creating gap5/tg_index config.status: creating gap5/gap5_cmd config.status: creating gap4/gap4 config.status: creating copy_reads/copy_reads config.status: creating trev/trev config.status: creating prefinish/prefinish config.status: creating pregap4/pregap4 config.status: creating spin/spin config.status: creating staden_config.h ---------------------------------------------------------------------- External packages used: curl: via /usr/bin/curl-config zlib: DIR (system) curses: DIR (system) liblzma: DIR io_lib: via /usr/bin/io_lib-config Tcl: via /usr/lib/tclConfig.sh Tk: via /usr/lib/tkConfig.sh tklib: /usr/share/tcltk/tklib0.7 Iwidgets: /usr/share/tcltk/iwidgets4.1.0 Itcl: /usr/lib/tcltk/x86_64-linux-gnu/itcl3.4 Itk: /usr/lib/tcltk/x86_64-linux-gnu/itk3.4 ---------------------------------------------------------------------- make[1]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_auto_build -a make -j4 make[1]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11' cd Misc && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./Misc/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./Misc SUBDIR=Misc all cd trev && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./trev/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./trev SUBDIR=trev all cd primer3 && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./primer3/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./primer3 SUBDIR=primer3 all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/Misc' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/trev' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/primer3' make[2]: warning: -j4 forced in submake: resetting jobserver mode. cd primer3/src && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/primer3/src' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/primer3' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/trev' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o crash.o -c crash.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o date.o -c date.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filenames.o -c filenames.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o files.o -c files.c cd pregap4 && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 all gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_lib.o -c primer3_lib.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_release.o -c primer3_release.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligotm.o -c oligotm.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -o dpal_primer.o -c dpal.c make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/pregap4' make[2]: warning: -j4 forced in submake: resetting jobserver mode. cd spin_emboss && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss all /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/spin_emboss' make[2]: warning: -j4 forced in submake: resetting jobserver mode. Nothing to build for Pregap4. make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/pregap4' /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' cd scripts && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./scripts SUBDIR=scripts all Nothing to build for spin_emboss. make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/spin_emboss' make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/scripts' make[2]: warning: -j4 forced in submake: resetting jobserver mode. cd data && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./data/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./data SUBDIR=data all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/data' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o format_output.o -c format_output.c /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' /build/staden-5my1Zk/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-5my1Zk/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' Nothing to build for scripts. make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/scripts' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find.o -c find.c Nothing to build for data. make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/data' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shell.o -c shell.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strings.o -c strings.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o usleep.o -c usleep.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o error.o -c error.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xerror.o -c xerror.c In file included from /usr/include/string.h:495, from strings.c:4: In function ‘strncpy’, inlined from ‘c2fstr’ at strings.c:31:5: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from strings.c:1: strings.c: In function ‘c2fstr’: strings.c:30:18: note: length computed here 30 | i = min((int)strlen(c),max_f); | ^~~~~~~~~ misc.h:87:23: note: in definition of macro ‘min’ 87 | #define min(A,B) ( ( (A) < (B) ) ? (A) : (B) ) | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o xalloc.o -c xalloc.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vlen.o -c vlen.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o boulder_input.o -c boulder_input.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o FtoC.o -c FtoC.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o getfile.o -c getfile.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bitmap.o -c bitmap.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array.o -c array.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o locks.o -c locks.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o array_arith.o -c array_arith.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_db.o -c parse_db.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstring.o -c dstring.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o string_alloc.o -c string_alloc.c parse_db.c: In function ‘parse_entry’: parse_db.c:234:52: warning: ‘%s’ directive writing up to 8191 bytes into a region of size 8162 [-Wformat-overflow=] 234 | sprintf(buf, "Warning - unknown identifier \"%s\"\n",word); | ^~ ~~~~ In file included from /usr/include/stdio.h:867, from parse_db.c:19: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 33 and 8224 bytes into a destination of size 8192 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p /build/staden-5my1Zk/staden-2.0.0+b11/lib 2>/dev/null touch /build/staden-5my1Zk/staden-2.0.0+b11/lib/.dir gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primer3_main.o -c primer3_main.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strtol64.o -c strtol64.c primer3_main.c: In function ‘pr_safe_malloc’: primer3_main.c:520:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 520 | write(2, pr_program_name, pr_program_name_len), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro ‘OOM_ERROR’ 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ primer3_main.c:521:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 521 | write(2, OOM_MESSAGE, OOM_MESSAGE_LEN), \ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ primer3_main.c:528:20: note: in expansion of macro ‘OOM_ERROR’ 528 | if (NULL == r) OOM_ERROR; | ^~~~~~~~~ primer3_main.c: In function ‘boulder_print_oligos’: primer3_main.c:416:25: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] 416 | else sprintf(suffix, "_%d", i); | ^~ primer3_main.c:416:23: note: directive argument in the range [1, 2147483646] 416 | else sprintf(suffix, "_%d", i); | ^~~~~ In file included from /usr/include/stdio.h:867, from primer3_main.c:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 3 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libmisc.so crash.o date.o filenames.o files.o find.o shell.o strings.o usleep.o error.o xerror.o xalloc.o vlen.o FtoC.o getfile.o bitmap.o array.o locks.o array_arith.o parse_db.o dstring.o string_alloc.o strtol64.o -lm primer3_main.c: In function ‘main’: primer3_main.c:234:25: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 2 [-Wformat-overflow=] 234 | else sprintf(suffix, "_%d", i); | ^~ primer3_main.c:234:23: note: directive argument in the range [1, 2147483647] 234 | else sprintf(suffix, "_%d", i); | ^~~~~ In file included from /usr/include/stdio.h:867, from primer3_main.c:7: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 3 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/Misc' cd tk_utils && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils all cd text_utils && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./text_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils SUBDIR=text_utils all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/text_utils' make[2]: warning: -j4 forced in submake: resetting jobserver mode. cd abi && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./abi/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./abi SUBDIR=abi all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/tk_utils' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/abi' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs.o -c text_output_stubs.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output_stubs2.o -c text_output_stubs2.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./abi -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o abiIO.o -c abiIO.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cli_arg.o -c cli_arg.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./abi -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o getABISampleName.o -c getABISampleName.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tclXkeylist.o -c tclXkeylist.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./abi -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIcomment.o -c getABIcomment.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tclXutil.o -c tclXutil.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_utils.o -c tcl_utils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./abi -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIdate.o -c getABIdate.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./abi -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o getABIfield.o -c getABIfield.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libtext_utils.so text_output_stubs.o text_output_stubs2.o -lmisc gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_debug.o -c tcl_debug.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/text_utils' cd alf && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./alf/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./alf SUBDIR=alf all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/alf' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABISampleName abiIO.o getABISampleName.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./alf -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o alfsplit.o -c alfsplit.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIcomment abiIO.o getABIcomment.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIdate abiIO.o getABIdate.o -lmisc -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o misc.o -c misc.c alfsplit.c: In function ‘main’: alfsplit.c:347:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 347 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:363:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 363 | fread (buf,512,1,inData) ; | ^~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c: In function ‘readIndexEntry’: alfsplit.c:129:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 129 | fread (ent->label,40,1,fil) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ alfsplit.c:135:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] 135 | fread (junk,70,1,fil) ; | ^~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text_output.o -c text_output.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkRaster.o -c tkRaster.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkRasterBuiltIn.o -c tkRasterBuiltIn.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o getABIfield abiIO.o getABIfield.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o alfsplit alfsplit.o -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sheet.o -c sheet.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/alf' cd g && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./g/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./g SUBDIR=g all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/g' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/abi' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o freetree.o -c freetree.c In file included from tkRaster.c:45: tkRaster.c: In function ‘DrawEnvIndex’: tkRaster.c:2266:62: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2266 | entryPtr = Tcl_FindHashEntry (&(RasterPtr->drawEnvTable), (char*)drawenvno); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2587:53: note: in definition of macro ‘Tcl_FindHashEntry’ 2587 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ tkRaster.c: In function ‘CreateDrawEnv’: tkRaster.c:2353:8: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2353 | (char*) (RasterPtr->drawEnvCount), | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2590:55: note: in definition of macro ‘Tcl_CreateHashEntry’ 2590 | (*((tablePtr)->createProc))(tablePtr, (const char *)(key), newPtr) | ^~~ tkRaster.c: In function ‘DestroyDrawEnv’: tkRaster.c:2381:6: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2381 | (char*)(drawenvptr->index)); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2587:53: note: in definition of macro ‘Tcl_FindHashEntry’ 2587 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ cd eba && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./eba/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./eba SUBDIR=eba all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/eba' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./eba -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o qual.o -c qual.