Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/g/gff2aplot/gff2aplot_2.0-14_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/gff2aplot-2.0-14sa376wp0/gff2aplot_2.0-14_amd64.buildinfo Get source package info: gff2aplot=2.0-14 Source URL: http://snapshot.notset.fr/mr/package/gff2aplot/2.0-14/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=2.37-5 binutils-common=2.37-5 binutils-x86-64-linux-gnu=2.37-5 bsdextrautils=2.37.2-2 bsdutils=1:2.37.2-2 build-essential=12.9 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.1-1 cpp-10=10.3.0-9 dash=0.5.11+git20210120+802ebd4-1 debconf=1.5.77 debhelper=13.5.1 debianutils=5.4-3 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=10.3.0-9 gcc=4:10.2.1-1 gcc-10=10.3.0-9 gcc-10-base=10.3.0-9 gcc-11-base=11.2.0-4 gettext=0.21-4 gettext-base=0.21-4 grep=3.7-1 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=2.3.1-1 libarchive-zip-perl=1.68-1 libasan6=11.2.0-4 libatomic1=11.2.0-4 libattr1=1:2.5.1-1 libaudit-common=1:3.0.5-1 libaudit1=1:3.0.5-1 libbinutils=2.37-5 libblkid1=2.37.2-2 libbz2-1.0=1.0.8-4 libc-bin=2.32-2 libc-dev-bin=2.32-2 libc6=2.32-2 libc6-dev=2.32-2 libcap-ng0=0.7.9-2.2+b1 libcc1-0=11.2.0-4 libcom-err2=1.46.4-1 libcrypt-dev=1:4.4.25-2 libcrypt1=1:4.4.25-2 libctf-nobfd0=2.37-5 libctf0=2.37-5 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.260 libdebhelper-perl=13.5.1 libdpkg-perl=1.20.9 libelf1=0.185-2 libfile-stripnondeterminism-perl=1.12.0-1 libgcc-10-dev=10.3.0-9 libgcc-s1=11.2.0-4 libgcrypt20=1.9.4-2 libgdbm-compat4=1.20-1 libgdbm6=1.20-1 libgmp10=2:6.2.1+dfsg-1 libgomp1=11.2.0-4 libgpg-error0=1.42-3 libgssapi-krb5-2=1.18.3-7 libicu67=67.1-7 libisl23=0.23-1 libitm1=11.2.0-4 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 liblsan0=11.2.0-4 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.39-3 libmagic1=1:5.39-3 libmount1=2.37.2-2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libpam-modules=1.4.0-10 libpam-modules-bin=1.4.0-10 libpam-runtime=1.4.0-10 libpam0g=1.4.0-10 libpcre2-8-0=10.36-2 libpcre3=2:8.39-13 libperl5.32=5.32.1-5 libpipeline1=1.5.3-1 libquadmath0=11.2.0-4 libseccomp2=2.5.2-1 libselinux1=3.1-3 libsigsegv2=2.13-1 libsmartcols1=2.37.2-2 libssl1.1=1.1.1l-1 libstdc++-10-dev=10.3.0-9 libstdc++6=11.2.0-4 libsub-override-perl=0.09-2 libsystemd0=247.9-1 libtinfo6=6.2+20201114-4 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-4 libubsan1=11.2.0-4 libuchardet0=0.0.7-1 libudev1=247.9-1 libunistring2=0.9.10-6 libuuid1=2.37.2-2 libxml2=2.9.12+dfsg-3 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+20201114-4 ncurses-bin=6.2+20201114-4 patch=2.7.6-7 perl=5.32.1-5 perl-base=5.32.1-5 perl-modules-5.32=5.32.1-5 po-debconf=1.0.21+nmu1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=2.96-7 tar=1.34+dfsg-1 util-linux=2.37.2-2 xz-utils=5.2.5-2 zlib1g=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/20210919T145255Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210919T145255Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210908T210625Z/ 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 gff2aplot=2.0-14 && mkdir -p /build/gff2aplot-ou119N && dpkg-source --no-check -x /*.dsc /build/gff2aplot-ou119N/gff2aplot-2.0 && chown -R builduser:builduser /build/gff2aplot-ou119N" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gff2aplot-ou119N/gff2aplot-2.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1631163531" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/gff2aplot-ou119N /tmp/gff2aplot-2.0-14sa376wp0 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20210908T210625Z 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.8zX8vDcKNZ 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.8zX8vDcKNZ Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-2). 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/20210908T210625Z unstable/main amd64 libfakeroot amd64 1.26-1 [47.3 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210908T210625Z unstable/main amd64 fakeroot amd64 1.26-1 [87.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (781 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 ... 4664 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.26-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.26-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.26-1_amd64.deb ... Unpacking fakeroot (1.26-1) ... Setting up libfakeroot:amd64 (1.26-1) ... Setting up fakeroot (1.26-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.32-2) ... 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/20210919T145255Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210919T145255Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210908T210625Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.8zX8vDcKNZ Get:1 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm InRelease [128 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20210908T210625Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main Sources [11.6 MB] Get:4 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.0 MB in 20s (1169 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.8zX8vDcKNZ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d gff2aplot=2.0-14 && mkdir -p /build/gff2aplot-ou119N && dpkg-source --no-check -x /*.dsc /build/gff2aplot-ou119N/gff2aplot-2.0 && chown -R builduser:builduser /build/gff2aplot-ou119N"' exec /tmp/mmdebstrap.8zX8vDcKNZ Reading package lists... NOTICE: 'gff2aplot' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/gff2aplot.git Please use: git clone https://salsa.debian.org/med-team/gff2aplot.