Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/segemehl/segemehl_0.3.4-5_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/segemehl-0.3.4-52efqskhx/segemehl_0.3.4-5_amd64.buildinfo Get source package info: segemehl=0.3.4-5 Source URL: http://snapshot.notset.fr/mr/package/segemehl/0.3.4-5/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.4-1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.51 bash=5.1-3+b1 binutils=2.37-4 binutils-common=2.37-4 binutils-x86-64-linux-gnu=2.37-4 bsdextrautils=2.37.2-1 bsdutils=1:2.37.2-1 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.2.1-6 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.4.1 debianutils=5.4-1 dh-autoreconf=20 dh-strip-nondeterminism=1.12.0-1 diffutils=1:3.7-5 dpkg=1.20.9 dpkg-dev=1.20.9 dwz=0.14-1 file=1:5.39-3 findutils=4.8.0-1 g++=4:10.2.1-1 g++-10=10.2.1-6 gcc=4:10.2.1-1 gcc-10=10.2.1-6 gcc-10-base=10.2.1-6 gcc-11-base=11.2.0-2 gettext=0.21-4 gettext-base=0.21-4 grep=3.6-1 groff-base=1.22.4-6 gzip=1.10-4 hostname=3.23 init-system-helpers=1.60 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-10 libarchive-zip-perl=1.68-1 libasan6=11.2.0-2 libatomic1=11.2.0-2 libattr1=1:2.4.48-6 libaudit-common=1:3.0.5-1 libaudit1=1:3.0.5-1 libbinutils=2.37-4 libblkid1=2.37.2-1 libbrotli1=1.0.9-2+b2 libbz2-1.0=1.0.8-4 libc-bin=2.31-16 libc-dev-bin=2.31-16 libc6=2.31-16 libc6-dev=2.31-16 libcap-ng0=0.7.9-2.2+b1 libcc1-0=11.2.0-2 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-1 libcrypt1=1:4.4.25-1 libctf-nobfd0=2.37-4 libctf0=2.37-4 libcurl3-gnutls=7.74.0-1.3+b1 libcurl4-gnutls-dev=7.74.0-1.3+b1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.4.1 libdeflate-dev=1.7-2 libdeflate0=1.7-2 libdpkg-perl=1.20.9 libelf1=0.185-2 libffi7=3.3-6 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.2.1-6 libgcc-s1=11.2.0-2 libgcrypt20=1.8.7-6 libgdbm-compat4=1.19-2 libgdbm6=1.19-2 libglib2.0-0=2.68.4-1 libgmp10=2:6.2.1+dfsg-1 libgnutls30=3.7.1-5 libgomp1=11.2.0-2 libgpg-error0=1.42-2 libgssapi-krb5-2=1.18.3-6 libhogweed6=3.7.3-1 libhts-dev=1.11-4 libhts3=1.11-4 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.23-1 libitm1=11.2.0-2 libk5crypto3=1.18.3-6 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-6 libkrb5support0=1.18.3-6 libldap-2.4-2=2.4.57+dfsg-3 liblsan0=11.2.0-2 liblz4-1=1.9.3-2 liblzma-dev=5.2.5-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-1 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libncurses-dev=6.2+20201114-2 libncurses6=6.2+20201114-2 libncursesw6=6.2+20201114-2 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.23.22-1 libpam-modules=1.4.0-9 libpam-modules-bin=1.4.0-9 libpam-runtime=1.4.0-9 libpam0g=1.4.0-9 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-5 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.2 libquadmath0=11.2.0-2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2.1 libsasl2-modules-db=2.1.27+dfsg-2.1 libseccomp2=2.5.1-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.37.2-1 libssh2-1=1.9.0-3 libssl1.1=1.1.1k-1 libstdc++-10-dev=10.2.1-6 libstdc++6=11.2.0-2 libsub-override-perl=0.09-2 libsystemd0=247.9-1 libtasn1-6=4.16.0-2 libtinfo6=6.2+20201114-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-2 libubsan1=11.2.0-2 libuchardet0=0.0.7-1 libudev1=247.9-1 libunistring2=0.9.10-6 libuuid1=2.37.2-1 libxml2=2.9.10+dfsg-6.7 libzstd1=1.4.8+dfsg-2.1 linux-libc-dev=5.10.46-4 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20201114-2 ncurses-bin=6.2+20201114-2 patch=2.7.6-7 perl=5.32.1-5 perl-base=5.32.1-5 perl-modules-5.32=5.32.1-5 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.7-1 sensible-utils=0.0.14 sysvinit-utils=2.96-7 tar=1.34+dfsg-1 util-linux=2.37.2-1 xz-utils=5.2.5-2 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/20210827T030044Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210827T030044Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220402T210321Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210822T204137Z/ 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 segemehl=0.3.4-5 && mkdir -p /build/segemehl-2SkcJD && dpkg-source --no-check -x /*.dsc /build/segemehl-2SkcJD/segemehl-0.3.4 && chown -R builduser:builduser /build/segemehl-2SkcJD" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/segemehl-2SkcJD/segemehl-0.3.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1629823741" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/segemehl-2SkcJD /tmp/segemehl-0.3.4-52efqskhx bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20210822T204137Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.fv2DuYx6bp 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.fv2DuYx6bp Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 134 kB of archives. After this operation, 397 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20210822T204137Z unstable/main amd64 libfakeroot amd64 1.25.3-1.1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210822T204137Z unstable/main amd64 fakeroot amd64 1.25.3-1.1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (1023 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 ... 4670 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1.1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1.1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1.1_amd64.deb ... Unpacking fakeroot (1.25.3-1.1) ... Setting up libfakeroot:amd64 (1.25.3-1.1) ... Setting up fakeroot (1.25.3-1.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-16) ... 