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./eba -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o conf.o -c conf.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSheet.o -c tkSheet.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSheet_common.o -c tkSheet_common.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o eba qual.o conf.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trace_print.o -c trace_print.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/eba' cd init_exp && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./init_exp/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./init_exp SUBDIR=init_exp all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/init_exp' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./init_exp -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o init_exp.o -c init_exp.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DDPAL_MAX_ALIGN=36 -DMAX_PRIMER_LENGTH=36 -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libprimer3.so primer3_lib.o primer3_release.o oligotm.o dpal_primer.o format_output.o boulder_input.o -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o postscript.o -c postscript.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o split.o -c split.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o primer3_core primer3_main.o -lprimer3 -lm -lm gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o init_exp init_exp.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/primer3/src' cd get_scf_field && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./get_scf_field/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/get_scf_field' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./get_scf_field -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o get_scf_field.o -c get_scf_field.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTrace.o -c tkTrace.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libg.so g-files.o g-db.o g-struct.o freetree.o g-error.o g-io.o g-connect.o g-request.o -lmisc gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceComp.o -c tkTraceComp.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/g' make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/init_exp' cd hetins && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./hetins/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./hetins SUBDIR=hetins all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/hetins' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o get_scf_field get_scf_field.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./hetins -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o hetins.o -c hetins.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/get_scf_field' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceIO.o -c tkTraceIO.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkTraceDisp.o -c tkTraceDisp.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o capture.o -c capture.c capture.c: In function ‘tcl_capture’: capture.c:33:7: warning: implicit declaration of function ‘mkostemp’; did you mean ‘mkstemp’? [-Wimplicit-function-declaration] 33 | fd = mkostemp(NULL, 0666); | ^~~~~~~~ | mkstemp capture.c:54:5: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result [-Wunused-result] 54 | read(fd, buf, statbuf.st_size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o canvas_box.o -c canvas_box.c tkTraceDisp.c: In function ‘trace_draw_numbers’: tkTraceDisp.c:746:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 746 | sprintf(number, "%d", cind); | ^ In file included from /usr/include/stdio.h:867, from tkTraceDisp.c:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o hetins hetins.o -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/hetins' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ruler_tick.o -c ruler_tick.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzyme_map.o -c restriction_enzyme_map.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o element_canvas.o -c element_canvas.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o container.o -c container.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o container_ruler.o -c container_ruler.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tcl_io_lib.o -c tcl_io_lib.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/usr/include -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libtk_utils.so cli_arg.o tclXkeylist.o tclXutil.o tcl_utils.o tcl_debug.o misc.o init.o text_output.o tkRaster.o tkRasterBuiltIn.o sheet.o tkSheet.o tkSheet_common.o trace_print.o postscript.o split.o tkTrace.o tkTraceComp.o tkTraceIO.o tkTraceDisp.o capture.o canvas_box.o ruler_tick.o restriction_enzyme_map.o element_canvas.o container.o container_ruler.o tcl_io_lib.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lmisc -lpng -lz make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/tk_utils' cd seq_utils && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/seq_utils' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_lib_old.o -c align_lib_old.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_ss.o -c align_ss.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_ss2.o -c align_ss2.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_sv.o -c align_sv.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dna_utils.o -c dna_utils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o genetic_code.o -c genetic_code.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o renz_utils.o -c renz_utils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_formats.o -c sequence_formats.c sequence_formats.c: In function ‘get_embl_format_seq’: sequence_formats.c:729:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 729 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:738:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 738 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c: In function ‘add_feat’: sequence_formats.c:481:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 481 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ sequence_formats.c:510:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 510 | fgets(line, loc_len, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o scramble.o -c scramble.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o base_comp.o -c base_comp.c renz_utils.c: In function ‘SetREnzColour’: renz_utils.c:1049:35: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 1049 | sprintf(colour, "#%02x%02x%02x", r, g, b); | ^ In file included from /usr/include/stdio.h:867, from renz_utils.c:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 8 and 26 bytes into a destination of size 7 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o open_reading_frames.o -c open_reading_frames.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edge.o -c edge.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o search_utils.o -c search_utils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align_lib.o -c align_lib.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o filter_words.o -c filter_words.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libseq_utils.so align.o align_lib_old.o align_ss.o align_ss2.o align_sv.o dna_utils.o genetic_code.o renz_utils.o sequence_formats.o scramble.o base_comp.o open_reading_frames.o edge.o search_utils.o align_lib.o read_matrix.o filter_words.o -ltext_utils -lmisc -lm make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./mutlib/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib SUBDIR=mutlib all cd vector_clip && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./vector_clip/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip all cd spin && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./spin/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./spin SUBDIR=spin all cd screen_seq && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./screen_seq/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/mutlib' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/vector_clip' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/spin' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/screen_seq' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg.o -c seq_reg.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./vector_clip -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o vector_clip.o -c vector_clip.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_reg_cmds.o -c seq_reg_cmds.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o raster_cmds.o -c raster_cmds.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_raster.o -c seq_raster.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o align.o -c align.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o basecall.o -c basecall.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./screen_seq -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o screen_seq.o -c screen_seq.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller.o -c caller.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_snr.o -c caller_snr.cpp seq_raster.c: In function ‘GetRasterZoom’: seq_raster.c:1512:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1512 | result = (int)gen.result; | ^ g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_base.o -c caller_base.cpp seq_raster.c: In function ‘seq_raster_callback’: seq_raster.c:3012:30: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3012 | jdata->info.result = (void *)zoom; | ^ seq_raster.c:3034:24: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 3034 | jdata->info.result = (void *)zoom; | ^ seq_reg_cmds.c: In function ‘GetActiveSeqName’: seq_reg_cmds.c:919:25: warning: zero-length gnu_printf format string [-Wformat-zero-length] 919 | vTcl_SetResult(interp, ""); | ^~ raster_cmds.c: In function ‘RasterResults’: raster_cmds.c:250:9: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 250 | zoom = (int)gen.result; | ^ screen_seq.c: In function ‘get_vfilenames’: screen_seq.c:133:18: warning: ‘%s’ directive writing up to 4096 bytes into a region of size between 1 and 4097 [-Wformat-overflow=] 133 | sprintf(tmp, "%s%s", base_name, file_name); | ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:867, from screen_seq.c:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 1 and 8193 bytes into a destination of size 4097 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ screen_seq.c: In function ‘get_vfilenames_old’: screen_seq.c:180:24: warning: ‘%s’ directive writing up to 4096 bytes into a region of size between 1 and 4097 [-Wformat-overflow=] 180 | sprintf(file_name, "%s%s", base_name, file_name); | ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:867, from screen_seq.c:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 1 and 8193 bytes into a destination of size 4097 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequtils.o -c sequtils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_results.o -c seq_results.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o screen_seq screen_seq.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_sendto.o -c seq_sendto.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/screen_seq' cd qclip && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./qclip/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./qclip SUBDIR=qclip all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/qclip' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o qclip.o -c qclip.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o consen.o -c consen.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./qclip -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c seq_sendto.c: In function ‘sender_callback.part.0’: seq_sendto.c:132:19: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 893 [-Wformat-overflow=] 132 | sprintf(cmd, "upvar #0 commn_[list %s] commn; " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 137 | cursor->abspos, cursor->abspos, job); | ~~~ seq_sendto.c:135:25: note: format string is defined here 135 | "{abspos %d} {job %s}}]", | ^~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from seq_sendto.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 135 or more bytes (assuming 1158) into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caller_level.o -c caller_level.