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 351 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main gff2aplot 2.0-14 (dsc) [2044 B] Get:2 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main gff2aplot 2.0-14 (tar) [328 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210919T145255Z bookworm/main gff2aplot 2.0-14 (diff) [20.7 kB] Fetched 351 kB in 1s (655 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'gff2aplot_2.0-14.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting gff2aplot in /build/gff2aplot-ou119N/gff2aplot-2.0 dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz dpkg-source: info: unpacking gff2aplot_2.0-14.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying non_lexical_loop_iterator.patch dpkg-source: info: applying 02-blat2gff.diff dpkg-source: info: applying 03-parseblast.diff dpkg-source: info: applying use-dpkg-buildflags.patch dpkg-source: info: applying mayhem.patch dpkg-source: info: applying fis-privacy-breach.patch dpkg-source: info: applying perl_5.28.patch dpkg-source: info: applying fix_install_ali2gff.patch dpkg-source: info: applying enhance_sprintf_buffer.patch dpkg-source: info: applying fix_README_used_for_test.patch dpkg-source: info: applying fix_gff_comments.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/gff2aplot-ou119N/gff2aplot-2.0 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1631163531" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.8zX8vDcKNZ dpkg-buildpackage: info: source package gff2aplot dpkg-buildpackage: info: source version 2.0-14 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/gff2aplot-ou119N/gff2aplot-2.0' rm -f src/ali2gff/ali2gff bin/ali2gff make[1]: Leaving directory '/build/gff2aplot-ou119N/gff2aplot-2.0' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j4 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/gff2aplot-ou119N/gff2aplot-2.0' ### /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. ### RUNNING MAKEFILE ### ### Finishing PERL script from "src/gff2aplot.pl" -> "bin/gff2aplot.pl" /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. ### Fri Nov 12 15:18:12 UTC 2021 -- builduser ### ### Finishing PERL script from "src/parseblast.pl" -> "bin/parseblast.pl" /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. ### Finishing PERL script from "src/blat2gff.pl" -> "bin/blat2gff.pl" /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. ### Finishing PERL script from "src/sim2gff.pl" -> "bin/sim2gff.pl" ### Making ALI2GFF... ### ### MAKEFILE DONE... make[2]: Entering directory '/build/gff2aplot-ou119N/gff2aplot-2.0/src/ali2gff' ### ali2gff.c: In function ‘main’: ali2gff.c:88:8: warning: variable ‘ptr’ set but not used [-Wunused-but-set-variable] 88 | char *ptr; | ^~~ ali2gff.c: In function ‘processMumfile’: ali2gff.c:527:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 527 | if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); | ~^ ~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld ali2gff.c:527:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 527 | if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); | ~^ ~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld ali2gff.c:768:51: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 768 | if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); | ~^ ~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld ali2gff.c:768:57: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 768 | if (DEBUG) fprintf(stderr,"gap data: length %d-20=%d\n%s\n%s\n%s\n",strlen(seq1),strlen(seq1)-20,seq1,seq2,err); | ~^ ~~~~~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld ali2gff.c: In function ‘processGFFfile’: ali2gff.c:355:71: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 355 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", xName,yName,source,xb,yb,xe,ye,scores,strands,frames); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from ali2gff.h:20, from ali2gff.c:64: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 25 or more bytes (assuming 4028) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:354:71: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 354 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",xName,yName,source,xb,yb,xe,ye,score ,strands,frames); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from ali2gff.h:20, from ali2gff.c:64: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 2034) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:351:71: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 351 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", xName,yName,source,xb,yb,xe,ye,scores,strands,frames,cptr); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from ali2gff.h:20, from ali2gff.c:64: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 25 or more bytes (assuming 