I: pbuilder: network access will be disabled during build I: Current time: Tue Mar 12 10:58:50 +14 2024 I: pbuilder-time-stamp: 1710190730 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [stringtie_2.2.1+ds-3.dsc] I: copying [./stringtie_2.2.1+ds.orig-debian-tests-data.tar.xz] I: copying [./stringtie_2.2.1+ds.orig.tar.xz] I: copying [./stringtie_2.2.1+ds-3.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jan 26 20:37:21 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./stringtie_2.2.1+ds-3.dsc: no acceptable signature found dpkg-source: info: extracting stringtie in stringtie-2.2.1+ds dpkg-source: info: unpacking stringtie_2.2.1+ds.orig.tar.xz dpkg-source: info: unpacking stringtie_2.2.1+ds.orig-debian-tests-data.tar.xz dpkg-source: info: unpacking stringtie_2.2.1+ds-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Makefile.patch dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2576/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Mar 11 20:59 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2576/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2576/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=0b1cee4100c54f8cb816ec5b9c233cb8 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2576 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.i6aIHmJr/pbuilderrc_De1D --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.i6aIHmJr/b2 --logfile b2/build.log stringtie_2.2.1+ds-3.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 10 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2576/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libbam-dev, libhts-dev, libbz2-dev, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19818 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libbam-dev; however: Package libbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbam-dev{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblocale-gettext-perl{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 51 newly installed, 0 to remove and 0 not upgraded. Need to get 25.2 MB of archives. After unpacking 88.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-6+b1 [15.3 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-1+b2 [39.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.14.1 [85.6 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 debhelper all 13.14.1 [890 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3+b1 [915 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libbam-dev i386 0.1.19+dfsg-6 [130 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libbz2-dev i386 1.0.8-5+b2 [31.4 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libpsl5 i386 0.21.2-1+b1 [59.7 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libssh2-1 i386 1.11.0-4 [224 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libcurl3-gnutls i386 8.5.0-2 [454 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.5.0-2 [574 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.19-1 [41.9 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.19-1 [50.5 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.0-1+b1 [68.5 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libhts3 i386 1.19+ds-1 [490 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.6.0-0.2 [281 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.19+ds-1 [1660 kB] Fetched 25.2 MB in 2s (11.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19818 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-6+b1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-6+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../03-libmagic1_1%3a5.45-2+b1_i386.deb ... Unpacking libmagic1:i386 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-2+b1_i386.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-3_i386.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.39.3-6_i386.deb ... Unpacking bsdextrautils (2.39.3-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../09-libpipeline1_1.5.7-1+b2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.0-3_i386.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.14.1_all.deb ... Unpacking libdebhelper-perl (13.14.1) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../23-libelf1_0.190-1+b1_i386.deb ... Unpacking libelf1:i386 (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1_i386.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../25-libicu72_72.1-4+b1_i386.deb ... Unpacking libicu72:i386 (72.1-4+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b2_i386.deb ... Unpacking libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-14+b1_i386.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.14.1_all.deb ... Unpacking debhelper (13.14.1) ... Selecting previously unselected package help2man. Preparing to unpack .../31-help2man_1.49.3_i386.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../32-zlib1g-dev_1%3a1.3.dfsg-3+b1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.3.dfsg-3+b1) ... Selecting previously unselected package libbam-dev. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2576/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2576/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/stringtie-2.2.1+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../stringtie_2.2.1+ds-3_source.changes dpkg-buildpackage: info: source package stringtie dpkg-buildpackage: info: source version 2.2.1+ds-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_auto_clean make -j7 clean make[2]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' rm -f stringtie stringtie.o* ./gclib/GBase.o ./gclib/GArgs.o ./gclib/GStr.o ./gclib/GSam.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/reproducible-path/stringtie-2.2.1+ds' rm -fr test_data rm -f SuperReads_RNA/global-1/SuperReadsR/all_tests make[1]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+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 \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_auto_build -- 'LINKER=$(CXX)' make -j7 "INSTALL=install --strip-program=true" LINKER=\$\(CXX\) make[2]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GBase.cpp -o gclib/GBase.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GArgs.cpp -o gclib/GArgs.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GStr.cpp -o gclib/GStr.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GSam.cpp -o gclib/GSam.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/gdna.cpp -o gclib/gdna.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/codons.cpp -o gclib/codons.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFastaIndex.cpp -o gclib/GFastaIndex.