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o spin_globals.o -c spin_globals.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dnatable.o -c dnatable.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o muttag.o -c muttag.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag.o -c mutationtag.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seq_plot_funcs.o -c seq_plot_funcs.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutationtag_utils.o -c mutationtag_utils.cpp gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o qclip qclip.o consen.o seqInfo.o -ltext_utils -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o pathutil.o -c pathutil.cpp make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/qclip' cd polyA_clip && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./polyA_clip/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/polyA_clip' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o polyA_clip.o -c polyA_clip.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./polyA_clip -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o seqInfo.o -c seqInfo.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o peakcall.o -c peakcall.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stringlist.o -c stringlist.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed.o -c seqed.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagarray.o -c tagarray.cpp gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o polyA_clip polyA_clip.o seqInfo.o -lseq_utils -ltext_utils -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqed.o -c tkSeqed.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/polyA_clip' cd stops && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./stops/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./stops SUBDIR=stops all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/stops' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./stops -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o stops.o -c stops.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trace.o -c trace.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqedUtils.o -c tkSeqedUtils.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o validate.o -c validate.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkSeqedNames.o -c tkSeqedNames.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_matrix.o -c read_matrix.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_align_lib.o -c sp_align_lib.cpp gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o stops stops.o -ltext_utils -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_write.o -c seqed_write.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqedInterface.o -c seqedInterface.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_translate.o -c seqed_translate.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_alignment.o -c sp_alignment.cpp make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/stops' cd make_weights && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./make_weights/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./make_weights SUBDIR=make_weights all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/make_weights' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./make_weights -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o make_weights.o -c make_weights.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o vector_clip vector_clip.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_restriction_enzymes.o -c seqed_restriction_enzymes.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_hash_lib.o -c sp_hash_lib.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqed_search.o -c seqed_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sequence_pair_display.o -c sequence_pair_display.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/vector_clip' cd find_renz && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./find_renz/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./find_renz SUBDIR=find_renz all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/find_renz' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./find_renz -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o find_renz.o -c find_renz.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o emboss_input_funcs.o -c emboss_input_funcs.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpam.o -c readpam.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o make_weights make_weights.o -lseq_utils -ltext_utils -lmisc -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o find_renz find_renz.o -lseq_utils -ltext_utils -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm sequence_pair_display.c: In function ‘update_seqs’: sequence_pair_display.c:316:20: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 316 | sprintf(tmp, "%10d", i*10); | ^ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/tkRaster.h:9, from seq_reg.h:6, from sequence_pair_display.c:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sequence_pair_display.c:344:20: warning: ‘__builtin___sprintf_chk’ writing a terminating nul past the end of the destination [-Wformat-overflow=] 344 | sprintf(tmp, "%10d", i*10); | ^ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/tkRaster.h:9, from seq_reg.h:6, from sequence_pair_display.c:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 11 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c: In function ‘emboss_graph_callback’: emboss_input_funcs.c:260:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 260 | jdata->info.result = (void *)id; | ^ emboss_input_funcs.c: In function ‘read_emboss_data_file’: emboss_input_funcs.c:402:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 402 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:437:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 437 | fscanf(fp, "##Number %d\n", &data->n_data_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:444:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 444 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:470:6: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 470 | fscanf(fp, "##Number %d\n", &data->n_graph_obj); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:477:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 477 | fgets(line, 1024, fp); | ^~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:518:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 518 | fscanf(fp, "%lf %lf\n", &pos, &p_array[i].score); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c: In function ‘init_emboss_stick_create’: emboss_input_funcs.c:658:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 658 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:659:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 659 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ emboss_input_funcs.c:660:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 660 | fgets(dummy1, 100, fp); | ^~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/make_weights' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o compare_spans.o -c compare_spans.c cd gap5 && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 SUBDIR=gap5 all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/gap5' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/find_renz' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_iface_g.o -c tg_iface_g.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o b+tree2.o -c b+tree2.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hache_table.o -c hache_table.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_gio.o -c tg_gio.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sp_matrix.o -c sp_matrix.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_hash.o -c sip_hash.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_similar_spans.o -c sip_similar_spans.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff.o -c tracediff.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_find_identity.o -c sip_find_identity.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_cache.o -c tg_cache.c sip_similar_spans.c: In function ‘similar_spans_callback’: sip_similar_spans.c:289:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 289 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_quick_scan.o -c sip_quick_scan.c sip_find_identity.c: In function ‘identities_callback’: sip_find_identity.c:210:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 210 | jdata->info.result = (void *)id; | ^ sip_quick_scan.c: In function ‘quick_scan_callback’: sip_quick_scan.c:234:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 234 | jdata->info.result = (void *)id; | ^ g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_helper.o -c tracediff_helper.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_align.o -c sip_align.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_globals.o -c sip_globals.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_cmds.o -c sip_cmds.c sip_align.c: In function ‘align_callback’: sip_align.c:181:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 181 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_contig.o -c tg_contig.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_sequence.o -c tg_sequence.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_results.o -c sip_results.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o rescan_matches.o -c rescan_matches.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_mutations.o -c tracediff_mutations.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o probs.o -c probs.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sim.o -c sim.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sip_sim.o -c sip_sim.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_globals.o -c nip_globals.c sip_sim.c: In function ‘sim_callback’: sip_sim.c:197:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 197 | jdata->info.result = (void *)id; | ^ g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_parameters.o -c tracediff_parameters.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracediff_validate.o -c tracediff_validate.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_cmds.o -c nip_cmds.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_base_comp.o -c nip_base_comp.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign.o -c tracealign.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_cache.o -c tracealign_cache.cpp nip_base_comp.c: In function ‘plot_base_comp_callback’: nip_base_comp.c:183:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 183 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_track.o -c tg_track.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_bin.o -c tg_bin.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_gene_search.o -c nip_gene_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_trna_search.o -c nip_trna_search.c nip_gene_search.c: In function ‘plot_gene_search_callback’: nip_gene_search.c:206:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 206 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_utils.o -c tg_utils.c nip_trna_search.c: In function ‘trna_search_callback’: nip_trna_search.c:173:24: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 173 | jdata->info.result = (void *)id; | ^ g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_helper.o -c tracealign_helper.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_register.o -c tg_register.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o codon_content.o -c codon_content.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_stop_codon.o -c nip_stop_codon.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o trna_search.o -c trna_search.c nip_stop_codon.c: In function ‘nip_stop_codons_callback’: nip_stop_codon.c:195:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 195 | jdata->info.result = (void *)id; | ^ g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_interpolate.o -c tracealign_interpolate.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_preprocess.o -c tracealign_preprocess.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tracks.o -c tg_tracks.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o splice_search.o -c splice_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_anno.o -c tg_anno.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_library.o -c tg_library.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tracealign_validate.o -c tracealign_validate.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan.o -c mutscan.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_splice_search.o -c nip_splice_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_string_search.o -c nip_string_search.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_helper.o -c mutscan_helper.