Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/a/aegean/aegean_0.16.0+dfsg-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/aegean-0.16.0+dfsg-2s6qjzblo/aegean_0.16.0+dfsg-2_amd64.buildinfo Get source package info: aegean=0.16.0+dfsg-2 Source URL: http://snapshot.notset.fr/mr/package/aegean/0.16.0+dfsg-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11 automake=1:1.16.1-4 autopoint=0.19.8.1-9 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.46 bash=5.0-4 binutils=2.32.51.20190821-2 binutils-common=2.32.51.20190821-2 binutils-x86-64-linux-gnu=2.32.51.20190821-2 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.7 bzip2=1.0.8-2 coreutils=8.30-3+b1 cpp=4:9.2.1-3 cpp-9=9.2.1-7 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.5.4 debianutils=4.9 dh-autoreconf=19 dh-strip-nondeterminism=1.6.0-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-1 fdisk=2.34-0.1 file=1:5.37-5 findutils=4.7.0-1 fontconfig=2.13.1-2+b1 fontconfig-config=2.13.1-2 fonts-dejavu-core=2.37-1 g++=4:9.2.1-3 g++-9=9.2.1-7 gcc=4:9.2.1-3 gcc-9=9.2.1-7 gcc-9-base=9.2.1-7 genometools-common=1.5.10+ds-3 gettext=0.19.8.1-9 gettext-base=0.19.8.1-9 grep=3.3-1 groff-base=1.22.4-3 gzip=1.9-3+b1 hostname=3.22+b1 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-4 libarchive-zip-perl=1.65-1 libasan5=9.2.1-7 libatomic1=9.2.1-7 libattr1=1:2.4.48-4 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2 libbinutils=2.32.51.20190821-2 libblkid-dev=2.34-0.1 libblkid1=2.34-0.1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.28-10 libc-dev-bin=2.28-10 libc6=2.28-10 libc6-dev=2.28-10 libcairo-gobject2=1.16.0-4 libcairo-script-interpreter2=1.16.0-4 libcairo2=1.16.0-4 libcairo2-dev=1.16.0-4 libcap-ng0=0.7.9-2+b1 libcc1-0=9.2.1-7 libcroco3=0.6.13-1 libdatrie1=0.2.12-3 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.249 libdpkg-perl=1.19.7 libelf1=0.176-1.1 libexpat1=2.2.7-2 libexpat1-dev=2.2.7-2 libfdisk1=2.34-0.1 libffi-dev=3.2.1-9 libffi6=3.2.1-9 libfile-stripnondeterminism-perl=1.6.0-1 libfontconfig1=2.13.1-2+b1 libfontconfig1-dev=2.13.1-2+b1 libfreetype6=2.9.1-4 libfreetype6-dev=2.9.1-4 libfribidi0=1.0.5-3.1 libgcc-9-dev=9.2.1-7 libgcc1=1:9.2.1-7 libgcrypt20=1.8.5-2 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libgenometools0=1.5.10+ds-3 libgenometools0-dev=1.5.10+ds-3 libglib2.0-0=2.60.6-2 libglib2.0-bin=2.60.6-2 libglib2.0-data=2.60.6-2 libglib2.0-dev=2.60.6-2 libglib2.0-dev-bin=2.60.6-2 libgmp10=2:6.1.2+dfsg-4 libgomp1=9.2.1-7 libgpg-error0=1.36-7 libgraphite2-3=1.3.13-8 libharfbuzz0b=2.6.1-2 libice-dev=2:1.0.9-2 libice6=2:1.0.9-2 libicu63=63.2-2 libisl19=0.20-2 libitm1=9.2.1-7 liblsan0=9.2.1-7 liblua5.1-0=5.1.5-8.1+b3 liblz4-1=1.8.3-1+b1 liblzma5=5.2.4-1+b1 liblzo2-2=2.10-0.1 libmagic-mgc=1:5.37-5 libmagic1=1:5.37-5 libmount-dev=2.34-0.1 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpdec2=2.4.2-2 libmpfr6=4.0.2-1 libncurses6=6.1+20190803-1 libncursesw6=6.1+20190803-1 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpango-1.0-0=1.42.4-7 libpangocairo-1.0-0=1.42.4-7 libpangoft2-1.0-0=1.42.4-7 libpcre16-3=2:8.39-12+b1 libpcre2-16-0=10.32-5+b1 libpcre2-32-0=10.32-5+b1 libpcre2-8-0=10.32-5+b1 libpcre2-dev=10.32-5+b1 libpcre2-posix0=10.32-5+b1 libpcre3=2:8.39-12+b1 libpcre3-dev=2:8.39-12+b1 libpcre32-3=2:8.39-12+b1 libpcrecpp0v5=2:8.39-12+b1 libperl5.28=5.28.1-6 libpipeline1=1.5.1-2 libpixman-1-0=0.36.0-1 libpixman-1-dev=0.36.0-1 libpng-dev=1.6.37-1 libpng16-16=1.6.37-1 libpth20=2.0.7-22 libpthread-stubs0-dev=0.4-1 libpython3-stdlib=3.7.3-1 libpython3.7-minimal=3.7.4-4 libpython3.7-stdlib=3.7.4-4 libquadmath0=9.2.1-7 libreadline8=8.0-3 