Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/s/stringtie/stringtie_2.1.4+ds-4_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/stringtie-2.1.4+ds-4brj2yzd3/stringtie_2.1.4+ds-4_amd64.buildinfo Get source package info: stringtie=2.1.4+ds-4 Source URL: http://snapshot.notset.fr/mr/package/stringtie/2.1.4+ds-4/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.69-11.1 automake=1:1.16.2-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.48 bash=5.1~rc2-1 binutils=2.35.1-2 binutils-common=2.35.1-2 binutils-x86-64-linux-gnu=2.35.1-2 bsdextrautils=2.36-3+b2 bsdutils=1:2.36-3+b2 build-essential=12.8 bzip2=1.0.8-4 coreutils=8.32-4+b1 cpp=4:10.2.0-1 cpp-10=10.2.0-16 dash=0.5.10.2-7 debconf=1.5.74 debhelper=13.2.1 debianutils=4.11.2 dh-autoreconf=19 dh-strip-nondeterminism=1.9.0-1 diffutils=1:3.7-3 dpkg=1.20.5 dpkg-dev=1.20.5 dwz=0.13-5 file=1:5.38-5 findutils=4.7.0+git20201010-2 g++=4:10.2.0-1 g++-10=10.2.0-16 gcc=4:10.2.0-1 gcc-10=10.2.0-16 gcc-10-base=10.2.0-16 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 grep=3.6-1 groff-base=1.22.4-5 gzip=1.10-2 help2man=1.47.16 hostname=3.23 init-system-helpers=1.58 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-8 libarchive-zip-perl=1.68-1 libasan6=10.2.0-16 libatomic1=10.2.0-16 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-3.1 libaudit1=1:2.8.5-3.1 libbam-dev=0.1.19-4 libbinutils=2.35.1-2 libblkid1=2.36-3+b2 libbrotli1=1.0.9-2+b1 libbz2-1.0=1.0.8-4 libc-bin=2.31-4 libc-dev-bin=2.31-4 libc6=2.31-4 libc6-dev=2.31-4 libcap-ng0=0.7.9-2.2 libcc1-0=10.2.0-16 libcom-err2=1.45.6-1 libcroco3=0.6.13-1 libcrypt-dev=1:4.4.17-1 libcrypt1=1:4.4.17-1 libctf-nobfd0=2.35.1-2 libctf0=2.35.1-2 libcurl3-gnutls=7.72.0-1 libcurl4-gnutls-dev=7.72.0-1 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.255 libdebhelper-perl=13.2.1 libdeflate-dev=1.6-1 libdeflate0=1.6-1 libdpkg-perl=1.20.5 libelf1=0.182-1 libffi7=3.3-4 libfile-stripnondeterminism-perl=1.9.0-1 libgcc-10-dev=10.2.0-16 libgcc-s1=10.2.0-16 libgcrypt20=1.8.7-2 libgdbm-compat4=1.18.1-5.1 libgdbm6=1.18.1-5.1 libglib2.0-0=2.66.2-1 libgmp10=2:6.2.0+dfsg-6 libgnutls30=3.6.15-4 libgomp1=10.2.0-16 libgpg-error0=1.38-2 libgssapi-krb5-2=1.17-10 libhogweed6=3.6-2 libhts-dev=1.11-2 libhts3=1.11-2 libicu67=67.1-4 libidn2-0=2.3.0-3 libisl22=0.22.1-1 libitm1=10.2.0-16 libk5crypto3=1.17-10 libkeyutils1=1.6.1-2 libkrb5-3=1.17-10 libkrb5support0=1.17-10 libldap-2.4-2=2.4.56+dfsg-1 liblocale-gettext-perl=1.07-4+b1 liblsan0=10.2.0-16 liblz4-1=1.9.2-2 liblzma-dev=5.2.4-1+b1 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.38-5 libmagic1=1:5.38-5 libmount1=2.36-3+b2 libmpc3=1.2.0-1 libmpfr6=4.1.0-3 libnettle8=3.6-2 libnghttp2-14=1.41.0-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnss-nis=3.1-4 libnss-nisplus=1.3-4 libp11-kit0=0.23.21-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpcre2-8-0=10.34-7 libpcre3=2:8.39-13 libperl5.32=5.32.0-4 libpipeline1=1.5.3-1 libpsl5=0.21.0-1.1 libquadmath0=10.2.0-16 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg-2 libsasl2-modules-db=2.1.27+dfsg-2 libseccomp2=2.5.0-3 libselinux1=3.1-2+b1 libsigsegv2=2.12-2 libsmartcols1=2.36-3+b2 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1h-1 libstdc++-10-dev=10.2.0-16 libstdc++6=10.2.0-16 libsub-override-perl=0.09-2 libsystemd0=246.6-2 libtasn1-6=4.16.0-2 libtinfo6=6.2+20200918-1 libtirpc-common=1.2.6-3 libtirpc-dev=1.2.6-3 libtirpc3=1.2.6-3 libtool=2.4.6-14 libtsan0=10.2.0-16 libubsan1=10.2.0-16 libuchardet0=0.0.7-1 libudev1=246.6-2 libunistring2=0.9.10-4 libuuid1=2.36-3+b2 libxml2=2.9.10+dfsg-6.2 libzstd1=1.4.5+dfsg-4 linux-libc-dev=5.9.6-1 login=1:4.8.1-1 lsb-base=11.1.0 m4=1.4.18-4 make=4.3-4 man-db=2.9.3-2 mawk=1.3.4.20200120-2 ncurses-base=6.2+20200918-1 ncurses-bin=6.2+20200918-1 patch=2.7.6-6 perl=5.32.0-4 perl-base=5.32.0-4 perl-modules-5.32=5.32.0-4 po-debconf=1.0.21 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-5 tar=1.30+dfsg-7 util-linux=2.36-3+b2 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20210123T144741Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201111T205648Z/ 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 stringtie=2.1.4+ds-4 && mkdir -p /build/stringtie-dCA9Qp && dpkg-source --no-check -x /*.dsc /build/stringtie-dCA9Qp/stringtie-2.1.4+ds && chown -R builduser:builduser /build/stringtie-dCA9Qp" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/stringtie-dCA9Qp/stringtie-2.1.4+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605341337" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/stringtie-dCA9Qp /tmp/stringtie-2.1.4+ds-4brj2yzd3 bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20201111T205648Z 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.FiOo7p295Z 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.FiOo7p295Z Reading package lists... Building dependency tree... util-linux is already the newest version (2.36-3+b2). 