Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/smalt/smalt_0.7.6-9_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/smalt-0.7.6-9ze5tzmgb/smalt_0.7.6-9_amd64.buildinfo Get source package info: smalt=0.7.6-9 Source URL: http://snapshot.notset.fr/mr/package/smalt/0.7.6-9/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11 automake=1:1.16.1-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.47 bash=5.0-5 binutils=2.33.1-6 binutils-common=2.33.1-6 binutils-x86-64-linux-gnu=2.33.1-6 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.2.1-21 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.7.3 debianutils=4.9.1 dh-autoreconf=19 dh-strip-nondeterminism=1.6.3-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-5 fdisk=2.34-0.1 file=1:5.37-6 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.2.1-21 gcc=4:9.2.1-3.1 gcc-9=9.2.1-21 gcc-9-base=9.2.1-21 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.3-1 groff-base=1.22.4-4 gzip=1.9-3+b1 hostname=3.23 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-5 libarchive-zip-perl=1.67-1 libasan5=9.2.1-21 libatomic1=9.2.1-21 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2+b1 libbambamc-dev=0.0.50-3 libbambamc0=0.0.50-3 libbinutils=2.33.1-6 libblkid1=2.34-0.1 libbrotli1=1.0.7-6 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.29-7 libc-dev-bin=2.29-7 libc6=2.29-7 libc6-dev=2.29-7 libcap-ng0=0.7.9-2.1+b1 libcc1-0=9.2.1-21 libcom-err2=1.45.4-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.10-9 libcrypt1=1:4.4.10-9 libcurl3-gnutls=7.67.0-2 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.250 libdebhelper-perl=12.7.3 libdeflate0=1.5-1 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libexpat1=2.2.9-1 libfdisk1=2.34-0.1 libffi6=3.2.1-9 libfile-stripnondeterminism-perl=1.6.3-1 libgcc-9-dev=9.2.1-21 libgcc1=1:9.2.1-21 libgcrypt20=1.8.5-3 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libglib2.0-0=2.62.4-1 libgmp10=2:6.1.2+dfsg-4 libgnutls30=3.6.11.1-2 libgomp1=9.2.1-21 libgpg-error0=1.36-7 libgssapi-krb5-2=1.17-6 libhogweed5=3.5.1+really3.5.1-2 libhts3=1.10.2-2 libicu63=63.2-2 libidn2-0=2.2.0-2 libisl22=0.22-2 libitm1=9.2.1-21 libk5crypto3=1.17-6 libkeyutils1=1.6-6 libkrb5-3=1.17-6 libkrb5support0=1.17-6 libldap-2.4-2=2.4.48+dfsg-1+b2 libldap-common=2.4.48+dfsg-1 liblsan0=9.2.1-21 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.37-6 libmagic1=1:5.37-6 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpdec2=2.4.2-2 libmpfr6=4.0.2-1 libncurses6=6.1+20191019-1 libncursesw6=6.1+20191019-1 libnettle7=3.5.1+really3.5.1-2 libnghttp2-14=1.40.0-1 libp11-kit0=0.23.18.1-2 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=5.30.0-9 libpipeline1=1.5.2-1 libpsl5=0.20.2-2 libpython3-stdlib=3.7.5-3 libpython3.7-minimal=3.7.6-1 libpython3.7-stdlib=3.7.6-1 libquadmath0=9.2.1-21 libreadline8=8.0-3 librtmp1=2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.4.2-2 libselinux1=3.0-1 libsigsegv2=2.12-2 libsmartcols1=2.34-0.1 libsqlite3-0=3.30.1+fossil191229-1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1d-2 libstdc++-9-dev=9.2.1-21 libstdc++6=9.2.1-21 libsub-override-perl=0.09-2 libsystemd0=244-3 libtasn1-6=4.15.0-2 libtinfo6=6.1+20191019-1 libtool=2.4.6-11 libtsan0=9.2.1-21 libubsan1=9.2.1-21 libuchardet0=0.0.6-3 libudev1=244-3 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libxml2=2.9.4+dfsg1-8 linux-libc-dev=5.4.6-1 login=1:4.8-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.0-2 mawk=1.3.3-19 mime-support=3.64 ncurses-base=6.1+20191019-1 ncurses-bin=6.1+20191019-1 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 pkg-config=0.29-6 po-debconf=1.0.21 python3=3.7.5-3 python3-minimal=3.7.5-3 python3.7=3.7.6-1 python3.7-minimal=3.7.6-1 readline-common=8.0-3 samtools=1.10-3 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-1 tar=1.30+dfsg-6+b1 util-linux=2.34-0.1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-1+b1 zlib1g-dev=1:1.2.11.dfsg-1+b1 --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/20200412T142911Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200101T211403Z/ 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 smalt=0.7.6-9 && mkdir -p /build/smalt-g13CqB && dpkg-source --no-check -x /*.dsc /build/smalt-g13CqB/smalt-0.7.6 && chown -R builduser:builduser /build/smalt-g13CqB" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/smalt-g13CqB/smalt-0.7.6 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1578048279" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/smalt-g13CqB /tmp/smalt-0.7.6-9ze5tzmgb bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20200101T211403Z 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.mzvJXYwZHn 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.mzvJXYwZHn Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). 