libseccomp2=2.4.1-2 libselinux1=2.9-2+b2 libselinux1-dev=2.9-2+b2 libsepol1=2.9-2+b2 libsepol1-dev=2.9-2+b2 libsigsegv2=2.12-2 libsm-dev=2:1.2.3-1 libsm6=2:1.2.3-1 libsmartcols1=2.34-0.1 libsqlite3-0=3.29.0-2 libssl1.1=1.1.1c-1 libstdc++-9-dev=9.2.1-7 libstdc++6=9.2.1-7 libsub-override-perl=0.09-2 libsystemd0=242-7 libthai-data=0.1.28-3 libthai0=0.1.28-3 libtinfo6=6.1+20190803-1 libtool=2.4.6-11 libtre5=0.8.0-6+b1 libtsan0=9.2.1-7 libubsan1=9.2.1-7 libuchardet0=0.0.6-3 libudev1=242-7 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libx11-6=2:1.6.7-1 libx11-data=2:1.6.7-1 libx11-dev=2:1.6.7-1 libxau-dev=1:1.0.8-1+b2 libxau6=1:1.0.8-1+b2 libxcb-render0=1.13.1-2 libxcb-render0-dev=1.13.1-2 libxcb-shm0=1.13.1-2 libxcb-shm0-dev=1.13.1-2 libxcb1=1.13.1-2 libxcb1-dev=1.13.1-2 libxdmcp-dev=1:1.1.2-3 libxdmcp6=1:1.1.2-3 libxext-dev=2:1.3.3-1+b2 libxext6=2:1.3.3-1+b2 libxml2=2.9.4+dfsg1-7+b3 libxrender-dev=1:0.9.10-1 libxrender1=1:0.9.10-1 linux-libc-dev=5.2.9-2 login=1:4.7-2 lsb-base=11.1.0 lua-filesystem=1.6.3-1+b1 lua-lpeg=1.0.0-2 lua-md5=1.2+git+1+8d87fee-1.1 m4=1.4.18-2 make=4.2.1-1.2 man-db=2.8.7-3 mawk=1.3.3-17+b3 mime-support=3.63 ncurses-base=6.1+20190803-1 ncurses-bin=6.1+20190803-1 patch=2.7.6-6 perl=5.28.1-6 perl-base=5.28.1-6 perl-modules-5.28=5.28.1-6 pkg-config=0.29-6 po-debconf=1.0.21 python3=3.7.3-1 python3-distutils=3.7.4-3 python3-lib2to3=3.7.4-3 python3-minimal=3.7.3-1 python3.7=3.7.4-4 python3.7-minimal=3.7.4-4 readline-common=8.0-3 sed=4.7-1 sensible-utils=0.0.12 sysvinit-utils=2.96~beta-1 tar=1.30+dfsg-6+b1 ucf=3.0038+nmu1 util-linux=2.34-0.1 uuid-dev=2.34-0.1 x11-common=1:7.7+19 x11proto-core-dev=2018.4-4 x11proto-dev=2018.4-4 x11proto-xext-dev=2018.4-4 xorg-sgml-doctools=1:1.11-1 xtrans-dev=1.3.5-1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-1+b1 zlib1g-dev=1:1.2.11.dfsg-1+b1 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20190917T214304Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20190909T044541Z/ 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 aegean=0.16.0+dfsg-2 && mkdir -p /build/aegean-sNsV2B && dpkg-source --no-check -x /*.dsc /build/aegean-sNsV2B/aegean-0.16.0+dfsg && chown -R builduser:builduser /build/aegean-sNsV2B" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/aegean-sNsV2B/aegean-0.16.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1568047935" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/aegean-sNsV2B /tmp/aegean-0.16.0+dfsg-2s6qjzblo bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20190909T044541Z 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.61OJ2VqMBw 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.61OJ2VqMBw Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20190909T044541Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20190909T044541Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (888 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 ... 4474 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.28-10) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20190917T214304Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20190909T044541Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.61OJ2VqMBw Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20190917T214304Z unstable InRelease [139 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20190909T044541Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20190917T214304Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20190917T214304Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20190917T214304Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20190917T214304Z