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_wtmatrix_search.o -c nip_wtmatrix_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_scaffold.o -c tg_scaffold.c nip_splice_search.c: In function ‘splice_search_callback’: nip_splice_search.c:183:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 183 | jdata->info.result = (void *)id; | ^ nip_string_search.c: In function ‘nip_string_search_callback’: nip_string_search.c:170:24: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 170 | jdata->info.result = (void *)id; | ^ g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_validate.o -c mutscan_validate.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_analysis.o -c mutscan_analysis.cpp nip_wtmatrix_search.c: In function ‘nip_wtmatrix_search_callback’: nip_wtmatrix_search.c:167:24: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 167 | jdata->info.result = (void *)id; | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_check.o -c tg_check.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_preprocess.o -c mutscan_preprocess.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_restriction_enzymes.o -c nip_restriction_enzymes.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mutscan_parameters.o -c mutscan_parameters.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o nip_canvas_box.o -c nip_canvas_box.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dinuc_freqs.o -c dinuc_freqs.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./spin -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libspin.so seq_reg.o seq_reg_cmds.o raster_cmds.o seq_raster.o sequtils.o seq_results.o seq_sendto.o spin_globals.o seq_plot_funcs.o seqed.o tkSeqed.o tkSeqedUtils.o tkSeqedNames.o seqed_write.o seqedInterface.o seqed_translate.o seqed_restriction_enzymes.o seqed_search.o sequence_pair_display.o emboss_input_funcs.o readpam.o compare_spans.o sip_hash.o sip_similar_spans.o sip_find_identity.o sip_quick_scan.o sip_align.o sip_globals.o sip_cmds.o sip_results.o rescan_matches.o probs.o sim.o sip_sim.o init.o nip_globals.o nip_cmds.o nip_base_comp.o nip_gene_search.o nip_trna_search.o codon_content.o nip_stop_codon.o trna_search.o splice_search.o nip_splice_search.o nip_string_search.o nip_wtmatrix_search.o nip_restriction_enzymes.o nip_canvas_box.o dinuc_freqs.o -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lseq_utils -lmisc gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/spin' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_tcl.o -c tg_tcl.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index.o -c tg_index.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap5_cmds.o -c newgap5_cmds.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap4_compat.o -c gap4_compat.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c cp /build/staden-5my1Zk/staden-2.0.0+b11/./mutlib/mutlib.def 2>&- make[2]: [/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib/Makefile:81: /build/staden-5my1Zk/staden-2.0.0+b11/lib/libmutlib.so] Error 1 (ignored) g++ -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -DMUTLIB_EXPORTS -DDYNMAT -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libmutlib.so align.o basecall.o caller.o caller_snr.o caller_base.o caller_level.o dnatable.o muttag.o mutationtag.o mutationtag_utils.o pathutil.o peakcall.o stringlist.o tagarray.o trace.o validate.o read_matrix.o sp_align_lib.o sp_alignment.o sp_hash_lib.o sp_matrix.o tracediff.o tracediff_helper.o tracediff_mutations.o tracediff_parameters.o tracediff_validate.o tracealign.o tracealign_cache.o tracealign_helper.o tracealign_interpolate.o tracealign_preprocess.o tracealign_validate.o mutscan.o mutscan_helper.o mutscan_validate.o mutscan_analysis.o mutscan_preprocess.o mutscan_parameters.o -lseq_utils -ltk_utils -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lmisc -lm -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/mutlib' cd gap4 && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 SUBDIR=gap4 all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/gap4' make[2]: warning: -j4 forced in submake: resetting jobserver mode. cd tracediff && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./tracediff/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./tracediff SUBDIR=tracediff all cd mutscan && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./mutscan/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./mutscan SUBDIR=mutscan all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/tracediff' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/mutscan' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutscan -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutscan -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o pathutil.o -c pathutil.cpp g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./tracediff -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-local.o -c gap-local.c g++ -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutscan -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o stringlist.o -c stringlist.cpp gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-remote.o -c gap-remote.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-if.o -c gap-if.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-init.o -c gap-init.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-dbstruct.o -c gap-dbstruct.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-create.o -c gap-create.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-io.o -c gap-io.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO1.o -c IO1.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io-reg.o -c io-reg.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o actf.o -c actf.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO2.o -c IO2.c g++ -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tracediff main.o -lmutlib -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lseq_utils -ltext_utils -lmisc -lm actf.c: In function ‘actf_lock’: actf.c:246:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result] 246 | write(fd, db_path, strlen(db_path)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o mutscan main.o pathutil.o stringlist.o -lmutlib -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltext_utils -lmisc -lm /usr/bin/ld: warning: libtk_utils.so, needed by /build/staden-5my1Zk/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/tracediff' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o seqInfo.o -c seqInfo.c /usr/bin/ld: warning: libtk_utils.so, needed by /build/staden-5my1Zk/staden-2.0.0+b11/lib/libmutlib.so, not found (try using -rpath or -rpath-link) gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/mutscan' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o parse_ft.o -c parse_ft.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o IO3.o -c IO3.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_utils.o -c io_utils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-error.o -c gap-error.c io_utils.c: In function ‘template_name_to_number’: io_utils.c:38:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 38 | return (int)Tcl_GetHashValue(hash); | ^ io_utils.c: In function ‘read_name_to_number’: io_utils.c:84:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 84 | return (int)Tcl_GetHashValue(hash); | ^ In file included from IO1.h:50, from io_utils.h:6, from io_utils.c:6: io_utils.c: In function ‘cache_template_name’: io_utils.c:549:25: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 549 | Tcl_SetHashValue(hash, (ClientData)number); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2573:69: note: in definition of macro ‘Tcl_SetHashValue’ 2573 | #define Tcl_SetHashValue(h, value) ((h)->clientData = (ClientData) (value)) | ^~~~~ io_utils.c: In function ‘cache_read_name’: io_utils.c:566:25: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 566 | Tcl_SetHashValue(hash, (ClientData)number); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2573:69: note: in definition of macro ‘Tcl_SetHashValue’ 2573 | #define Tcl_SetHashValue(h, value) ((h)->clientData = (ClientData) (value)) | ^~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stack_dump.o -c stack_dump.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o io_handle.o -c io_handle.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkAppInit.o -c tkAppInit.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap-tcl.o -c gap-tcl.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tk-io-reg.o -c tk-io-reg.c tk-io-reg.c: In function ‘tk_contig_register_cmd’: tk-io-reg.c:965:15: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 895 and 964 [-Wformat-overflow=] 965 | sprintf(buf, "{id %d} {seq %"PRIrec"} {pos %d} {abspos %d} {refs %d} " | ^~~~~~~~~~~~~~~~ ...... 973 | job); | ~~~ tk-io-reg.c:966:22: note: format string is defined here 966 | "{sent_by %d} {job %s}", | ^~ In file included from /usr/include/stdio.h:867, from tk-io-reg.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 62 and 1154 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_cli_arg.o -c gap_cli_arg.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_globals.o -c gap_globals.c tk-io-reg.c: In function ‘tk_result_is_consistency’: tk-io-reg.c:604:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 604 | if (args.cons_id == (int)gen.data) { | ^ tk-io-reg.c: In function ‘tk_contig_register_cmd’: tk-io-reg.c:1031:15: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 904 and 964 [-Wformat-overflow=] 1031 | sprintf(buf, "{id %d} {seq %d} {pos %d} {abspos %d} {refs %d} " | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 1039 | job); | ~~~ tk-io-reg.c:1032:22: note: format string is defined here 1032 | "{sent_by %d} {job %s}", | ^~ In file included from /usr/include/stdio.h:867, from tk-io-reg.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 62 and 1145 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o newgap_cmds.o -c newgap_cmds.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o init.o -c init.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consen.o -c consen.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consensus.o -c consensus.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_hash.o -c gap_hash.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_depth.o -c read_depth.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qual.o -c qual.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o qualIO.o -c qualIO.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_range.o -c gap_range.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depth_track.o -c depth_track.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o bubbl3.o -c bubbl3.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagdb.o -c tagdb.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notedb.o -c notedb.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_draw.o -c template_draw.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o active_tags.o -c active_tags.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dbcheck.o -c dbcheck.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tag_plot.o -c tag_plot.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clones.o -c clones.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o extract.o -c extract.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o preass.o -c preass.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list.o -c list.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reactions.o -c reactions.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o probe.o -c probe.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template.o -c template.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_contigs.o -c export_contigs.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o export_snps.o -c export_snps.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o template_display.o -c template_display.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ruler_display.o -c ruler_display.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash.o -c hash.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_array.o -c gap_array.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o import_gff.o -c import_gff.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o show_relationships.o -c show_relationships.c find_oligo.c: In function ‘StringMatch’: find_oligo.c:957:19: warning: ‘%ld’ directive writing between 1 and 19 bytes into a region of size 10 [-Wformat-overflow=] 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); | ^~~ find_oligo.c:957:20: note: format string is defined here 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); find_oligo.c:957:19: note: directive argument in the range [0, 9223372036854775807] 957 | sprintf(name1, "%"PRIrec"", ABS(c1[j])); | ^~~ In file included from /usr/include/stdio.h:867, from /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/hache_table.h:5, from /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/g-struct.h:24, from /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/g.h:1, from tg_struct.h:4, from tg_gio.h:4, from io_utils.h:6, from find_oligo.c:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 20 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fij.o -c fij.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o hash_lib.o -c hash_lib.