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/20200101T211403Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200101T211403Z 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 (881 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 ... 4507 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 (2.29-7) ... 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/20200412T142911Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20200101T211403Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.mzvJXYwZHn Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20200412T142911Z unstable InRelease [146 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20200101T211403Z 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/20200412T142911Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200412T142911Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20200412T142911Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20200412T142911Z unstable/main amd64 Packages [11.2 MB] Fetched 33.9 MB in 29s (1183 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.mzvJXYwZHn I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d smalt=0.7.6-9 && mkdir -p /build/smalt-g13CqB && dpkg-source --no-check -x /*.dsc /build/smalt-g13CqB/smalt-0.7.6 && chown -R builduser:builduser /build/smalt-g13CqB"' exec /tmp/mmdebstrap.mzvJXYwZHn Reading package lists... NOTICE: 'smalt' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/smalt.git Please use: git clone https://salsa.debian.org/med-team/smalt.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 72.3 MB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main smalt 0.7.6-9 (dsc) [2064 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main smalt 0.7.6-9 (tar) [72.3 MB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main smalt 0.7.6-9 (diff) [8756 B] Fetched 72.3 MB in 60s (1199 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'smalt_0.7.6-9.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting smalt in /build/smalt-g13CqB/smalt-0.7.6 dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz dpkg-source: info: unpacking smalt_0.7.6-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 2to3.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/smalt-g13CqB/smalt-0.7.6 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1578048279" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.mzvJXYwZHn dpkg-buildpackage: info: source package smalt dpkg-buildpackage: info: source version 0.7.6-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe 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/smalt-g13CqB/smalt-0.7.6' dh_auto_clean rm -rf test/*.pyc misc/*.pyc test/tmp make[1]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a debian/rules override_dh_autoreconf make[1]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6' echo "Do nothing - fails because auf broken upstream autoconf stuff" Do nothing - fails because auf broken upstream autoconf stuff make[1]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6' # see upstream INSTALL file CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for icc... no 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 style of include used by make... GNU checking dependency style of gcc... gcc3 checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for ranlib... ranlib checking for a Python interpreter with version >= 2.6... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.7 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.7/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.7/site-packages checking for samtools... yes checking for sam_open in -lbam... no checking for BAMBAMC... yes checking for gzread in -lz... 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 math.h usability... yes checking math.h presence... yes checking for math.h... yes checking pthread.h usability... yes checking pthread.h presence... yes checking for pthread.h... yes checking semaphore.h usability... yes checking semaphore.h presence... yes checking for semaphore.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking emmintrin.h usability... yes checking emmintrin.h presence... yes checking for emmintrin.h... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating test/data/Makefile config.status: creating misc/Makefile config.status: creating config.h config.status: executing depfiles commands make[1]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6' dh_auto_build -a make -j4 make[1]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6' make all-recursive make[2]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6' Making all in src make[3]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT elib.o -MD -MP -MF .deps/elib.Tpo -c -o elib.o elib.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT filio.o -MD -MP -MF .deps/filio.Tpo -c -o filio.o filio.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT sequence.o -MD -MP -MF .deps/sequence.Tpo -c -o sequence.o sequence.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-score.o -MD -MP -MF .deps/libsgm_a-score.Tpo -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c sequence.c: In function ‘seqFastqGetConstSequence’: sequence.c:2079:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2079 | if (length) | ^~ sequence.c:2081:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2081 | return NULL; | ^~~~~~ sequence.c: In function ‘seqFastqGetSequence’: sequence.c:2094:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2094 | if (length) | ^~ sequence.c:2096:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2096 | return NULL; | ^~~~~~ sequence.c: In function ‘seqIOopen’: sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=] 489 | strcpy(p->fmode, "r"); | ^~~~~~~~~~~~~~~~~~~~~ sequence.c:491:3: note: here 491 | case SEQIO_WRITE_GZIP_FASTA: | ^~~~ score.c:49:21: warning: ‘LN0P25’ defined but not used [-Wunused-const-variable=] 49 | static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */ | ^~~~~~ mv -f .deps/filio.Tpo .deps/filio.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-diffstr.o -MD -MP -MF .deps/libsgm_a-diffstr.Tpo -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c mv -f .deps/elib.Tpo .deps/elib.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-alibuffer.o -MD -MP -MF .deps/libsgm_a-alibuffer.Tpo -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c mv -f .deps/libsgm_a-alibuffer.Tpo .deps/libsgm_a-alibuffer.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-alignment.o -MD -MP -MF .deps/libsgm_a-alignment.Tpo -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c mv -f .deps/libsgm_a-score.Tpo .deps/libsgm_a-score.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-swsimd.o -MD -MP -MF .deps/libsgm_a-swsimd.Tpo -c -o libsgm_a-swsimd.o `test -f 'swsimd.c' || echo './'`swsimd.c alignment.c:478:13: warning: ‘blankALITRACK’ defined but not used [-Wunused-function] 478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp) | ^~~~~~~~~~~~~ mv -f .deps/libsgm_a-swsimd.Tpo .deps/libsgm_a-swsimd.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-sort.o -MD -MP -MF .deps/libsgm_a-sort.Tpo -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c mv -f .deps/libsgm_a-alignment.Tpo .deps/libsgm_a-alignment.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-array.o -MD -MP -MF .deps/libsgm_a-array.Tpo -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c mv -f .deps/libsgm_a-diffstr.Tpo .deps/libsgm_a-diffstr.Po mv -f .deps/libsgm_a-array.Tpo .deps/libsgm_a-array.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-interval.o -MD -MP -MF .deps/libsgm_a-interval.Tpo -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashidx.o -MD -MP -MF .deps/libsgm_a-hashidx.Tpo -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c mv -f .deps/libsgm_a-sort.Tpo .deps/libsgm_a-sort.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-hashhit.o -MD -MP -MF .deps/libsgm_a-hashhit.Tpo -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c hashidx.c: In function ‘countPerfectKey’: hashidx.c:191:77: warning: unused parameter ‘tuplectr’ [-Wunused-parameter] 191 | static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ hashidx.c: In function ‘countCollisionKey’: hashidx.c:206:79: warning: unused parameter ‘tuplectr’ [-Wunused-parameter] 206 | static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ hashidx.c: In function ‘collectWords’: hashidx.c:223:74: warning: unused parameter ‘tuplectr’ [-Wunused-parameter] 223 | static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ hashidx.c: In function ‘countWords’: hashidx.c:265:72: warning: unused parameter ‘tuplectr’ [-Wunused-parameter] 265 | static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr) | ~~~~~~~~~~^~~~~~~~ At top level: hashidx.c:446:18: warning: ‘getWordHisto’ defined but not used [-Wunused-function] 446 | static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp) | ^~~~~~~~~~~~ hashidx.c:63:19: warning: ‘HASHTABFIL_READERRMSG’ defined but not used [-Wunused-const-variable=] 63 | static const char HASHTABFIL_READERRMSG[] = "when reading hash table file"; | ^~~~~~~~~~~~~~~~~~~~~ mv -f .deps/libsgm_a-interval.Tpo .deps/libsgm_a-interval.