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/20201111T205648Z unstable/main amd64 libfakeroot amd64 1.25.3-1 [47.0 kB] Get:2 http://snapshot.notset.fr/archive/debian/20201111T205648Z unstable/main amd64 fakeroot amd64 1.25.3-1 [87.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 134 kB in 0s (850 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 ... 4694 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.25.3-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.25.3-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.25.3-1_amd64.deb ... Unpacking fakeroot (1.25.3-1) ... Setting up libfakeroot:amd64 (1.25.3-1) ... Setting up fakeroot (1.25.3-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.31-4) ... 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/20210123T144741Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20201111T205648Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.FiOo7p295Z Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20210123T144741Z unstable InRelease [153 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20201111T205648Z 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/20210123T144741Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210123T144741Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20210123T144741Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20210123T144741Z unstable/main amd64 Packages [11.7 MB] Fetched 34.4 MB in 30s (1159 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.FiOo7p295Z I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d stringtie=2.1.4+ds-4 && mkdir -p /build/stringtie-dCA9Qp && dpkg-source --no-check -x /*.dsc /build/stringtie-dCA9Qp/stringtie-2.1.4+ds && chown -R builduser:builduser /build/stringtie-dCA9Qp"' exec /tmp/mmdebstrap.FiOo7p295Z Reading package lists... NOTICE: 'stringtie' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/stringtie.git Please use: git clone https://salsa.debian.org/med-team/stringtie.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1045 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main stringtie 2.1.4+ds-4 (dsc) [2413 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main stringtie 2.1.4+ds-4 (tar) [789 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main stringtie 2.1.4+ds-4 (tar) [244 kB] Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main stringtie 2.1.4+ds-4 (diff) [9076 B] Fetched 1045 kB in 1s (1165 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'stringtie_2.1.4+ds-4.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting stringtie in /build/stringtie-dCA9Qp/stringtie-2.1.4+ds dpkg-source: info: unpacking stringtie_2.1.4+ds.orig.tar.xz dpkg-source: info: unpacking stringtie_2.1.4+ds.orig-debian-tests-data.tar.xz dpkg-source: info: unpacking stringtie_2.1.4+ds-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile.patch I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/stringtie-dCA9Qp/stringtie-2.1.4+ds && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1605341337" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.FiOo7p295Z dpkg-buildpackage: info: source package stringtie dpkg-buildpackage: info: source version 2.1.4+ds-4 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 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' dh_auto_clean install -d /build/stringtie-dCA9Qp/stringtie-2.1.4\+ds/debian/.debhelper/generated/_source/home make -j4 clean make[2]: Entering directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' rm -f stringtie stringtie.o* ./gclib/GBase.o ./gclib/GArgs.o ./gclib/GStr.o ./gclib/GBam.o ./gclib/gdna.o ./gclib/codons.o ./gclib/GFastaIndex.o ./gclib/GFaSeqGet.o ./gclib/gff.o ./gclib/GThreads.o rlink.o tablemaker.o tmerge.o rm -f core.