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o do_fij.o -c do_fij.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o str_finder.o -c str_finder.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_assemble.o -c auto_assemble.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o gap_canvas_box.o -c gap_canvas_box.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dis_readings.o -c dis_readings.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_repeats.o -c find_repeats.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_extend.o -c contig_extend.c template_display.c: In function ‘template_callback’: template_display.c:2354:36: warning: ‘%s’ directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] 2354 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, t->frame, | ^~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from template_display.c:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 21 or more bytes (assuming 120) into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o break_contig.o -c break_contig.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_haplotypes.o -c find_haplotypes.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o quality_plot.o -c quality_plot.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair.o -c readpair.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_selector.o -c contig_selector.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o complement.o -c complement.c readpair.c: In function ‘readpair_obj_func’: readpair.c:175:43: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 989 and 999 [-Wformat-overflow=] 175 | sprintf(cmd, "CreateTemplateDisplay %d {%s}", | ^~ 176 | *handle, c_list); | ~~~~~~ In file included from /usr/include/stdio.h:867, from readpair.c:18: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 27 and 1060 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o cs-object.o -c cs-object.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o interval_tree.o -c interval_tree.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-files.o -c g-files.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o list_proc.o -c list_proc.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dstrand.o -c dstrand.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo_sel.o -c oligo_sel.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-db.o -c g-db.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o alter_rel.o -c alter_rel.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-struct.o -c g-struct.c oligo_sel.c: In function ‘primer_top’: oligo_sel.c:276:29: warning: ‘%s’ directive writing up to 256 bytes into a region of size between 58 and 98 [-Wformat-overflow=] 276 | sprintf(tmpbuf, "%s %s %s.%d %s %d %c", | ^~ 277 | tempname, gelname, dbname, *temnum, oligo, oligostart, | ~~~~~~ In file included from /usr/include/stdio.h:867, from oligo_sel.c:23: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 10 or more bytes (assuming 306) into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-error.o -c g-error.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-alloc.o -c g-alloc.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-io.o -c g-io.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o restriction_enzymes.o -c restriction_enzymes.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o stop_codon.o -c stop_codon.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o assemble_direct.o -c assemble_direct.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-connect.o -c g-connect.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o g-request.o -c g-request.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_view.o -c editor_view.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o check_assembly.o -c check_assembly.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_join.o -c editor_join.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_search.o -c editor_search.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU2.o -c tagU2.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o mess.o -c mess.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_oligo.o -c find_oligo.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db.o -c copy_db.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contig_order.o -c contig_order.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c copy_db.c: In function ‘copy_read_name’: copy_db.c:118:18: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 9 [-Wformat-overflow=] 118 | sprintf(num, "#%d", iter++); | ^~ copy_db.c:118:16: note: directive argument in the range [1, 2147483646] 118 | sprintf(num, "#%d", iter++); | ^~~~~ In file included from /usr/include/stdio.h:867, from copy_db.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 3 and 12 bytes into a destination of size 10 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o clip.o -c clip.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o primlib.o -c primlib.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o editor_oligo.o -c editor_oligo.c tman_display.c: In function ‘repositionSeq’: tman_display.c:279:21: warning: ‘ xview moveto ’ directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:279:18: note: assuming directive output of 12 bytes 279 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 28 and 2096 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c: In function ‘manageTrace’: tman_display.c:250:21: warning: ‘ left_cutoff ’ directive writing 13 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 250 | sprintf(buf, "%s left_cutoff %d", dc->path, leftCutOff); | ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 15 and 1048 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c:253:21: warning: ‘ right_cutoff ’ directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 253 | sprintf(buf, "%s right_cutoff %d", dc->path, leftCutOff + cutLength); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 16 and 1049 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o notes.o -c notes.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_display.o -c consistency_display.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o consistency_canvas_box.o -c consistency_canvas_box.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tg_index_common.o -c tg_index_common.c consistency_display.c: In function ‘consistency_join’: consistency_display.c:160:15: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 160 | gen.data = (void *)remove_dup; | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o baf.o -c baf.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maq.o -c maq.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o confidence_graph.o -c confidence_graph.c confidence_graph.c: In function ‘confidence_callback’: confidence_graph.c:531:26: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 531 | jdata->generic.data = (void *)conf->cons_id; | ^ confidence_graph.c:624:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 624 | confidence_join(io, c, conf, (int)jdata->generic.data); | ^ notes.c: In function ‘time_t2str’: notes.c:829:21: warning: ‘ (’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 829 | sprintf(buf, "%s (%ld)", buf2, (long)t); | ^~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from notes.c:11: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 1047 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o maqmap.o -c maqmap.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_index.o -c sam_index.c consistency_display.c: In function ‘consistency_callback’: consistency_display.c:883:36: warning: ‘%s’ directive writing up to 99 bytes into a region of size 82 [-Wformat-overflow=] 883 | sprintf(cmd, "RulerWindowSize %d %s %s ", 1, c->frame, | ^~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from consistency_display.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 21 or more bytes (assuming 120) into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o sam_pileup.o -c sam_pileup.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o reading_coverage.o -c reading_coverage.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o readpair_coverage.o -c readpair_coverage.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o ace.o -c ace.c reading_coverage.c: In function ‘reading_coverage_callback’: reading_coverage.c:552:26: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 552 | jdata->generic.data = (void *)rcov->cons_id; | ^ reading_coverage.c:645:43: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 645 | reading_coverage_join(io, c, rcov, (int)jdata->generic.data); | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o strand_coverage.o -c strand_coverage.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o find_fragments.o -c find_fragments.c readpair_coverage.c: In function ‘readpair_coverage_callback’: readpair_coverage.c:500:26: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 500 | jdata->generic.data = (void *)rcov->cons_id; | ^ readpair_coverage.c:594:44: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 594 | readpair_coverage_join(io, c, rcov, (int)jdata->generic.data); | ^ strand_coverage.c: In function ‘strand_coverage_callback’: strand_coverage.c:503:26: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 503 | jdata->generic.data = (void *)scov->cons_id; | ^ strand_coverage.c:541:42: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 541 | strand_coverage_join(io, c, scov, (int)jdata->generic.data); | ^ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o caf.o -c caf.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o fasta.o -c fasta.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o vseqs.o -c vseqs.c In file included from vseqs.c:3: vseqs.c: In function ‘new_vcontig’: vseqs.c:60:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 60 | hash = Tcl_CreateHashEntry(&db->num_hash, (char *)rnum, | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2590:55: note: in definition of macro ‘Tcl_CreateHashEntry’ 2590 | (*((tablePtr)->createProc))(tablePtr, (const char *)(key), newPtr) | ^~~ vseqs.c: In function ‘new_vrseq’: vseqs.c:158:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 158 | hash = Tcl_CreateHashEntry(&vc->num_hash, (char *)(vrseq->rnum), &new); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2590:55: note: in definition of macro ‘Tcl_CreateHashEntry’ 2590 | (*((tablePtr)->createProc))(tablePtr, (const char *)(key), newPtr) | ^~~ vseqs.c: In function ‘del_vrseq’: vseqs.c:215:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 215 | hash = Tcl_FindHashEntry(&vc->num_hash, (char *)(vrseq->rnum)); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2587:53: note: in definition of macro ‘Tcl_FindHashEntry’ 2587 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ vseqs.c: In function ‘vrseq_index2ptr’: vseqs.c:409:45: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 409 | hash = Tcl_FindHashEntry(&vc->num_hash, (char *)num); | ^ /usr/include/tcl8.6/tcl-private/generic/tcl.h:2587:53: note: in definition of macro ‘Tcl_FindHashEntry’ 2587 | (*((tablePtr)->findProc))(tablePtr, (const char *)(key)) | ^~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o legacy_f2c.o -c legacy_f2c.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o f2c.o -c f2c.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o afg.o -c afg.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o shuffle_pads.o -c shuffle_pads.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o auto_break.o -c auto_break.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o depad_seq_tree.o -c depad_seq_tree.c In file included from /usr/include/string.h:495, from caf.c:11: In function ‘strncpy’, inlined from ‘read_data’ at caf.c:1044:3, inlined from ‘import_caf’ at caf.c:1295:12, inlined from ‘parse_caf’ at caf.c:1396:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ caf.c: In function ‘parse_caf’: caf.c:1036:16: note: length computed here 1036 | tm_len = strlen(value); | ^~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from caf.c:11: In function ‘strncpy’, inlined from ‘read_data’ at caf.c:1033:3, inlined from ‘import_caf’ at caf.c:1295:12, inlined from ‘parse_caf’ at caf.c:1396:9: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ caf.c: In function ‘parse_caf’: caf.c:1027:16: note: length computed here 1027 | tr_len = strlen(value); | ^~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEditor.o -c tkEditor.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdNames.o -c tkEdNames.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libgap5.so -L/build/staden-5my1Zk/staden-2.0.0+b11/lib newgap5_cmds.o gap4_compat.o gap_hash.o hash_lib.o qual.o qualIO.o gap_globals.o tagdb.o init.o notedb.o active_tags.o list_proc.o gap-error.o stack_dump.o tk-io-reg.o tkAppInit.o consen.o contig_selector.o cs-object.o find_repeats.o readpair.o check_assembly.o consensus.o read_depth.o gap_range.o template_display.o depth_track.o template_draw.o quality_plot.o tag_plot.o fij.o do_fij.o break_contig.o dis_readings.o export_contigs.o export_snps.o find_oligo.o import_gff.o shuffle_pads.o str_finder.o restriction_enzymes.o gap_canvas_box.o contig_extend.o auto_break.o find_haplotypes.o interval_tree.o g-files.o g-db.o g-struct.o g-error.o g-alloc.o g-io.o g-connect.o g-request.o tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o editor_view.o editor_join.o editor_search.o tkEdNames.o tkEditor.o tman_interface.o tman_display.o primlib.o editor_oligo.o tg_index_common.o baf.o maq.o maqmap.o sam_index.o sam_pileup.o ace.o caf.o fasta.o afg.o depad_seq_tree.