unstable/main amd64 Packages [11.0 MB] Fetched 33.7 MB in 29s (1155 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.61OJ2VqMBw I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d aegean=0.16.0+dfsg-2 && mkdir -p /build/aegean-sNsV2B && dpkg-source --no-check -x /*.dsc /build/aegean-sNsV2B/aegean-0.16.0+dfsg && chown -R builduser:builduser /build/aegean-sNsV2B"' exec /tmp/mmdebstrap.61OJ2VqMBw Reading package lists... NOTICE: 'aegean' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/aegean.git Please use: git clone https://salsa.debian.org/med-team/aegean.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 546 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main aegean 0.16.0+dfsg-2 (dsc) [2235 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main aegean 0.16.0+dfsg-2 (tar) [535 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main aegean 0.16.0+dfsg-2 (diff) [9340 B] Fetched 546 kB in 1s (787 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'aegean_0.16.0+dfsg-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting aegean in /build/aegean-sNsV2B/aegean-0.16.0+dfsg dpkg-source: info: unpacking aegean_0.16.0+dfsg.orig.tar.xz dpkg-source: info: unpacking aegean_0.16.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_hardening dpkg-source: info: applying fix_m64_on_some_archs dpkg-source: info: applying remove_license dpkg-source: info: applying adjust_datapath dpkg-source: info: applying follow_links dpkg-source: info: applying includepaths dpkg-source: info: applying 2to3.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/aegean-sNsV2B/aegean-0.16.0+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1568047935" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.61OJ2VqMBw dpkg-buildpackage: info: source package aegean dpkg-buildpackage: info: source version 0.16.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' rm -rf bin/parseval bin/canon-gff3 bin/locuspocus bin/gaeval bin/xtractore bin/pmrna bin/tidygff3 bin/unittests libaegean.a obj/AgnAttributeFilterStream.o obj/AgnCliquePair.o obj/AgnCompareReportHTML.o obj/AgnCompareReportText.o obj/AgnComparison.o obj/AgnFilterStream.o obj/AgnGaevalVisitor.o obj/AgnGeneStream.o obj/AgnInferCDSVisitor.o obj/AgnInferExonsVisitor.o obj/AgnInferParentStream.o obj/AgnLocus.o obj/AgnLocusFilterStream.o obj/AgnLocusMapVisitor.o obj/AgnLocusRefineStream.o obj/AgnLocusStream.o obj/AgnMrnaRepVisitor.o obj/AgnPseudogeneFixVisitor.o obj/AgnRemoveChildrenVisitor.o obj/AgnTranscriptClique.o obj/AgnTypecheck.o obj/AgnUnitTest.o obj/AgnUtils.o inc/core/AgnVersion.h bin/*.dSYM make[1]: Leaving directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' dh_auto_build -- prefix=/build/aegean-sNsV2B/aegean-0.16.0+dfsg/debian/tmp 64bit=yes errorcheck=no make -j4 "INSTALL=install --strip-program=true" prefix=/build/aegean-sNsV2B/aegean-0.16.0\+dfsg/debian/tmp 64bit=yes errorcheck=no make[2]: Entering directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' [print inc/core/AgnVersion.h] [compile AgnAttributeFilterStream] [compile AgnCliquePair] [compile AgnCompareReportHTML] [compile AgnCompareReportText] In file included from /usr/include/string.h:494, from src/core/AgnCompareReportText.c:11: In function ‘strncpy’, inlined from ‘compare_report_text_comp_class_summary’ at src/core/AgnCompareReportText.c:287:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/core/AgnCompareReportText.c: In function ‘compare_report_text_comp_class_summary’: src/core/AgnCompareReportText.c:287:3: note: length computed here 287 | strncpy(header + 