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/20210827T030044Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210827T030044Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220402T210321Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20210822T204137Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.fv2DuYx6bp Get:1 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm InRelease [112 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20210822T204137Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main Sources [11.6 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220402T210321Z unstable/main amd64 Packages [12.4 MB] Fetched 35.4 MB in 29s (1208 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.fv2DuYx6bp I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d segemehl=0.3.4-5 && mkdir -p /build/segemehl-2SkcJD && dpkg-source --no-check -x /*.dsc /build/segemehl-2SkcJD/segemehl-0.3.4 && chown -R builduser:builduser /build/segemehl-2SkcJD"' exec /tmp/mmdebstrap.fv2DuYx6bp Reading package lists... NOTICE: 'segemehl' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/segemehl.git Please use: git clone https://salsa.debian.org/med-team/segemehl.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 254 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main segemehl 0.3.4-5 (dsc) [2032 B] Get:2 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main segemehl 0.3.4-5 (tar) [244 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210827T030044Z bookworm/main segemehl 0.3.4-5 (diff) [7788 B] Fetched 254 kB in 0s (867 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'segemehl_0.3.4-5.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting segemehl in /build/segemehl-2SkcJD/segemehl-0.3.4 dpkg-source: info: unpacking segemehl_0.3.4.orig.tar.xz dpkg-source: info: unpacking segemehl_0.3.4-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying rpath.patch dpkg-source: info: applying cross.patch dpkg-source: info: applying arm64.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/segemehl-2SkcJD/segemehl-0.3.4 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1629823741" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.fv2DuYx6bp dpkg-buildpackage: info: source package segemehl dpkg-buildpackage: info: source version 0.3.4-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j10 clean make[1]: Entering directory '/build/segemehl-2SkcJD/segemehl-0.3.4' Cleaning... rm -f -r build segemehl haarz make[1]: Leaving directory '/build/segemehl-2SkcJD/segemehl-0.3.4' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/segemehl-2SkcJD/segemehl-0.3.4' dh_auto_build -- all make -j10 "INSTALL=install --strip-program=true" all make[2]: Entering directory '/build/segemehl-2SkcJD/segemehl-0.3.4' Building... library for source build/md5.o Building... library for source build/vstack.o Building... library for source build/queryalign.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/md5.o libs/md5.c Building... library for source build/annotation.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vstack.o libs/vstack.c cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/queryalign.o libs/queryalign.c Building... library for source build/bitVector.o Building... library for source build/locus.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/annotation.o libs/annotation.c Building... library for source build/debug.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitVector.o libs/bitVector.c Building... library for source build/seqclip.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/locus.o libs/locus.c Building... library for source build/kdseed.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/seqclip.o libs/seqclip.c cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/debug.o libs/debug.c Building... library for source build/stack.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdseed.o libs/kdseed.c cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stack.o libs/stack.c In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/sw.h:38, from libs/seqclip.c:44: libs/seqclip.c: In function ‘bl_Find3PrimeGreedy’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/seqclip.c:529:9: note: in expansion of macro ‘FREEMEMORY’ 529 | FREEMEMORY(space, adapter); | ^~~~~~~~~~ libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this ‘if’ clause 528 | if(adapter) | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: libs/annotation.c: In function ‘bl_annotationitemDestruct’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:149:23: note: in expansion of macro ‘FREEMEMORY’ 149 | if(item->chromname) FREEMEMORY(space, item->chromname); | ^~~~~~~~~~ libs/annotation.c:149:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 149 | if(item->chromname) FREEMEMORY(space, item->chromname); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:150:18: note: in expansion of macro ‘FREEMEMORY’ 150 | if(item->name) FREEMEMORY(space, item->name); | ^~~~~~~~~~ libs/annotation.c:150:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 150 | if(item->name) FREEMEMORY(space, item->name); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:151:21: note: in expansion of macro ‘FREEMEMORY’ 151 | if(item->itemRgb) FREEMEMORY(space, item->itemRgb); | ^~~~~~~~~~ libs/annotation.c:151:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 151 | if(item->itemRgb) FREEMEMORY(space, item->itemRgb); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:152:24: note: in expansion of macro ‘FREEMEMORY’ 152 | if(item->blockSizes) FREEMEMORY(space, item->blockSizes); | ^~~~~~~~~~ libs/annotation.c:152:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 152 | if(item->blockSizes) FREEMEMORY(space, item->blockSizes); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:153:25: note: in expansion of macro ‘FREEMEMORY’ 153 | if(item->blockStarts) FREEMEMORY(space, item->blockStarts); | ^~~~~~~~~~ libs/annotation.c:153:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 153 | if(item->blockStarts) FREEMEMORY(space, item->blockStarts); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:154:26: note: in expansion of macro ‘FREEMEMORY’ 154 | if(item->blockRefseqs) FREEMEMORY(space, item->blockRefseqs); | ^~~~~~~~~~ libs/annotation.c:154:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 154 | if(item->blockRefseqs) FREEMEMORY(space, item->blockRefseqs); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:155:26: note: in expansion of macro ‘FREEMEMORY’ 155 | if(item->blockStrands) FREEMEMORY(space, item->blockStrands); | ^~~~~~~~~~ libs/annotation.c:155:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 155 | if(item->blockStrands) FREEMEMORY(space, item->blockStrands); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:156:20: note: in expansion of macro ‘FREEMEMORY’ 156 | if(item->source) FREEMEMORY(space, item->source); | ^~~~~~~~~~ libs/annotation.c:156:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 156 | if(item->source) FREEMEMORY(space, item->source); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: libs/annotation.c: In function ‘bl_annotationtrackDestruct’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:409:24: note: in expansion of macro ‘FREEMEMORY’ 409 | if(track->trackname) FREEMEMORY(space, track->trackname); | ^~~~~~~~~~ libs/annotation.c:409:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 409 | if(track->trackname) FREEMEMORY(space, track->trackname); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:410:23: note: in expansion of macro ‘FREEMEMORY’ 410 | if(track->filename) FREEMEMORY(space, track->filename); | ^~~~~~~~~~ libs/annotation.c:410:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 410 | if(track->filename) FREEMEMORY(space, track->filename); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:411:26: note: in expansion of macro ‘FREEMEMORY’ 411 | if(track->description) FREEMEMORY(space, track->description); | ^~~~~~~~~~ libs/annotation.c:411:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 411 | if(track->description) FREEMEMORY(space, track->description); | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:418:20: note: in expansion of macro ‘FREEMEMORY’ 418 | if(track->items) FREEMEMORY(space, track->items) ; | ^~~~~~~~~~ libs/annotation.c:418:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 418 | if(track->items) FREEMEMORY(space, track->items) ; | ^~ In file included from include/stringutils.h:27, from libs/annotation.c:29: libs/annotation.c: In function ‘bl_annotationmultitrackDestruct’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/annotation.c:455:20: note: in expansion of macro ‘FREEMEMORY’ 455 | if(track->items) FREEMEMORY(space, track->items) ; | ^~~~~~~~~~ libs/annotation.c:455:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 455 | if(track->items) FREEMEMORY(space, track->items) ; | ^~ Building... library for source build/bamio.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bamio.o libs/bamio.c Building... library for source build/vqueue.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vqueue.o libs/vqueue.c Building... library for source build/aluruSort.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/aluruSort.o libs/aluruSort.c Building... library for source build/segemehl_helper.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/segemehl_helper.o libs/segemehl_helper.c Building... library for source build/bitArray.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitArray.o libs/bitArray.c Building... library for source build/sw.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sw.o libs/sw.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from include/bamio.h:21, from libs/bamio.c:32: libs/bamio.c: In function ‘bl_bamCrossSectionDestruct’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/bamio.c:468:20: note: in expansion of macro ‘FREEMEMORY’ 468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d); | ^~~~~~~~~~ libs/bamio.c:468:5: note: some parts of macro expansion are not guarded by this ‘if’ clause 468 | if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d); | ^~ Building... library for source build/kdchain.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/kdchain.o libs/kdchain.c Building... library for source build/vtprogressbar.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/vtprogressbar.o libs/vtprogressbar.c Building... library for source build/karlin.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/karlin.o libs/karlin.c Building... library for source build/bgzip.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bgzip.o libs/bgzip.c Building... library for source build/gzidx.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/gzidx.o libs/gzidx.c Building... library for source build/portable_endian.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/portable_endian.o libs/portable_endian.c Building... library for source build/container.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/container.o libs/container.c Building... library for source build/bedfiles.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bedfiles.o libs/bedfiles.c Building... library for source build/segemehl.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/segemehl.o libs/segemehl.c Building... library for source build/memory.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/memory.o libs/memory.c Building... library for source build/junctions.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/junctions.o libs/junctions.c Building... library for source build/pigeon.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/pigeon.o libs/pigeon.c In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/segemehl.h:44, from libs/pigeon.c:35: libs/pigeon.c: In function ‘pigeon’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/pigeon.c:352:13: note: in expansion of macro ‘FREEMEMORY’ 352 | if(check) FREEMEMORY(space, check); | ^~~~~~~~~~ libs/pigeon.c:352:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 352 | if(check) FREEMEMORY(space, check); | ^~ Building... library for source build/radixsort.