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tkEdUtils.o -c tkEdUtils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edInterface.o -c edInterface.c /usr/bin/ld: tg_index_common.o: in function `bttmp_file_open': ./gap5/tg_index_common.c:105: warning: the use of `tmpnam' is dangerous, better use `mkstemp' gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o tg_index.bin tg_iface_g.o b+tree2.o hache_table.o tg_gio.o tg_cache.o tg_contig.o tg_sequence.o tg_track.o tg_bin.o tg_utils.o tg_register.o tg_tracks.o tg_anno.o tg_library.o tg_scaffold.o tg_check.o actf.o gap_cli_arg.o tg_tcl.o tg_index.o -lgap5 -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -ltk_utils -lz -llzma -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -lprimer3 -lmisc -lm /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-5my1Zk/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/gap5' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edUtils2.o -c edUtils2.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagU1.o -c tagU1.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o undo.o -c undo.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edExtend.o -c edExtend.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edCommands.o -c edCommands.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o edMutations.o -c edMutations.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tagEditor.o -c tagEditor.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o searchUtils.o -c searchUtils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_interface.o -c tman_interface.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_display.o -c tman_display.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_cons.o -c tman_cons.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o tman_diff.o -c tman_diff.c tman_display.c: In function ‘repositionSeq’: tman_display.c:281:21: warning: ‘ xview moveto ’ directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~ tman_display.c:281:18: note: assuming directive output of 12 bytes 281 | sprintf(buf, "%s xview moveto %g;%s icursor %d\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 28 and 2096 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c: In function ‘manageTrace’: tman_display.c:252:21: warning: ‘ left_cutoff ’ directive writing 13 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 252 | sprintf(buf, "%s left_cutoff %d", dc->path, leftCutOff); | ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 15 and 1048 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tman_display.c:255:21: warning: ‘ right_cutoff ’ directive writing 14 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 255 | sprintf(buf, "%s right_cutoff %d", dc->path, leftCutOff + cutLength); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/tcl8.6/tcl-private/generic/tcl.h:120, from /usr/include/tcl8.6/tk-private/generic/tk.h:19, from tman_display.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 16 and 1049 bytes into a destination of size 1024 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o contigEditor.o -c contigEditor.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o join.o -c join.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o oligo.o -c oligo.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_db_main.o -c copy_db_main.c copy_db_main.c: In function ‘main’: copy_db_main.c:86:2: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result] 86 | scanf("%c", &ans); | ^~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o text-io-reg.o -c text-io-reg.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o copy_db gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o copy_db.o copy_db_main.o text-io-reg.o io_utils.o io_handle.o -lg -ltext_utils -lmisc -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/. -I/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libgap.so -L/build/staden-5my1Zk/staden-2.0.0+b11/lib gap-local.o gap-remote.o gap-if.o gap-init.o gap-dbstruct.o gap-create.o gap-error.o stack_dump.o gap-io.o IO1.o io-reg.o actf.o IO2.o seqInfo.o parse_ft.o IO3.o io_utils.o io_handle.o gap-tcl.o tk-io-reg.o gap_cli_arg.o gap_globals.o newgap_cmds.o init.o consen.o gap_hash.o qual.o qualIO.o bubbl3.o tagdb.o notedb.o active_tags.o dbcheck.o clones.o extract.o preass.o list.o reactions.o probe.o template.o template_display.o ruler_display.o gap_canvas_box.o hash.o gap_array.o show_relationships.o fij.o hash_lib.o do_fij.o auto_assemble.o dis_readings.o find_repeats.o break_contig.o quality_plot.o readpair.o contig_selector.o complement.o cs-object.o list_proc.o dstrand.o oligo_sel.o primlib.o alter_rel.o restriction_enzymes.o stop_codon.o assemble_direct.o check_assembly.o tagU2.o mess.o find_oligo.o copy_db.o contig_order.o clip.o notes.o consistency_display.o consistency_canvas_box.o confidence_graph.o reading_coverage.o readpair_coverage.o strand_coverage.o find_fragments.o vseqs.o legacy_f2c.o f2c.o shuffle_pads.o auto_break.o tkEditor.o tkEdNames.o tkEdUtils.o edInterface.o edUtils2.o tagU1.o undo.o edExtend.o edCommands.o edMutations.o tagEditor.o searchUtils.o tman_interface.o tman_display.o tman_cons.o tman_diff.o contigEditor.o join.o oligo.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lseq_utils -ltk_utils -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lg -lmutlib -lmisc -lprimer3 -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/gap4' cd prefinish && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish SUBDIR=prefinish all cd haplo && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./haplo/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./haplo SUBDIR=haplo all cd copy_reads && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads all cd convert && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./convert/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./convert SUBDIR=convert all make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/prefinish' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/haplo' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/copy_reads' make[2]: warning: -j4 forced in submake: resetting jobserver mode. make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/convert' make[2]: warning: -j4 forced in submake: resetting jobserver mode. gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish.o -c finish.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_hash.o -c finish_hash.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./haplo -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_tcl.o -c haplo_tcl.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./haplo -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_snps.o -c haplo_snps.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads_globals.o -c copy_reads_globals.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_long.o -c finish_long.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./haplo -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_split.o -c haplo_split.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_main.o -c finish_main.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o copy_reads.o -c copy_reads.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./haplo -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o haplo_cons.o -c haplo_cons.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./convert -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o list.o -c list.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./convert -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o main.o -c main.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./convert -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o dapIO.o -c dapIO.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./convert -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o dapDB.o -c dapDB.c main.c: In function ‘get_db’: main.c:87:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 87 | fgets(name, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:92:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] 92 | fgets(version, sizeof(IOString), stdin); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./convert -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o bapIO.o -c bapIO.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./convert -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o bapDB.o -c bapDB.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_utils.o -c finish_utils.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./convert -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o gapDB.o -c gapDB.c copy_reads.c: In function ‘create_si_struct’: copy_reads.c:125:26: warning: ‘%s’ directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 125 | sprintf(comment, "%s %s", tag_text, io_name(io)); | ^~ In file included from /usr/include/stdio.h:867, from copy_reads.c:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./convert -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o process.o -c process.c copy_reads.c: In function ‘copy_reads’: copy_reads.c:409:27: warning: ‘%s’ directive writing up to 255 bytes into a region of size 99 [-Wformat-overflow=] 409 | sprintf(comment, "%s %s", tag_text, io_name(io_to)); | ^~ In file included from /usr/include/stdio.h:867, from copy_reads.c:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 2 or more bytes (assuming 257) into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_walk.o -c finish_walk.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./convert -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -o flat_sd.o -c flat_sd.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o staden_convert list.o main.o dapIO.o dapDB.o bapIO.o bapDB.o gapDB.o process.o flat_sd.o -lm -lgap -lg -lprimer3 -lmutlib -ltk_utils -lseq_utils -lmisc -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_reverse.o -c finish_reverse.c gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libcopy_reads.so copy_reads_globals.o copy_reads.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./haplo -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./haplo -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itk/generic -I/build/staden-5my1Zk/staden-2.0.0+b11/./incrTcl-3.3cvs/itcl/generic -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libhaplo.so haplo_tcl.o haplo_snps.o haplo_split.o haplo_cons.o -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -ltk_utils -lmisc -lgap make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/copy_reads' make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/haplo' /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-5my1Zk/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/convert' gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_filter.o -c finish_filter.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o finish_pcr.o -c finish_pcr.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o dust.o -c dust.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o insert_size_dist.o -c insert_size_dist.