* make[2]: Leaving directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' rm -f debian/stringtie.1 rm -fr test_data rm -f SuperReads_RNA/global-1/SuperReadsR/all_tests make[1]: Leaving directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/stringtie.substvars debian/files rm -fr -- debian/stringtie/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a install -d /build/stringtie-dCA9Qp/stringtie-2.1.4\+ds/debian/.debhelper/generated/_source/home debian/rules override_dh_auto_build make[1]: Entering directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' dh_auto_build -- 'LINKER=$(CXX)' make -j4 "INSTALL=install --strip-program=true" LINKER=\$\(CXX\) make[2]: Entering directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GBase.cpp -o gclib/GBase.o g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GArgs.cpp -o gclib/GArgs.o g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GStr.cpp -o gclib/GStr.o g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GBam.cpp -o gclib/GBam.o In file included from gclib/GBam.cpp:1: gclib/GBam.h:24:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 24 | struct { | ^ g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gdna.cpp -o gclib/gdna.o g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/codons.cpp -o gclib/codons.o g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o gclib/GFastaIndex.cpp: In member function ‘int GFastaIndex::loadIndex(const char*)’: gclib/GFastaIndex.cpp:55:22: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘uint*’ {aka ‘unsigned int*’} [-Wformat=] 55 | sscanf(p, "%d%lld%d%d", &len, &offset, &line_len, &line_blen); | ~^ ~~~~ | | | | int* uint* {aka unsigned int*} | %d g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gff.cpp -o gclib/gff.o In file included from gclib/gff.cpp:1: gclib/gff.h:228:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 228 | struct { | ^ gclib/gff.h:231:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 231 | struct { | ^ gclib/gff.h:327:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 327 | struct { | ^ gclib/gff.h:689:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 689 | struct { | ^ gclib/gff.h:1148:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1148 | struct { | ^ g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GThreads.cpp -o gclib/GThreads.o g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c rlink.cpp -o rlink.o g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tablemaker.cpp -o tablemaker.o g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tmerge.cpp -o tmerge.o In file included from rlink.h:5, from rlink.cpp:1: ./gclib/gff.h:228:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 228 | struct { | ^ ./gclib/gff.h:231:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 231 | struct { | ^ ./gclib/gff.h:327:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 327 | struct { | ^ ./gclib/gff.h:689:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 689 | struct { | ^ ./gclib/gff.h:1148:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1148 | struct { | ^ In file included from rlink.h:6, from rlink.cpp:1: ./gclib/GBam.h:24:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 24 | struct { | ^ In file included from rlink.h:5, from tablemaker.cpp:2: ./gclib/gff.h:228:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 228 | struct { | ^ ./gclib/gff.h:231:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 231 | struct { | ^ ./gclib/gff.h:327:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 327 | struct { | ^ ./gclib/gff.h:689:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 689 | struct { | ^ ./gclib/gff.h:1148:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1148 | struct { | ^ In file included from rlink.h:5, from tmerge.h:5, from tmerge.cpp:1: ./gclib/gff.h:228:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 228 | struct { | ^ ./gclib/gff.h:231:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 231 | struct { | ^ ./gclib/gff.h:327:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 327 | struct { | ^ ./gclib/gff.h:689:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 