4, label, strlen(label)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:494, from src/core/AgnCompareReportText.c:11: In function ‘strncpy’, inlined from ‘compare_report_text_summary_struc’ at src/core/AgnCompareReportText.c:589:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/core/AgnCompareReportText.c: In function ‘compare_report_text_summary_struc’: src/core/AgnCompareReportText.c:589:3: note: length computed here 589 | strncpy(buffer + 14, units, strlen(units)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:494, from src/core/AgnCompareReportText.c:11: In function ‘strncpy’, inlined from ‘compare_report_text_summary_struc’ at src/core/AgnCompareReportText.c:599:3: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:106:10: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/core/AgnCompareReportText.c: In function ‘compare_report_text_summary_struc’: src/core/AgnCompareReportText.c:599:3: note: length computed here 599 | strncpy(buffer + 15, units, strlen(units)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [compile AgnComparison] [compile AgnFilterStream] [compile AgnGaevalVisitor] [compile AgnGeneStream] [compile AgnInferCDSVisitor] [compile AgnInferExonsVisitor] src/core/AgnInferCDSVisitor.c: In function ‘infer_cds_visitor_visit_feature_node’: src/core/AgnInferCDSVisitor.c:453:25: warning: ‘start_codon’ may be used uninitialized in this function [-Wmaybe-uninitialized] 453 | right_codon_range = gt_genome_node_get_range(*(GtGenomeNode **)start_codon); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/core/AgnInferCDSVisitor.c:430:19: note: ‘start_codon’ was declared here 430 | GtFeatureNode **start_codon, **stop_codon; | ^~~~~~~~~~~ [compile AgnInferParentStream] [compile AgnLocus] [compile AgnLocusFilterStream] [compile AgnLocusMapVisitor] [compile AgnLocusRefineStream] [compile AgnLocusStream] [compile AgnMrnaRepVisitor] [compile AgnPseudogeneFixVisitor] [compile AgnRemoveChildrenVisitor] [compile AgnTranscriptClique] [compile AgnTypecheck] [compile AgnUnitTest] [compile AgnUtils] [compile ParsEval] [compile CanonGFF3] [compile LocusPocus] [compile GAEVAL] [compile Xtractore] [compile bin/pmrna] [compile bin/tidygff3] [compile unit tests] [create libaegean] ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libaegean.a make[2]: Leaving directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' make[1]: Leaving directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' dh_auto_test -- useshared=yes 64bit=yes testthreads=5 make -j4 test useshared=yes 64bit=yes testthreads=5 make[2]: Entering directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' AEGeAn Unit Tests AEGeAn::AgnAttributeFilterStream | SUCCESS | Pogonomyrmex barbatus (partial) | PASS AEGeAn::AgnPseudogeneFixVisitor | SUCCESS | Gene, no pseudo attribute | PASS | Gene, bogus pseudo attribute | PASS | Corrected pseudogene | PASS | Uncorrected pseudogene | PASS | iLocus with gene & pseudogene | PASS AEGeAn::AgnInferParentStream | SUCCESS | Test 1: basic | PASS | Test 2: 2 top-level | PASS | Test 3: 2 top-level, inferred parent | PASS | Test 4: multichild | PASS | Test 5: multichild, inferred parent | PASS AEGeAn::AgnMrnaRepVisitor | SUCCESS | TAIR10: test 1 | PASS AEGeAn::AgnRemoveChildrenVisitor | SUCCESS | Test 1: grape (Gaze) | PASS AEGeAn::AgnTranscriptClique | SUCCESS | simple check | PASS | two mRNAs | PASS | copy check | PASS AEGeAn::AgnCliquePair | SUCCESS | perfect match vs. self | PASS | CDS match | PASS | non-match | PASS AEGeAn::AgnLocus | SUCCESS | grape test 1 | PASS | grape test 2 | PASS | filter by CDS length | PASS | filter by exon number | PASS AEGeAn::AgnFilterStream | SUCCESS | mRNA | PASS | exon | PASS | CDS | PASS | intron | PASS | exon+intron | PASS | CDS+intron | PASS AEGeAn::AgnInferCDSVisitor | SUCCESS | grape test sans UTRs | PASS | grape test with UTRs, strand check | PASS | grape test 3 | PASS | grape test 4 | PASS AEGeAn::AgnInferExonsVisitor | SUCCESS | grape test sans UTRs | PASS | grape test with UTRs, strand check | PASS | grape test 3 | PASS | grape test 4 | PASS AEGeAn::AgnGeneStream | SUCCESS | 1 gene, 2 mRNAs | PASS | 1 gene, 2 mRNAs (one sans CDS) | PASS | mRNA only | PASS | mRNA boundaries | PASS AEGeAn::AgnLocusStream | SUCCESS | grape test (pairwise) | PASS | Pdom test (pairwise) | PASS | Amel test (Augustus) | PASS | Delta=200 | PASS AEGeAn::AgnLocusRefineStream | SUCCESS | Atta cephalotes (syndrome): coords | PASS | Atta cephalotes (syndrome): elen | PASS | Megachile rotundata CST: coords | PASS | Megachile rotundata CST: elen | PASS AEGeAn::AgnGaevalVisitor | SUCCESS | range intersect (1) | PASS | range intersect (2) | PASS | range intersect (3) | PASS | union (1) | PASS | union (2) | PASS | union (3) | PASS | intersect (1) | PASS | intersect (2) | PASS | intersect (3) | PASS | intersect (4) | PASS | intersect (5) | PASS | calculate coverage | PASS | introns confirmed (no gaps) | PASS | introns confirmed (gaps) | PASS | calculate integrity | PASS ===== Unit tests passed for all 15 classes! ===== AEGeAn Functional Tests GFF3 I/O: 'AT1G05320' | codons | PASS | sansexons | PASS | sansutrs | PASS | withprot | PASS GFF3 I/O: 'FBgn0035002' | codons | PASS | sansexons | PASS | sansutrs | PASS AEGeAn::LocusPocus | default | PASS | end skip | PASS | Apis mellifera plap | PASS | Apis mellifera plap (CDS) | PASS | Apis mellifera LSM | PASS | Megachile rotundata CST (intron) | PASS | iiLocus lengths (Amel OGS Group7.16) | PASS | Nasonia vitripennis (intron gene) | PASS | A. echinatior (intron gene + ncRNA) | PASS AEGeAn::Xtractore | major royal jelly | PASS AEGeAn::CanonGFF3 | A. mellifera gene multitrans | PASS AEGeAn::GAEVAL | sans CDS | PASS | Pdom | PASS AEGeAn::ParsEval | Amel Group7.16 (text) | PASS | Amel Group7.16 (delta=500) | PASS | Amel Group7.16 (HTML) | PASS AEGeAn::align-convert.py | GAEVAL example1 | PASS | GAEVAL example5 | PASS AEGeAn::pmrna | A. mellifera Shal | PASS | A. mellifera dock | PASS | A. mellifera pseudo | PASS AEGeAn::tidygff3 | A. dorsata exception | PASS make[2]: Leaving directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' make[1]: Leaving directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' dh_auto_install -- 64bit=yes prefix=/build/aegean-sNsV2B/aegean-0.16.0+dfsg/debian/tmp make -j4 install DESTDIR=/build/aegean-sNsV2B/aegean-0.16.0\+dfsg/debian/aegean AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" 64bit=yes prefix=/build/aegean-sNsV2B/aegean-0.16.0\+dfsg/debian/tmp make[2]: Entering directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' cp bin/parseval bin/canon-gff3 bin/locuspocus bin/gaeval bin/xtractore bin/pmrna bin/tidygff3 /build/aegean-sNsV2B/aegean-0.16.0+dfsg/debian/tmp/bin/. cp libaegean.a /build/aegean-sNsV2B/aegean-0.16.0+dfsg/debian/tmp/lib/. cp inc/core/*.h /build/aegean-sNsV2B/aegean-0.16.0+dfsg/debian/tmp/include/aegean/. cp -r data/share/* /build/aegean-sNsV2B/aegean-0.16.0+dfsg/debian/tmp/share/aegean/. make[2]: Leaving directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' make[1]: Leaving directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' dh_install -a debian/rules override_dh_installdocs make[1]: Entering directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' cp /build/aegean-sNsV2B/aegean-0.16.0+dfsg/README.md /build/aegean-sNsV2B/aegean-0.16.0+dfsg/README dh_installdocs make[1]: Leaving directory '/build/aegean-sNsV2B/aegean-0.16.0+dfsg' dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_missing: bin/canon-gff3 exists in debian/tmp but is not installed to anywhere dh_missing: bin/gaeval exists in debian/tmp but is not installed to anywhere dh_missing: bin/xtractore exists in debian/tmp but is not installed to anywhere dh_missing: bin/tidygff3 exists in debian/tmp but is not installed to anywhere dh_missing: bin/locuspocus exists in debian/tmp but is not installed to anywhere dh_missing: bin/parseval exists in debian/tmp but is not installed to anywhere dh_missing: bin/pmrna exists in debian/tmp but is not installed to anywhere dh_missing: lib/libaegean.a exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnCliquePair.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnInferCDSVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnTranscriptClique.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/aegean.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnUnitTest.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnRemoveChildrenVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnCompareReportHTML.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnCompareReportText.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnGeneStream.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnLocus.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnLocusFilterStream.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnLocusMapVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnFilterStream.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnComparison.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnAttributeFilterStream.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnLocusStream.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnLocusRefineStream.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnInferExonsVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnMrnaRepVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnGaevalVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnUtils.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnTypecheck.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnVersion.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnPseudogeneFixVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: include/aegean/AgnInferParentStream.h exists in debian/tmp but is not installed to anywhere The following debhelper tools have reported what they installed (with files per package) * dh_install: aegean (8) * dh_installdocs: aegean (1) * dh_installman: aegean (7) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built For a short-term work-around: Add the files to debian/not-installed dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'aegean-dbgsym' in '../aegean-dbgsym_0.16.0+dfsg-2_amd64.deb'. dpkg-deb: building package 'aegean' in '../aegean_0.16.0+dfsg-2_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../aegean_0.16.0+dfsg-2_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/aegean-sNsV2B /tmp/aegean-0.16.0+dfsg-2s6qjzblo I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.61OJ2VqMBw... I: success in 379.2127 seconds md5: aegean-dbgsym_0.16.0+dfsg-2_amd64.deb: OK md5: aegean_0.16.0+dfsg-2_amd64.deb: OK sha1: aegean-dbgsym_0.16.0+dfsg-2_amd64.deb: OK sha1: aegean_0.16.0+dfsg-2_amd64.deb: OK sha256: aegean-dbgsym_0.16.0+dfsg-2_amd64.deb: OK sha256: aegean_0.16.0+dfsg-2_amd64.deb: OK Checksums: OK