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_size_dist.o -c read_size_dist.c gcc -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -o read_conf_dist.o -c read_conf_dist.c gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_size_dist read_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o insert_size_dist insert_size_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm gcc -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o read_conf_dist read_conf_dist.o -lg -lgap -ltk_utils -lprimer3 -lmutlib -lseq_utils -lmisc -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -ldl -lz -lpthread -lm -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread -lcurl -lz -lm gcc -shared -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -g -O2 -fdebug-prefix-map=/build/staden-5my1Zk/staden-2.0.0+b11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DUSE_NON_CONST -I/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish -I/build/staden-5my1Zk/staden-2.0.0+b11/./Misc -I/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 -I/build/staden-5my1Zk/staden-2.0.0+b11/./g -I"/usr/include/tcl8.6/tk-private/generic" -I"/usr/include/tcl8.6/tk-private/unix" -I"/usr/include/tcl8.6/tk-private/generic/ttk" -I"/usr/include/tcl8.6/tcl-private/generic" -I"/usr/include/tcl8.6/tcl-private/unix" -I/usr/include -I/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils -I/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src -I/build/staden-5my1Zk/staden-2.0.0+b11 -DSVN_VERSION="" -fPIC -L/build/staden-5my1Zk/staden-2.0.0+b11/lib -Wl,-z,relro -Wl,-z,now -Wl,--export-dynamic -Wl,-rpath,/usr/lib/staden -o /build/staden-5my1Zk/staden-2.0.0+b11/lib/libprefinish.so finish.o finish_hash.o finish_long.o finish_main.o finish_utils.o finish_walk.o finish_reverse.o finish_filter.o finish_pcr.o dust.o -L/usr/lib/x86_64-linux-gnu -ltk8.6 -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -lX11 -lXss -lXext -lXft -lfontconfig -lfreetype -lfontconfig -lpthread -ldl -lz -lpthread -lm -lseq_utils -ltk_utils -lmisc -lgap -lprimer3 /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-5my1Zk/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-5my1Zk/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) /usr/bin/ld: warning: libtext_utils.so, needed by /build/staden-5my1Zk/staden-2.0.0+b11/lib/libseq_utils.so, not found (try using -rpath or -rpath-link) make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/prefinish' make[1]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_auto_test -a create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_auto_install make -j4 install DESTDIR=/build/staden-5my1Zk/staden-2.0.0\+b11/debian/tmp AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11' mkdir -p /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden mkdir -p /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin mkdir -p /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc mkdir -p /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden mkdir -p /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir -p /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl mkdir -p /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/doc mkdir -p /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/man cp shlib.conf /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp ./staden.profile /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden make JOB=install make[3]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11' cd Misc && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./Misc/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./Misc SUBDIR=Misc install cd trev && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./trev/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./trev SUBDIR=trev install cd primer3 && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./primer3/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./primer3 SUBDIR=primer3 install cd primer3/src && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./primer3/src SUBDIR=primer3/src install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/Misc' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/trev' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/primer3' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/primer3/src' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libmisc.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden install trev /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Nothing to be done for 'install'. make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/primer3' cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libprimer3.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cd pregap4 && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./pregap4 SUBDIR=pregap4 install mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/Misc' cp /build/staden-5my1Zk/staden-2.0.0+b11/./trev/trev.tcl /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/trev make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/pregap4' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/primer3/src' cd spin_emboss && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss SUBDIR=spin_emboss install cp /build/staden-5my1Zk/staden-2.0.0+b11/./trev/trevrc /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cd hetins && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./hetins/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./hetins SUBDIR=hetins install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/spin_emboss' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/trev' make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/hetins' make[4]: warning: -j4 forced in submake: resetting jobserver mode. /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/../global.mk:233: warning: ignoring old recipe for target 'clean' cd scripts && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./scripts SUBDIR=scripts install /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/../global.mk:233: warning: ignoring old recipe for target 'clean' install pregap4 /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin/pregap4 make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/scripts' make[4]: warning: -j4 forced in submake: resetting jobserver mode. mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 cp /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/*.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/tclIndex /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss cp /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/*.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/widget_licence /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/tclIndex /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4 /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/../global.mk:233: warning: ignoring old recipe for target 'clean' cp hetins /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/hetins' cp /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/assemble4 /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cp /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/create_emboss_files /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules cd data && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./data/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./data SUBDIR=data install cp /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/fasta-split /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/data' make[4]: warning: -j4 forced in submake: resetting jobserver mode. mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/acdtcl/* /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin_emboss/acdtcl cp /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/fasta2exp /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cp /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/modules/*.p4m /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/modules cp /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/splitseq_da /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts cp /build/staden-5my1Zk/staden-2.0.0+b11/./scripts/staden_help /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts /build/staden-5my1Zk/staden-2.0.0+b11/./data/Makefile:9: warning: overriding recipe for target 'clean' /build/staden-5my1Zk/staden-2.0.0+b11/./data/../global.mk:233: warning: ignoring old recipe for target 'clean' cp: cannot stat '/build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/acdtcl/*': No such file or directory make[4]: [/build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/Makefile:30: install] Error 1 (ignored) cp /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/emboss_menu /build/staden-5my1Zk/staden-2.0.0+b11/./spin_emboss/spin_embossrc /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/scripts' mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/spin_emboss' cp /build/staden-5my1Zk/staden-2.0.0+b11/./data/alus/* /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/alus cd tk_utils && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils SUBDIR=tk_utils install cd text_utils && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./text_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./text_utils SUBDIR=text_utils install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/tk_utils' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/templates/*.p4t /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/templates make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/text_utils' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp: cannot stat '/build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/templates/*.p4t': No such file or directory make[4]: [/build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/Makefile:42: install] Error 1 (ignored) cp /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/naming_schemes/*.p4t /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/pregap4/naming_schemes cp /build/staden-5my1Zk/staden-2.0.0+b11/./pregap4/pregap4rc /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libtk_utils.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libtext_utils.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/pregap4' make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/text_utils' cd abi && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./abi/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./abi SUBDIR=abi install cd alf && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./alf/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./alf SUBDIR=alf install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/abi' make[4]: warning: -j4 forced in submake: resetting jobserver mode. mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils cp /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/*.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/tclIndex /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/tk_utils make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/alf' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp getABISampleName getABIcomment getABIdate getABIfield /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp alfsplit /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/abi' make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/alf' cd g && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./g/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./g SUBDIR=g install cd eba && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./eba/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./eba SUBDIR=eba install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/g' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/eba' make[4]: warning: -j4 forced in submake: resetting jobserver mode. mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data cp eba /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libg.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/stash /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/eba' cp /build/staden-5my1Zk/staden-2.0.0+b11/./data/blast_data/* /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/blast_data cd init_exp && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./init_exp/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./init_exp SUBDIR=init_exp install make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/g' cp /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/2bars_*.bmp /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/help_config /build/staden-5my1Zk/staden-2.0.0+b11/./tk_utils/tk_utilsrc /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/init_exp' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cd get_scf_field && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./get_scf_field/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./get_scf_field SUBDIR=get_scf_field install make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/tk_utils' make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/get_scf_field' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cd seq_utils && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils SUBDIR=seq_utils install mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes cp /build/staden-5my1Zk/staden-2.0.0+b11/./data/gcodes/* /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/gcodes make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/seq_utils' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp init_exp /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/init_exp' cp get_scf_field /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/get_scf_field' cp /build/staden-5my1Zk/staden-2.0.0+b11/./data/vectors/* /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc/vectors cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libseq_utils.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils/align_lib_nuc_matrix /build/staden-5my1Zk/staden-2.0.0+b11/./seq_utils/nuc_matrix /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-5my1Zk/staden-2.0.0+b11/./data/RENZYM.* /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/seq_utils' cd mutlib && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./mutlib/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./mutlib SUBDIR=mutlib install cp /build/staden-5my1Zk/staden-2.0.0+b11/./data/renzyme_bairoch /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cd spin && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./spin/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./spin SUBDIR=spin install cd vector_clip && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./vector_clip/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./vector_clip SUBDIR=vector_clip install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/mutlib' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/spin' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/vector_clip' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp vector_clip /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin install spin /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libmutlib.