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT libsgm_a-segment.o -MD -MP -MF .deps/libsgm_a-segment.Tpo -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c segment.c:1375:12: warning: ‘checkCANDARRsequential’ defined but not used [-Wunused-function] 1375 | static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs) | ^~~~~~~~~~~~~~~~~~~~~~ segment.c:1330:13: warning: ‘labelSEGCANDWithinInsertRange’ defined but not used [-Wunused-function] 1330 | static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/sequence.Tpo .deps/sequence.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-smalt.o -MD -MP -MF .deps/smalt-smalt.Tpo -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c smalt.c: In function ‘cleanupSmaltOutput’: smalt.c:659:39: warning: unused parameter ‘errmsgp’ [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ mv -f .deps/libsgm_a-hashidx.Tpo .deps/libsgm_a-hashidx.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-menu.o -MD -MP -MF .deps/smalt-menu.Tpo -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c mv -f .deps/libsgm_a-hashhit.Tpo .deps/libsgm_a-hashhit.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-threads.o -MD -MP -MF .deps/smalt-threads.Tpo -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c mv -f .deps/smalt-smalt.Tpo .deps/smalt-smalt.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-infmt.o -MD -MP -MF .deps/smalt-infmt.Tpo -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c mv -f .deps/libsgm_a-segment.Tpo .deps/libsgm_a-segment.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-results.o -MD -MP -MF .deps/smalt-results.Tpo -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c mv -f .deps/smalt-infmt.Tpo .deps/smalt-infmt.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-resultpairs.o -MD -MP -MF .deps/smalt-resultpairs.Tpo -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c mv -f .deps/smalt-threads.Tpo .deps/smalt-threads.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-report.o -MD -MP -MF .deps/smalt-report.Tpo -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c results.c: In function ‘resultSetInferInsertSize’: results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare] 2470 | rp->sidx == rp->sidx) { | ^~ mv -f .deps/smalt-menu.Tpo .deps/smalt-menu.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-rmap.o -MD -MP -MF .deps/smalt-rmap.Tpo -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c mv -f .deps/smalt-resultpairs.Tpo .deps/smalt-resultpairs.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt-insert.o -MD -MP -MF .deps/smalt-insert.Tpo -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c mv -f .deps/smalt-report.Tpo .deps/smalt-report.Po rm -f libseq.a mv -f .deps/smalt-insert.Tpo .deps/smalt-insert.Po ar cru libseq.a elib.o filio.o sequence.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseq.a rm -f libsgm.a ar cru libsgm.a libsgm_a-score.o libsgm_a-diffstr.o libsgm_a-alibuffer.o libsgm_a-alignment.o libsgm_a-swsimd.o libsgm_a-sort.o libsgm_a-array.o libsgm_a-interval.o libsgm_a-hashidx.o libsgm_a-hashhit.o libsgm_a-segment.o libseq.a ar: `u' modifier ignored since `D' is the default (see `U') ranlib libsgm.a mv -f .deps/smalt-rmap.Tpo .deps/smalt-rmap.Po mv -f .deps/smalt-results.Tpo .deps/smalt-results.Po gcc -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt smalt-smalt.o smalt-menu.o smalt-threads.o smalt-infmt.o smalt-results.o smalt-resultpairs.o smalt-report.o smalt-rmap.o smalt-insert.o libsgm.a libseq.a -lbambamc -lz -lm -lpthread -lz make[3]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/src' Making all in test make[3]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/test' make[4]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/test' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/test' make[3]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/test' Making all in misc make[3]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/misc' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT simread.o -MD -MP -MF .deps/simread.Tpo -c -o simread.o simread.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT rsample.o -MD -MP -MF .deps/rsample.Tpo -c -o rsample.o rsample.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT fetchseq.o -MD -MP -MF .deps/fetchseq.Tpo -c -o fetchseq.o fetchseq.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT splitreads.o -MD -MP -MF .deps/splitreads.Tpo -c -o splitreads.o splitreads.c mv -f .deps/splitreads.Tpo .deps/splitreads.Po mv -f .deps/fetchseq.Tpo .deps/fetchseq.