689 | struct { | ^ In file included from rlink.h:6, from tablemaker.cpp:2: ./gclib/GBam.h:24:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 24 | struct { | ^ ./gclib/gff.h:1148:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1148 | struct { | ^ In file included from rlink.h:6, from tmerge.h:5, from tmerge.cpp:1: ./gclib/GBam.h:24:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 24 | struct { | ^ In file included from rlink.h:10, from rlink.cpp:1: ./gclib/GIntHash.hh:292:2: warning: extra ‘;’ [-Wpedantic] 292 | }; | ^ In file included from rlink.h:10, from tmerge.h:5, from tmerge.cpp:1: ./gclib/GIntHash.hh:292:2: warning: extra ‘;’ [-Wpedantic] 292 | }; | ^ In file included from rlink.h:10, from tablemaker.cpp:2: ./gclib/GIntHash.hh:292:2: warning: extra ‘;’ [-Wpedantic] 292 | }; | ^ rlink.cpp: In function ‘void count_good_junctions(BundleData*)’: rlink.cpp:14102:22: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘CJunction*’ [-Wformat=] 14102 | sprintf(sbuf, "%p", junction[j]); | ~^ | | | void* rlink.cpp:14118:25: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘CJunction*’ [-Wformat=] 14118 | sprintf(sbuf, "%p", junction[equal[s]]); | ~^ | | | void* rlink.cpp:14128:22: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘CJunction*’ [-Wformat=] 14128 | sprintf(sbuf, "%p", ejunction[j]); | ~^ | | | void* rlink.cpp:14144:25: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘CJunction*’ [-Wformat=] 14144 | sprintf(sbuf, "%p", ejunction[equal[s]]); | ~^ | | | void* rlink.cpp:14184:22: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘CJunction*’ [-Wformat=] 14184 | sprintf(sbuf, "%p", rd.juncs[i-1]); | ~^ | | | void* g++ -g -O2 -fdebug-prefix-map=/build/stringtie-dCA9Qp/stringtie-2.1.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -I/usr/include/bamtools/api/ -DDEBUG -D_DEBUG -DGDEBUG -Wall -Wextra -I. -I./gclib -I/usr/include/samtools -I/usr/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c++0x -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c stringtie.cpp -o stringtie.o In file included from rlink.h:5, from stringtie.cpp:2: ./gclib/gff.h:228:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 228 | struct { | ^ ./gclib/gff.h:231:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 231 | struct { | ^ ./gclib/gff.h:327:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 327 | struct { | ^ ./gclib/gff.h:689:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 689 | struct { | ^ ./gclib/gff.h:1148:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1148 | struct { | ^ In file included from rlink.h:6, from stringtie.cpp:2: ./gclib/GBam.h:24:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 24 | struct { | ^ In file included from rlink.h:10, from stringtie.cpp:2: ./gclib/GIntHash.hh:292:2: warning: extra ‘;’ [-Wpedantic] 292 | }; | ^ g++ -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o stringtie gclib/GBase.o gclib/GArgs.o gclib/GStr.o gclib/GBam.o gclib/gdna.o gclib/codons.o gclib/GFastaIndex.o gclib/GFaSeqGet.o gclib/gff.o gclib/GThreads.o rlink.o tablemaker.o tmerge.o stringtie.o -pthread -lhts -lbam -lz WARNING: built DEBUG version [much slower], use "make clean release" for a faster, optimized version of the program. make[2]: Leaving directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' make[1]: Leaving directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' rm -f debian/stringtie.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' echo "Disabling tests, as they require network access." Disabling tests, as they require network access. make[1]: Leaving directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a rm -f -- debian/stringtie.substvars rm -fr -- debian/.debhelper/generated/stringtie/ debian/stringtie/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' help2man ./stringtie -n StringTie -s 1 -o debian/stringtie.1 dh_auto_install install -d /build/stringtie-dCA9Qp/stringtie-2.1.4\+ds/debian/stringtie make[1]: Leaving directory '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' dh_install -a install -d debian/stringtie/usr/bin cp --reflink=auto -a ./stringtie debian/stringtie/usr/bin/ install -d debian/.debhelper/generated/stringtie dh_installdocs -a install -d debian/stringtie/usr/share/doc/stringtie