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/vector_clip' cp /build/staden-5my1Zk/staden-2.0.0+b11/./data/m13mp18_primers /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/mutlib' mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin cd qclip && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./qclip/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./qclip SUBDIR=qclip install cp /build/staden-5my1Zk/staden-2.0.0+b11/./data/vector_primer /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cd screen_seq && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./screen_seq/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./screen_seq SUBDIR=screen_seq install cp /build/staden-5my1Zk/staden-2.0.0+b11/./spin/*.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./spin/tclIndex /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/spin cp /build/staden-5my1Zk/staden-2.0.0+b11/./data/pam250 /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/qclip' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/screen_seq' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/data' cd polyA_clip && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./polyA_clip/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./polyA_clip SUBDIR=polyA_clip install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/polyA_clip' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp qclip /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp screen_seq /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/qclip' cd stops && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./stops/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./stops SUBDIR=stops install make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/screen_seq' make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/stops' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cd make_weights && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./make_weights/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./make_weights SUBDIR=make_weights install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/make_weights' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp polyA_clip /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp stops /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/polyA_clip' cp make_weights /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/stops' cd find_renz && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./find_renz/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./find_renz SUBDIR=find_renz install make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/make_weights' cd mutscan && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./mutscan/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./mutscan SUBDIR=mutscan install cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libspin.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cd gap5 && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./gap5 SUBDIR=gap5 install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/find_renz' make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/mutscan' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/gap5' make[4]: warning: -j4 forced in submake: resetting jobserver mode. cp /build/staden-5my1Zk/staden-2.0.0+b11/./spin/*.wts /build/staden-5my1Zk/staden-2.0.0+b11/./spin/niprc /build/staden-5my1Zk/staden-2.0.0+b11/./spin/siprc /build/staden-5my1Zk/staden-2.0.0+b11/./spin/spinrc /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp mutscan /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp find_renz /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/find_renz' make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/mutscan' cd tracediff && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./tracediff/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./tracediff SUBDIR=tracediff install cd gap4 && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./gap4 SUBDIR=gap4 install make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/spin' make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/tracediff' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/gap4' make[4]: warning: -j4 forced in submake: resetting jobserver mode. install gap5 /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 cp /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/*.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/tclIndex /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 cp tracediff /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/tracediff' cp copy_db /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin install gap4 /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap cp /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/*.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/tclIndex /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap cp /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/../gap4/acd2tag.tcl /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/gap5 cp /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/gap5rc /build/staden-5my1Zk/staden-2.0.0+b11/./gap5/gap5rc_menu_full /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libgap5.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp tg_index.bin /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libgap.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden install tg_index /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin install gap5_cmd /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/gap5' cp /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/gaprc /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/gaprc_menu_full /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/gaprc_menu_mito /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/GTAGDB /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/NOTEDB /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/cap2rc /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/cap3rc /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/fak2rc /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/phraprc /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/*.bitmap /build/staden-5my1Zk/staden-2.0.0+b11/./gap4/*.gif /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/gap4' cd prefinish && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./prefinish SUBDIR=prefinish install cd haplo && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./haplo/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./haplo SUBDIR=haplo install cd copy_reads && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads SUBDIR=copy_reads install cd convert && make -f /build/staden-5my1Zk/staden-2.0.0+b11/./convert/Makefile -w -j4 --jobserver-auth=3,4 BUILD=/build/staden-5my1Zk/staden-2.0.0+b11 SRC=/build/staden-5my1Zk/staden-2.0.0+b11/./convert SUBDIR=convert install make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/haplo' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/copy_reads' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/prefinish' make[4]: warning: -j4 forced in submake: resetting jobserver mode. make[4]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11/convert' make[4]: warning: -j4 forced in submake: resetting jobserver mode. mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo install copy_reads /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-5my1Zk/staden-2.0.0+b11/./haplo/*.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./haplo/tclIndex /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/haplo mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp /build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads/copy_reads.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads/copy_reads_main.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads/tclIndex /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/copy_reads cp /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/*.tcl /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/*.itcl /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/*.itk /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/help /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/args.template /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/tclIndex /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp staden_convert /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libcopy_reads.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libhaplo.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/convert' cp /build/staden-5my1Zk/staden-2.0.0+b11/./copy_reads/copy_readsrc /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc cp /build/staden-5my1Zk/staden-2.0.0+b11/./haplo/haplorc /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/copy_reads' make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/haplo' cp /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/config.prefinish /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish cp /build/staden-5my1Zk/staden-2.0.0+b11/lib/libprefinish.so /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/staden install prefinish /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/bin cp /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/finish_sanger /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/finish_cDNA /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/finish_cDNA_ends_only \ /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/scripts mkdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/rules/*.rule /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/tcl/prefinish/rules cp /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/config.prefinish /build/staden-5my1Zk/staden-2.0.0+b11/./prefinish/prefinishrc /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/share/staden/etc make[4]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11/prefinish' make[3]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11' make[2]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11' # Remove file causing lintian errors that is targeting at windows find debian -name help_windows.tcl -delete # Remove some empty directories find debian -type d -empty -name acdtcl -delete find debian -type d -empty -name templates -delete # Build system is not prepared for multi-arch mv /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu/* /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib rmdir /build/staden-5my1Zk/staden-2.0.0+b11/debian/tmp/usr/lib/x86_64-linux-gnu make[1]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_install -a dh_installdocs -a dh_installdocs: warning: Could not parse doc-base for doc-base Document id; skipping dh_installchangelogs -a debian/rules override_dh_installman-arch make[1]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_installman # due to a file name conflict spin.1 is moved out of the way #826684 mkdir -p debian/staden/usr/lib/debian-med/share/man/man1/ mv debian/staden/usr/share/man/man1/spin.1 debian/staden/usr/lib/debian-med/share/man/man1/ gzip -9 debian/staden/usr/lib/debian-med/share/man/man1/spin.1 make[1]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a debian/rules override_dh_fixperms make[1]: Entering directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_fixperms # scripts should be executable chmod a+x debian/*/usr/share/staden/tcl/gap5/contig_graph.tcl chmod a+x debian/*/usr/share/staden/tcl/gap5/gap5_cmd.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/add_stops.tcl chmod a+x debian/*/usr/share/staden/tcl/prefinish/finish_sanger.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_ext.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_galeon.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_int.tcl chmod a+x debian/*/usr/share/staden/tcl/tk_utils/help_netscape.tcl make[1]: Leaving directory '/build/staden-5my1Zk/staden-2.0.0+b11' dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'staden-dbgsym' in '../staden-dbgsym_2.0.0+b11-4+b1_amd64.deb'. dpkg-deb: building package 'staden' in '../staden_2.0.0+b11-4+b1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../staden_2.0.0+b11-4+b1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/staden-5my1Zk /tmp/staden-2.0.0+b11-4+b13tb_3szx I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.a0vGgZY_vO... I: success in 774.2951 seconds md5: staden-dbgsym_2.0.0+b11-4+b1_amd64.deb: OK md5: staden_2.0.0+b11-4+b1_amd64.deb: OK sha1: staden-dbgsym_2.0.0+b11-4+b1_amd64.deb: OK sha1: staden_2.0.0+b11-4+b1_amd64.deb: OK sha256: staden-dbgsym_2.0.0+b11-4+b1_amd64.deb: OK sha256: staden_2.0.0+b11-4+b1_amd64.deb: OK Checksums: OK