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/radixsort.o libs/radixsort.c Building... library for source build/sort.o Building... library for source build/match.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sort.o libs/sort.c cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/match.o libs/match.c Building... library for source build/charsequence.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/charsequence.o libs/charsequence.c In file included from libs/charsequence.c:26: libs/charsequence.c: In function ‘destructSequence’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/charsequence.c:467:4: note: in expansion of macro ‘FREEMEMORY’ 467 | FREEMEMORY(space, sequence->sequence); | ^~~~~~~~~~ libs/charsequence.c:466:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 466 | if (sequence->sequence != NULL) | ^~ In file included from libs/charsequence.c:26: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/charsequence.c:470:5: note: in expansion of macro ‘FREEMEMORY’ 470 | FREEMEMORY(space, sequence->alphabetname); | ^~~~~~~~~~ libs/charsequence.c:469:2: note: some parts of macro expansion are not guarded by this ‘if’ clause 469 | if (sequence->alphabetname != NULL) | ^~ In file included from libs/charsequence.c:26: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/charsequence.c:472:2: note: in expansion of macro ‘FREEMEMORY’ 472 | FREEMEMORY(space, sequence->url); | ^~~~~~~~~~ libs/charsequence.c:471:5: note: some parts of macro expansion are not guarded by this ‘if’ clause 471 | if (sequence->url != NULL) | ^~ In file included from libs/charsequence.c:26: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/charsequence.c:474:2: note: in expansion of macro ‘FREEMEMORY’ 474 | FREEMEMORY(space, sequence->info); | ^~~~~~~~~~ libs/charsequence.c:473:5: note: some parts of macro expansion are not guarded by this ‘if’ clause 473 | if (sequence->info != NULL) | ^~ libs/charsequence.c: In function ‘loadSequence’: libs/charsequence.c:296:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 296 | fread(s, sizeof(CharSequence), 1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/charsequence.c:304:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 304 | fread(s->description, sizeof(char), s->descrlen+1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/charsequence.c:305:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 305 | fread(s->alphabetname, sizeof(char), s->namelen+1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/charsequence.c:306:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 306 | fread(s->url, sizeof(char), s->urllen+1, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/charsequence.c:307:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 307 | fread(sequence, sizeof(char), s->length, infile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Building... library for source build/stringutils.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/stringutils.o libs/stringutils.c Building... library for source build/manout.o Building... library for source build/samio.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manout.o libs/manout.c cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samio.o libs/samio.c In file included from include/stringutils.h:27, from libs/stringutils.c:39: libs/stringutils.c: In function ‘destructStringset’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/stringutils.c:274:9: note: in expansion of macro ‘FREEMEMORY’ 274 | FREEMEMORY(space, s->strings[i].str); | ^~~~~~~~~~ libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this ‘if’ clause 273 | if(s->strings[i].str != NULL) | ^~ Building... library for source build/brendel.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/brendel.o libs/brendel.c Building... library for source build/info.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/info.o libs/info.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: libs/samio.c: In function ‘bl_samDestructTag’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:102:15: note: in expansion of macro ‘FREEMEMORY’ 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); | ^~~~~~~~~~ libs/samio.c:102:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 102 | if(kv->tag) FREEMEMORY(NULL, kv->tag); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:103:15: note: in expansion of macro ‘FREEMEMORY’ 103 | if(kv->val) FREEMEMORY(NULL, kv->val); | ^~~~~~~~~~ libs/samio.c:103:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 103 | if(kv->val) FREEMEMORY(NULL, kv->val); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:104:16: note: in expansion of macro ‘FREEMEMORY’ 104 | if(kv->type) FREEMEMORY(NULL, kv->type); | ^~~~~~~~~~ libs/samio.c:104:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 104 | if(kv->type) FREEMEMORY(NULL, kv->type); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:105:15: note: in expansion of macro ‘FREEMEMORY’ 105 | if(kv->key) FREEMEMORY(NULL, kv->key); | ^~~~~~~~~~ libs/samio.c:105:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 105 | if(kv->key) FREEMEMORY(NULL, kv->key); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: libs/samio.c: In function ‘bl_samDestruct’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:112:21: note: in expansion of macro ‘FREEMEMORY’ 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); | ^~~~~~~~~~ libs/samio.c:112:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 112 | if(samrec->qname) FREEMEMORY(NULL, samrec->qname); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:113:21: note: in expansion of macro ‘FREEMEMORY’ 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); | ^~~~~~~~~~ libs/samio.c:113:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 113 | if(samrec->rname) FREEMEMORY(NULL, samrec->rname); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:114:21: note: in expansion of macro ‘FREEMEMORY’ 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); | ^~~~~~~~~~ libs/samio.c:114:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 114 | if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:115:21: note: in expansion of macro ‘FREEMEMORY’ 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); | ^~~~~~~~~~ libs/samio.c:115:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 115 | if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:116:21: note: in expansion of macro ‘FREEMEMORY’ 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); | ^~~~~~~~~~ libs/samio.c:116:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 116 | if(samrec->seq) FREEMEMORY(NULL, samrec->seq); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:117:21: note: in expansion of macro ‘FREEMEMORY’ 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); | ^~~~~~~~~~ libs/samio.c:117:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 117 | if(samrec->qual) FREEMEMORY(NULL, samrec->qual); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from include/samio.h:23, from libs/samio.c:33: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/samio.c:121:20: note: in expansion of macro ‘FREEMEMORY’ 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); | ^~~~~~~~~~ libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 121 | if(samrec->tags) FREEMEMORY(NULL, samrec->tags); | ^~ libs/info.c: In function ‘timestr_r’: libs/info.c:64:50: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~ libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from libs/info.c:41: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 16 and 67 bytes into a destination of size 26 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/info.c: In function ‘infomsg’: libs/info.c:64:50: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~ libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from libs/info.c:41: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 16 and 67 bytes into a destination of size 26 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/info.c: In function ‘nfolevel’: libs/info.c:64:50: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~ libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647] 64 | sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from libs/info.c:41: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 16 and 67 bytes into a destination of size 26 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Building... library for source build/gzip.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/gzip.o libs/gzip.c Building... library for source build/sufarray.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/sufarray.o libs/sufarray.c Building... library for source build/fileBins.o Building... library for source build/splitalign.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileBins.o libs/fileBins.c cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/splitalign.o libs/splitalign.c Building... library for source build/iupac.o Building... library for source build/bitvectoralg.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/iupac.o libs/iupac.c cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/bitvectoralg.o libs/bitvectoralg.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, from libs/sufarray.c:39: libs/sufarray.c: In function ‘destructSufArr’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:613:5: note: in expansion of macro ‘FREEMEMORY’ 613 | FREEMEMORY(space, arr->lcpctab); | ^~~~~~~~~~ libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 612 | if (arr->lcpctab != NULL) | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, from libs/sufarray.c:39: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:615:5: note: in expansion of macro ‘FREEMEMORY’ 615 | FREEMEMORY(space, arr->inv_suftab); | ^~~~~~~~~~ libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 614 | if (arr->inv_suftab != NULL) | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, from libs/sufarray.c:39: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:619:5: note: in expansion of macro ‘FREEMEMORY’ 619 | FREEMEMORY(space, arr->idvtab); | ^~~~~~~~~~ libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 618 | if (arr->idvtab != NULL) | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, from libs/sufarray.c:39: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:624:5: note: in expansion of macro ‘FREEMEMORY’ 624 | FREEMEMORY(space, arr->suflink); | ^~~~~~~~~~ libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 620 | if (arr->suflink != NULL) | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, from libs/sufarray.c:39: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:627:5: note: in expansion of macro ‘FREEMEMORY’ 627 | FREEMEMORY(space, arr->chldtab); | ^~~~~~~~~~ libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 626 | if (arr->chldtab != NULL) | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, from libs/sufarray.c:39: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:629:5: note: in expansion of macro ‘FREEMEMORY’ 629 | FREEMEMORY(space, arr->mdfive); | ^~~~~~~~~~ libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 628 | if (arr->mdfive) | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, from libs/sufarray.c:39: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:631:5: note: in expansion of macro ‘FREEMEMORY’ 631 | FREEMEMORY(space, arr->llvtab); | ^~~~~~~~~~ libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 630 | if(arr->llvtab != NULL) | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/sufarray.h:45, from libs/sufarray.c:39: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/sufarray.c:636:5: note: in expansion of macro ‘FREEMEMORY’ 636 | FREEMEMORY(space, arr->id); | ^~~~~~~~~~ libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 632 | if(arr->id != NULL) | ^~ libs/sufarray.c: In function ‘readSuffixarray’: libs/sufarray.c:428:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 428 | fread(&nmemb, sizeof(Uint), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:430:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 430 | fread(suftab, sizeof(Uint), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:431:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 431 | fread(&flags, sizeof(char), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:436:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 436 | fread(lcpctab, sizeof(unsigned char), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:438:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 438 | fread(&llvmemb, sizeof(Uint), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:440:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 440 | fread(llvtab, sizeof(PairUint), llvmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:446:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 446 | fread(chldtab, sizeof(childtab), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:484:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | fread(suflink, sizeof(Uint), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:508:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 508 | fread(id, sizeof(signed char), nmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:511:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 511 | fread(&idvmemb, sizeof(Uint), 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:515:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 515 | fread(idvtab, sizeof(PairLSint), idvmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:519:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 519 | fread(idvutab, sizeof(PairUint), idvmemb, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libs/sufarray.c:530:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(mdfive, sizeof(unsigned char), 16, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Building... library for source build/intervaltree.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/intervaltree.o libs/intervaltree.c Building... library for source build/haarz.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/haarz.o libs/haarz.c In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/bitvectoralg.h:32, from include/splitalign.h:29, from libs/splitalign.c:32: libs/splitalign.c: In function ‘bl_fixSplitAlignHoffmann’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1323:25: note: in expansion of macro ‘FREEMEMORY’ 1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); | ^~~~~~~~~~ libs/splitalign.c:1323:7: note: some parts of macro expansion are not guarded by this ‘if’ clause 1323 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); | ^~ In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/bitvectoralg.h:32, from include/splitalign.h:29, from libs/splitalign.c:32: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1324:25: note: in expansion of macro ‘FREEMEMORY’ 1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); | ^~~~~~~~~~ libs/splitalign.c:1324:7: note: some parts of macro expansion are not guarded by this ‘if’ clause 1324 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); | ^~ In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/bitvectoralg.h:32, from include/splitalign.h:29, from libs/splitalign.c:32: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1325:26: note: in expansion of macro ‘FREEMEMORY’ 1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); | ^~~~~~~~~~ libs/splitalign.c:1325:7: note: some parts of macro expansion are not guarded by this ‘if’ clause 1325 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); | ^~ In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/bitvectoralg.h:32, from include/splitalign.h:29, from libs/splitalign.c:32: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1326:26: note: in expansion of macro ‘FREEMEMORY’ 1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); | ^~~~~~~~~~ libs/splitalign.c:1326:7: note: some parts of macro expansion are not guarded by this ‘if’ clause 1326 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); | ^~ In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/bitvectoralg.h:32, from include/splitalign.h:29, from libs/splitalign.c:32: libs/splitalign.c: In function ‘bl_fixSplitAlignBrendel’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1565:27: note: in expansion of macro ‘FREEMEMORY’ 1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); | ^~~~~~~~~~ libs/splitalign.c:1565:9: note: some parts of macro expansion are not guarded by this ‘if’ clause 1565 | if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]); | ^~ In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/bitvectoralg.h:32, from include/splitalign.h:29, from libs/splitalign.c:32: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1566:27: note: in expansion of macro ‘FREEMEMORY’ 1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); | ^~~~~~~~~~ libs/splitalign.c:1566:9: note: some parts of macro expansion are not guarded by this ‘if’ clause 1566 | if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]); | ^~ In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/bitvectoralg.h:32, from include/splitalign.h:29, from libs/splitalign.c:32: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1567:28: note: in expansion of macro ‘FREEMEMORY’ 1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); | ^~~~~~~~~~ libs/splitalign.c:1567:9: note: some parts of macro expansion are not guarded by this ‘if’ clause 1567 | if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]); | ^~ In file included from include/stringutils.h:27, from