4028) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:350:71: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 350 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",xName,yName,source,xb,yb,xe,ye,score ,strands,frames,cptr); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from ali2gff.h:20, from ali2gff.c:64: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 2034) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:300:71: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 300 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", yName,xName,source,yb,xb,ye,xe,scores,strands,frames); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from ali2gff.h:20, from ali2gff.c:64: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 25 or more bytes (assuming 4028) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:299:71: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 299 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",yName,xName,source,yb,xb,ye,xe,score,strands,frames); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from ali2gff.h:20, from ali2gff.c:64: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 2034) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:296:71: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 296 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", yName,xName,source,yb,xb,ye,xe,scores,strands,frames,cptr); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from ali2gff.h:20, from ali2gff.c:64: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 25 or more bytes (assuming 4028) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:295:71: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 295 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",yName,xName,source,yb,xb,ye,xe,score,strands,frames,cptr); | ^~ ~~~~~ In file included from /usr/include/stdio.h:866, from ali2gff.h:20, from ali2gff.c:64: /usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 30 or more bytes (assuming 2034) into a destination of size 1000 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processMumfile’: ali2gff.c:732:12: warning: ‘score’ may be used uninitialized in this function [-Wmaybe-uninitialized] 732 | score = (score - errCount)/score; // match percentage | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c: In function ‘processSimfile’: ali2gff.c:1073:15: warning: ‘yrev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1073 | ye = yrev-ye; | ~~~~^~~ ali2gff.c:1064:41: warning: ‘yseqLen_4’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) { | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ ali2gff.c:1064:15: warning: ‘xseqLen_4’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) { | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:519, from ali2gff.h:22, from ali2gff.c:64: In function ‘strncpy’, inlined from ‘main’ at ali2gff.c:135:2: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:91:10: warning: ‘__builtin_strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation] 91 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/build/gff2aplot-ou119N/gff2aplot-2.0/src/ali2gff' mkdir -p ./bin cp ./src/ali2gff/ali2gff \ ./bin/ali2gff /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. mode of 'bin/gff2aplot.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/parseblast.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/blat2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) mode of 'bin/sim2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x) make[1]: Leaving directory '/build/gff2aplot-ou119N/gff2aplot-2.0' dh_auto_test -a make -j4 test make[1]: Entering directory '/build/gff2aplot-ou119N/gff2aplot-2.0' ### SORRY !!! Tests were not implemented yet... make[1]: Leaving directory '/build/gff2aplot-ou119N/gff2aplot-2.0' create-stamp debian/debhelper-build-stamp dh_prep -a dh_installdirs -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/gff2aplot-ou119N/gff2aplot-2.0' for script in `find bin -name "*.pl"` ; do mv $script bin/`basename $script .pl` ; done make[1]: Leaving directory '/build/gff2aplot-ou119N/gff2aplot-2.0' dh_install -a dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/gff2aplot-ou119N/gff2aplot-2.0' dh_installexamples # Fix path names, silence GS find debian/*/usr/share/doc/*/examples -name README -exec sed -i \ -e 's?^$BIN/\([0-9a-z]\+\)\.pl?\1?' \ -e 's?^$BIN/\([0-9a-z]\+\) ?\1 ?' \ -e 's?^GS=.*;?GS="gs -q" ;?' \{\} \; make[1]: Leaving directory '/build/gff2aplot-ou119N/gff2aplot-2.0' 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 'gff2aplot' in '../gff2aplot_2.0-14_amd64.deb'. dpkg-deb: building package 'gff2aplot-dbgsym' in '../gff2aplot-dbgsym_2.0-14_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../gff2aplot_2.0-14_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/gff2aplot-ou119N /tmp/gff2aplot-2.0-14sa376wp0 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.8zX8vDcKNZ... I: success in 1360.0020 seconds md5: gff2aplot-dbgsym_2.0-14_amd64.deb: OK md5: gff2aplot_2.0-14_amd64.deb: OK sha1: gff2aplot-dbgsym_2.0-14_amd64.deb: OK sha1: gff2aplot_2.0-14_amd64.deb: OK sha256: gff2aplot-dbgsym_2.0-14_amd64.deb: OK sha256: gff2aplot_2.0-14_amd64.deb: OK Checksums: OK