install -p -m0644 debian/copyright debian/stringtie/usr/share/doc/stringtie/copyright dh_installchangelogs -a install -p -m0644 debian/changelog debian/stringtie/usr/share/doc/stringtie/changelog.Debian dh_installman -a install -d debian/stringtie/usr/share/man/man1/ install -p -m0644 ./debian/stringtie.1 debian/stringtie/usr/share/man/man1/stringtie.1 man-recode --to-code UTF-8 --suffix .dh-new debian/stringtie/usr/share/man/man1/stringtie.1 mv debian/stringtie/usr/share/man/man1/stringtie.1.dh-new debian/stringtie/usr/share/man/man1/stringtie.1 chmod 0644 -- debian/stringtie/usr/share/man/man1/stringtie.1 dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/stringtie chmod a-x usr/share/doc/stringtie/changelog.Debian usr/share/man/man1/stringtie.1 gzip -9nf usr/share/doc/stringtie/changelog.Debian usr/share/man/man1/stringtie.1 cd '/build/stringtie-dCA9Qp/stringtie-2.1.4+ds' dh_fixperms -a find debian/stringtie ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/stringtie/usr/share/doc -type f -a -true -a ! -regex 'debian/stringtie/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/stringtie/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/stringtie/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/stringtie -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/stringtie/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -a dh_dwz -a -a dwz -- debian/stringtie/usr/bin/stringtie dh_strip -a -a install -d debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/32 objcopy --only-keep-debug --compress-debug-sections debian/stringtie/usr/bin/stringtie debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/32/69c98ca1764d8b799357daa52a4876ecef0d9a.debug chmod 0644 -- debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/32/69c98ca1764d8b799357daa52a4876ecef0d9a.debug strip --remove-section=.comment --remove-section=.note debian/stringtie/usr/bin/stringtie objcopy --add-gnu-debuglink debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/32/69c98ca1764d8b799357daa52a4876ecef0d9a.debug debian/stringtie/usr/bin/stringtie install -d debian/.debhelper/stringtie/dbgsym-root/usr/share/doc ln -s stringtie debian/.debhelper/stringtie/dbgsym-root/usr/share/doc/stringtie-dbgsym dh_makeshlibs -a -a rm -f debian/stringtie/DEBIAN/shlibs dh_shlibdeps -a -a install -d debian/stringtie/DEBIAN dpkg-shlibdeps -Tdebian/stringtie.substvars debian/stringtie/usr/bin/stringtie dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/stringtie.substvars echo misc:Pre-Depends= >> debian/stringtie.substvars install -d debian/.debhelper/stringtie/dbgsym-root/DEBIAN dpkg-gencontrol -pstringtie -ldebian/changelog -Tdebian/stringtie.substvars -Pdebian/.debhelper/stringtie/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -DPackage=stringtie-dbgsym "-DDepends=stringtie (= \${binary:Version})" "-DDescription=debug symbols for stringtie" -DBuild-Ids=3269c98ca1764d8b799357daa52a4876ecef0d9a -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/stringtie/dbgsym-root/DEBIAN/control dpkg-gencontrol -pstringtie -ldebian/changelog -Tdebian/stringtie.substvars -Pdebian/stringtie chmod 0644 -- debian/stringtie/DEBIAN/control dh_md5sums -a cd debian/stringtie >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/stringtie/DEBIAN/md5sums cd debian/.debhelper/stringtie/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/stringtie/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/stringtie .. dpkg-deb --root-owner-group --build debian/.debhelper/stringtie/dbgsym-root .. dpkg-deb: building package 'stringtie-dbgsym' in '../stringtie-dbgsym_2.1.4+ds-4_amd64.deb'. dpkg-deb: building package 'stringtie' in '../stringtie_2.1.4+ds-4_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../stringtie_2.1.4+ds-4_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/stringtie-dCA9Qp /tmp/stringtie-2.1.4+ds-4brj2yzd3 I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.FiOo7p295Z... I: success in 695.4236 seconds md5: stringtie-dbgsym_2.1.4+ds-4_amd64.deb: OK md5: stringtie_2.1.4+ds-4_amd64.deb: OK sha1: stringtie-dbgsym_2.1.4+ds-4_amd64.deb: OK sha1: stringtie_2.1.4+ds-4_amd64.deb: OK sha256: stringtie-dbgsym_2.1.4+ds-4_amd64.deb: OK sha256: stringtie_2.1.4+ds-4_amd64.deb: OK Checksums: OK