include/biofiles.h:43, from include/alignment.h:38, from include/bitvectoralg.h:32, from include/splitalign.h:29, from libs/splitalign.c:32: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/splitalign.c:1568:28: note: in expansion of macro ‘FREEMEMORY’ 1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); | ^~~~~~~~~~ libs/splitalign.c:1568:9: note: some parts of macro expansion are not guarded by this ‘if’ clause 1568 | if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]); | ^~ In file included from libs/fileBins.c:51: libs/fileBins.c: In function ‘bl_fileBinsSortLine’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/fileBins.c:901:18: note: in expansion of macro ‘FREEMEMORY’ 901 | if(fileSort) FREEMEMORY(space, line); | ^~~~~~~~~~ libs/fileBins.c:901:5: note: some parts of macro expansion are not guarded by this ‘if’ clause 901 | if(fileSort) FREEMEMORY(space, line); | ^~ Building... library for source build/manopt.o Building... library for source build/mathematics.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mathematics.o libs/mathematics.c cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/manopt.o libs/manopt.c In file included from include/mathematics.h:117, from libs/intervaltree.c:27: libs/intervaltree.c: In function ‘bl_intervaltreeDestruct’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/intervaltree.c:443:19: note: in expansion of macro ‘FREEMEMORY’ 443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions); | ^~~~~~~~~~ libs/intervaltree.c:443:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 443 | if(root->ncoll) FREEMEMORY(NULL, root->collisions); | ^~ Building... library for source build/multicharseq.o In file included from include/mathematics.h:117, from libs/mathematics.c:38: libs/mathematics.c: In function ‘destructVector’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/mathematics.c:251:23: note: in expansion of macro ‘FREEMEMORY’ 251 | if (v->elements) FREEMEMORY(space, v->elements); | ^~~~~~~~~~ libs/mathematics.c:251:6: note: some parts of macro expansion are not guarded by this ‘if’ clause 251 | if (v->elements) FREEMEMORY(space, v->elements); | ^~ cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/multicharseq.o libs/multicharseq.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from libs/multicharseq.c:38: libs/multicharseq.c: In function ‘destructMultiCharSeq’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/multicharseq.c:212:7: note: in expansion of macro ‘FREEMEMORY’ 212 | FREEMEMORY(space, mseq->markpos); | ^~~~~~~~~~ libs/multicharseq.c:211:2: note: some parts of macro expansion are not guarded by this ‘if’ clause 211 | if (mseq->markpos != NULL) | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from libs/multicharseq.c:38: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/multicharseq.c:214:7: note: in expansion of macro ‘FREEMEMORY’ 214 | FREEMEMORY(space, mseq->map); | ^~~~~~~~~~ libs/multicharseq.c:213:2: note: some parts of macro expansion are not guarded by this ‘if’ clause 213 | if (mseq->map != NULL) | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/multicharseq.h:43, from libs/multicharseq.c:38: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/multicharseq.c:216:7: note: in expansion of macro ‘FREEMEMORY’ 216 | FREEMEMORY(space, mseq->ref); | ^~~~~~~~~~ libs/multicharseq.c:215:5: note: some parts of macro expansion are not guarded by this ‘if’ clause 215 | if (mseq->ref != NULL) | ^~ Building... library for source build/filebuffer.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/filebuffer.o libs/filebuffer.c Building... library for source build/mapfrag.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mapfrag.o libs/mapfrag.c Building... library for source build/mappingqual.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/mappingqual.o libs/mappingqual.c Building... library for source build/nw.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/nw.o libs/nw.c Building... library for source build/alignment.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/alignment.o libs/alignment.c In file included from include/mathematics.h:117, from libs/alignment.c:38: libs/alignment.c: In function ‘wrapAlignment’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/alignment.c:97:18: note: in expansion of macro ‘FREEMEMORY’ 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); | ^~~~~~~~~~ libs/alignment.c:97:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 97 | if(al->rmvseq) FREEMEMORY(NULL, al->v); | ^~ In file included from include/mathematics.h:117, from libs/alignment.c:38: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/alignment.c:98:18: note: in expansion of macro ‘FREEMEMORY’ 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); | ^~~~~~~~~~ libs/alignment.c:98:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 98 | if(al->rmuseq) FREEMEMORY(NULL, al->u); | ^~ Building... library for source build/matealign.o Building... library for source build/biofiles.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/matealign.o libs/matealign.c cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/biofiles.o libs/biofiles.c In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/locus.h:41, from include/mapfrag.h:39, from libs/matealign.c:32: libs/matealign.c: In function ‘bl_matealign’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/matealign.c:313:15: note: in expansion of macro ‘FREEMEMORY’ 313 | if(npos[0]) FREEMEMORY(NULL, spos[0]); | ^~~~~~~~~~ libs/matealign.c:313:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 313 | if(npos[0]) FREEMEMORY(NULL, spos[0]); | ^~ In file included from include/stringutils.h:27, from include/charsequence.h:43, from include/locus.h:41, from include/mapfrag.h:39, from libs/matealign.c:32: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/matealign.c:314:15: note: in expansion of macro ‘FREEMEMORY’ 314 | if(npos[1]) FREEMEMORY(NULL, spos[1]); | ^~~~~~~~~~ libs/matealign.c:314:3: note: some parts of macro expansion are not guarded by this ‘if’ clause 314 | if(npos[1]) FREEMEMORY(NULL, spos[1]); | ^~ Building... library for source build/fileio.