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT mixreads.o -MD -MP -MF .deps/mixreads.Tpo -c -o mixreads.o mixreads.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT splitmates.o -MD -MP -MF .deps/splitmates.Tpo -c -o splitmates.o splitmates.c simread.c: In function ‘simulateSingleRead’: simread.c:534:49: warning: ‘%s’ directive writing up to 4095 bytes into a region of size between 3815 and 4070 [-Wformat-overflow=] 534 | sprintf(read_name, "%s_%9.9i_%s_%9.9u_%lli_%c_%s", readnamprefix, readnum, | ^~ 535 | refnamp, so+1, (long long signed) sidx, (is_reverse)? 'R':'F', alistr); | ~~~~~~ In file included from /usr/include/stdio.h:867, from simread.c:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 27 or more bytes (assuming 4377) into a destination of size 4096 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ simread.c:534:49: warning: ‘%s’ directive writing up to 4095 bytes into a region of size between 3815 and 4070 [-Wformat-overflow=] 534 | sprintf(read_name, "%s_%9.9i_%s_%9.9u_%lli_%c_%s", readnamprefix, readnum, | ^~ 535 | refnamp, so+1, (long long signed) sidx, (is_reverse)? 'R':'F', alistr); | ~~~~~~ In file included from /usr/include/stdio.h:867, from simread.c:29: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 27 or more bytes (assuming 4377) into a destination of size 4096 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/rsample.Tpo .deps/rsample.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT readstats.o -MD -MP -MF .deps/readstats.Tpo -c -o readstats.o readstats.c mv -f .deps/readstats.Tpo .deps/readstats.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT trunkreads.o -MD -MP -MF .deps/trunkreads.Tpo -c -o trunkreads.o trunkreads.c mv -f .deps/splitmates.Tpo .deps/splitmates.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqcol.o -MD -MP -MF .deps/basqcol.Tpo -c -o basqcol.o basqcol.c mv -f .deps/mixreads.Tpo .deps/mixreads.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT basqual.o -MD -MP -MF .deps/basqual.Tpo -c -o basqual.o basqual.c mv -f .deps/trunkreads.Tpo .deps/trunkreads.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT simqual.o -MD -MP -MF .deps/simqual.Tpo -c -o simqual.o simqual.c mv -f .deps/basqcol.Tpo .deps/basqcol.Po gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT diffstr.o -MD -MP -MF .deps/diffstr.Tpo -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c mv -f .deps/simqual.Tpo .deps/simqual.Po mv -f .deps/simread.Tpo .deps/simread.Po gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o mixreads mixreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz mv -f .deps/basqual.Tpo .deps/basqual.Po gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz mv -f .deps/diffstr.Tpo .deps/diffstr.Po gcc -I../src/ -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o simqual simqual.o basqual.o diffstr.o ../src/libseq.a -lm -lz make[3]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/misc' make[3]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6' make[3]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6' make[2]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6' make[1]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6' dh_auto_test -a make -j4 check VERBOSE=1 make[1]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6' Making check in src make[2]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/src' Making check in test make[2]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/test' make[3]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/test' make sequenceReverseComplement_test smalt_Xali_test make[4]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/test' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT sequenceReverseComplement_test.o -MD -MP -MF .deps/sequenceReverseComplement_test.Tpo -c -o sequenceReverseComplement_test.o sequenceReverseComplement_test.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-smalt.o -MD -MP -MF .deps/smalt_Xali_test-smalt.Tpo -c -o smalt_Xali_test-smalt.o `test -f '../src/smalt.c' || echo './'`../src/smalt.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-menu.o -MD -MP -MF .deps/smalt_Xali_test-menu.Tpo -c -o smalt_Xali_test-menu.o `test -f '../src/menu.c' || echo './'`../src/menu.c gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-threads.o -MD -MP -MF .deps/smalt_Xali_test-threads.Tpo -c -o smalt_Xali_test-threads.o `test -f '../src/threads.c' || echo './'`../src/threads.c mv -f .deps/sequenceReverseComplement_test.Tpo .deps/sequenceReverseComplement_test.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-infmt.o -MD -MP -MF .deps/smalt_Xali_test-infmt.Tpo -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c ../src/smalt.c: In function ‘cleanupSmaltOutput’: ../src/smalt.c:659:39: warning: unused parameter ‘errmsgp’ [-Wunused-parameter] 659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op) | ~~~~~~~~^~~~~~~ mv -f .deps/smalt_Xali_test-infmt.Tpo .deps/smalt_Xali_test-infmt.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-results.o -MD -MP -MF .deps/smalt_Xali_test-results.Tpo -c -o smalt_Xali_test-results.o `test -f '../src/results.c' || echo './'`../src/results.c ../src/results.c: In function ‘resultSetInferInsertSize’: ../src/results.c:2470:11: warning: self-comparison always evaluates to true [-Wtautological-compare] 2470 | rp->sidx == rp->sidx) { | ^~ mv -f .deps/smalt_Xali_test-threads.Tpo .deps/smalt_Xali_test-threads.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-resultpairs.o -MD -MP -MF .deps/smalt_Xali_test-resultpairs.Tpo -c -o smalt_Xali_test-resultpairs.o `test -f '../src/resultpairs.c' || echo './'`../src/resultpairs.c mv -f .deps/smalt_Xali_test-menu.Tpo .deps/smalt_Xali_test-menu.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-insert.o -MD -MP -MF .deps/smalt_Xali_test-insert.Tpo -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c mv -f .deps/smalt_Xali_test-smalt.Tpo .deps/smalt_Xali_test-smalt.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-report.o -MD -MP -MF .deps/smalt_Xali_test-report.Tpo -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c mv -f .deps/smalt_Xali_test-resultpairs.Tpo .deps/smalt_Xali_test-resultpairs.Po gcc -DHAVE_CONFIG_H -I. -I.. -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -MT smalt_Xali_test-rmap.o -MD -MP -MF .deps/smalt_Xali_test-rmap.Tpo -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c mv -f .deps/smalt_Xali_test-insert.Tpo .deps/smalt_Xali_test-insert.Po gcc -I../src/ -I../test -Wall -Wextra -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz mv -f .deps/smalt_Xali_test-results.Tpo .deps/smalt_Xali_test-results.Po mv -f .deps/smalt_Xali_test-report.Tpo .deps/smalt_Xali_test-report.Po mv -f .deps/smalt_Xali_test-rmap.Tpo .deps/smalt_Xali_test-rmap.Po gcc -I../src/ -I../test -Wall -Wextra -msse2 -g -O2 -fdebug-prefix-map=/build/smalt-g13CqB/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o smalt_Xali_test smalt_Xali_test-smalt.o smalt_Xali_test-menu.o smalt_Xali_test-threads.o smalt_Xali_test-infmt.o smalt_Xali_test-results.o smalt_Xali_test-resultpairs.o smalt_Xali_test-insert.o smalt_Xali_test-report.o smalt_Xali_test-rmap.o ../src/libsgm.a ../src/libseq.a -lbambamc -lz -lm -lpthread -lz make[4]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/test' make check-TESTS make[4]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/test' PASS: splitReads_test.py PASS: results_split_test.py PASS: ouform_cigar_test.py PASS: sample_test.py PASS: cigar_test.py PASS: mthread_test.py PASS: ioform_test.py PASS: xali_test.py PASS: bam_cigar_test.py ================== All 9 tests passed ================== make[4]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/test' make[3]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/test' make[2]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/test' Making check in misc make[2]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6/misc' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6/misc' make[2]: Entering directory '/build/smalt-g13CqB/smalt-0.7.6' make[2]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6' make[1]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6' 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/smalt-g13CqB/smalt-0.7.6' # upstream install does install more files than needed make[1]: Leaving directory '/build/smalt-g13CqB/smalt-0.7.6' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dwz: debian/smalt/usr/bin/smalt: DWARF compression not beneficial - old size 279991 new size 280073 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 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-9_amd64.deb'. dpkg-deb: building package 'smalt' in '../smalt_0.7.6-9_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../smalt_0.7.6-9_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/smalt-g13CqB /tmp/smalt-0.7.6-9ze5tzmgb I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.mzvJXYwZHn... I: success in 727.6968 seconds md5: smalt-dbgsym_0.7.6-9_amd64.deb: OK md5: smalt_0.7.6-9_amd64.deb: OK sha1: smalt-dbgsym_0.7.6-9_amd64.deb: OK sha1: smalt_0.7.6-9_amd64.deb: OK sha256: smalt-dbgsym_0.7.6-9_amd64.deb: OK sha256: smalt_0.7.6-9_amd64.deb: OK Checksums: OK