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/fileio.o libs/fileio.c Building... library for source build/merge.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/merge.o libs/merge.c libs/fileio.c: In function ‘bl_rm’: libs/fileio.c:220:3: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 220 | system(cmd); | ^~~~~~~~~~~ Building... library for source build/samheader.o cc -g -O2 -ffile-prefix-map=/build/segemehl-2SkcJD/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o build/samheader.o libs/samheader.c In file included from include/stringutils.h:27, from libs/merge.c:34: libs/merge.c: In function ‘se_mergeWorker’: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/merge.c:1096:20: note: in expansion of macro ‘FREEMEMORY’ 1096 | if(curkey) FREEMEMORY(NULL, curkey); | ^~~~~~~~~~ libs/merge.c:1096:9: note: some parts of macro expansion are not guarded by this ‘if’ clause 1096 | if(curkey) FREEMEMORY(NULL, curkey); | ^~ In file included from include/stringutils.h:27, from libs/merge.c:34: include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros] 32 | #define FREEMEMORY(X,PTR) free(PTR); PTR=NULL | ^~~~ libs/merge.c:1216:26: note: in expansion of macro ‘FREEMEMORY’ 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); | ^~~~~~~~~~ libs/merge.c:1216:5: note: some parts of macro expansion are not guarded by this ‘if’ clause 1216 | if(!reads && curkey) FREEMEMORY(NULL, curkey); | ^~ Linking segemehl cc build/md5.o build/vstack.o build/queryalign.o build/annotation.o build/bitVector.o build/locus.o build/seqclip.o build/debug.o build/kdseed.o build/stack.o build/bamio.o build/vqueue.o build/aluruSort.o build/segemehl_helper.o build/bitArray.o build/sw.o build/kdchain.o build/vtprogressbar.o build/karlin.o build/bgzip.o build/gzidx.o build/portable_endian.o build/container.o build/bedfiles.o build/memory.o build/junctions.o build/pigeon.o build/radixsort.o build/sort.o build/match.o build/charsequence.o build/stringutils.o build/samio.o build/manout.o build/brendel.o build/info.o build/gzip.o build/sufarray.o build/fileBins.o build/splitalign.o build/iupac.o build/bitvectoralg.o build/intervaltree.o build/manopt.o build/mathematics.o build/multicharseq.o build/filebuffer.o build/mapfrag.o build/mappingqual.o build/nw.o build/alignment.o build/matealign.o build/biofiles.o build/fileio.o build/merge.o build/samheader.o build/segemehl.o -o ./segemehl.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now Linking haarz cc build/md5.o build/vstack.o build/queryalign.o build/annotation.o build/bitVector.o build/locus.o build/seqclip.o build/debug.o build/kdseed.o build/stack.o build/bamio.o build/vqueue.o build/aluruSort.o build/segemehl_helper.o build/bitArray.o build/sw.o build/kdchain.o build/vtprogressbar.o build/karlin.o build/bgzip.o build/gzidx.o build/portable_endian.o build/container.o build/bedfiles.o build/memory.o build/junctions.o build/pigeon.o build/radixsort.o build/sort.o build/match.o build/charsequence.o build/stringutils.o build/samio.o build/manout.o build/brendel.o build/info.o build/gzip.o build/sufarray.o build/fileBins.o build/splitalign.o build/iupac.o build/bitvectoralg.o build/intervaltree.o build/manopt.o build/mathematics.o build/multicharseq.o build/filebuffer.o build/mapfrag.o build/mappingqual.o build/nw.o build/alignment.o build/matealign.o build/biofiles.o build/fileio.o build/merge.o build/samheader.o build/haarz.o -o ./haarz.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now make[2]: Leaving directory '/build/segemehl-2SkcJD/segemehl-0.3.4' make[1]: Leaving directory '/build/segemehl-2SkcJD/segemehl-0.3.4' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install -a debian/rules override_dh_install make[1]: Entering directory '/build/segemehl-2SkcJD/segemehl-0.3.4' mv segemehl.x segemehl mv haarz.x haarz find . -name "*.x" dh_install make[1]: Leaving directory '/build/segemehl-2SkcJD/segemehl-0.3.4' dh_installdocs -a dh_installchangelogs -a dh_installexamples -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 -a dh_strip -a -a dh_makeshlibs -a -a dh_shlibdeps -a -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'segemehl' in '../segemehl_0.3.4-5_amd64.deb'. dpkg-deb: building package 'segemehl-dbgsym' in '../segemehl-dbgsym_0.3.4-5_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../segemehl_0.3.4-5_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/segemehl-2SkcJD /tmp/segemehl-0.3.4-52efqskhx I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.fv2DuYx6bp... I: success in 335.2734 seconds md5: Value of 'md5' differs for segemehl-dbgsym_0.3.4-5_amd64.deb md5: Size differs for segemehl-dbgsym_0.3.4-5_amd64.deb md5: Value of 'md5' differs for segemehl_0.3.4-5_amd64.deb md5: Size differs for segemehl_0.3.4-5_amd64.deb sha1: Value of 'sha1' differs for segemehl-dbgsym_0.3.4-5_amd64.deb sha1: Size differs for segemehl-dbgsym_0.3.4-5_amd64.deb sha1: Value of 'sha1' differs for segemehl_0.3.4-5_amd64.deb sha1: Size differs for segemehl_0.3.4-5_amd64.deb sha256: Value of 'sha256' differs for segemehl-dbgsym_0.3.4-5_amd64.deb sha256: Size differs for segemehl-dbgsym_0.3.4-5_amd64.deb sha256: Value of 'sha256' differs for segemehl_0.3.4-5_amd64.deb sha256: Size differs for segemehl_0.3.4-5_amd64.deb Checksums: FAIL Cannot generate diffoscope for segemehl-dbgsym_0.3.4-5_amd64.deb: Cannot find URL: http://snapshot.notset.fr/mr/file/33e5d6b5c07ea7071636761d1f33c87baa44a5384f6238916a81ddb6ff3a0ebe/download Cannot generate diffoscope for segemehl_0.3.4-5_amd64.deb: RetryError[]