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o In file included from gclib/GStr.h:5, from gclib/GStr.cpp:2: gclib/GStr.cpp: In static member function 'static GStr::Data* GStr::new_data(uint, uint)': gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ gclib/GStr.cpp: In static member function 'static GStr::Data* GStr::new_data(const char*, uint)': gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:39:9: note: in expansion of macro 'GMALLOC' 39 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp:38:15: note: 'data' was declared here 38 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'void GStr::make_unique()' at gclib/GStr.cpp:91:30: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'void GStr::make_unique()': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::cut(int, int)' at gclib/GStr.cpp:890:26: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In function 'GStr& GStr::cut(int, int)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -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/GSam.cpp:1: gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'void GStr::make_unique()' at gclib/GStr.cpp:91:30, inlined from 'char* GStr::detach()' at gclib/GStr.cpp:130:13: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'char* GStr::detach()': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(const char*, uint)', inlined from 'GStr::GStr(const char*, uint)' at gclib/GStr.cpp:157:19: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:39:9: note: in expansion of macro 'GMALLOC' 39 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In constructor 'GStr::GStr(const char*, uint)': gclib/GStr.cpp:38:15: note: 'data' was declared here 38 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::trim(char)' at gclib/GStr.cpp:463:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::trim(char)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::trim(const char*)' at gclib/GStr.cpp:482:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::trim(const char*)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::trimL(char)' at gclib/GStr.cpp:572:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::trimL(char)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::trimL(const char*)' at gclib/GStr.cpp:590:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::trimL(const char*)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::padR(uint, char)' at gclib/GStr.cpp:605:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::padR(uint, char)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::padL(uint, char)' at gclib/GStr.cpp:615:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::padL(uint, char)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::padC(uint, char)' at gclib/GStr.cpp:626:23: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::padC(uint, char)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c gclib/GThreads.cpp -o gclib/GThreads.o In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::tr(const char*, const char*)' at gclib/GStr.cpp:786:25: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::tr(const char*, const char*)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c rlink.cpp -o rlink.o In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::paste(const GStr&, int, int)' at gclib/GStr.cpp:917:30: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::paste(const GStr&, int, int)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::paste(const char*, int, int)' at gclib/GStr.cpp:950:30: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::paste(const char*, int, int)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ In file included from gclib/gff.cpp:1: gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::insert(const GStr&, int)' at gclib/GStr.cpp:975:30: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::insert(const GStr&, int)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ gclib/gff.cpp: In constructor 'GffLine::GffLine(GffReader*, const char*)': gclib/gff.cpp:426:19: warning: unknown escape sequence: '\%' 426 | GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'GStr& GStr::insert(const char*, int)' at gclib/GStr.cpp:1000:30: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'GStr& GStr::insert(const char*, int)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tablemaker.cpp -o tablemaker.o g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tmerge.cpp -o tmerge.o In static member function 'static GStr::Data* GStr::new_data(uint, uint)', inlined from 'size_t GStr::read(FILE*, const char*, size_t)' at gclib/GStr.cpp:1380:22: gclib/GBase.h:176:28: warning: 'data' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/GStr.cpp:21:9: note: in expansion of macro 'GMALLOC' 21 | GMALLOC(data, sizeof(Data)+len+addcap); | ^~~~~~~ gclib/GStr.cpp: In member function 'size_t GStr::read(FILE*, const char*, size_t)': gclib/GStr.cpp:20:15: note: 'data' was declared here 20 | Data* data; | ^~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/stringtie-2.2.1+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++11 -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 tablemaker.cpp:2: ./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ ./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ ./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ ./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ ./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ In file included from rlink.h:6: ./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ In file included from rlink.h:5, from tmerge.h:5, from tmerge.cpp:1: ./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ ./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ ./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ ./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ In file included from rlink.h:5, from rlink.cpp:1: ./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ ./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ ./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ ./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ tablemaker.cpp: In function 'void rc_update_exons(RC_BundleData&)': tablemaker.cpp:205:29: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 205 | bind2nd( minus(), avg)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438, from /usr/include/c++/13/functional:49, from ./gclib/khashl.hh:25, from ./gclib/GHashMap.hh:8, from ./gclib/GFastaIndex.h:11, from ./gclib/GFaSeqGet.h:3, from ./gclib/gff.h:9: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ tablemaker.cpp:212:29: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 212 | bind2nd( minus(), mavg)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ ./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ ./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ In file included from rlink.h:6: ./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ In file included from rlink.h:6: ./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ In file included from rlink.h:5, from stringtie.cpp:2: ./gclib/gff.h:242:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 242 | struct { | ^ ./gclib/gff.h:245:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 245 | struct { | ^ ./gclib/gff.h:343:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 343 | struct { | ^ ./gclib/gff.h:706:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 706 | struct { | ^ ./gclib/gff.h:1165:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1165 | struct { | ^ In file included from rlink.h:6: ./gclib/GSam.h:32:16: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 32 | struct { | ^ stringtie.cpp: In function 'int main(int, char**)': stringtie.cpp:468:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] 468 | if (tstackSize::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = unsigned int; _Up = unsigned int; bool _IsMove = true]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = true; _II = unsigned int*; _OI = unsigned int*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = true; _II = unsigned int*; _OI = unsigned int*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42, inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = true; _II = unsigned int*; _OI = unsigned int*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31, inlined from '_OI std::move(_II, _II, _OI) [with _II = unsigned int*; _OI = unsigned int*]' at /usr/include/c++/13/bits/stl_algobase.h:665:38, inlined from 'void GVec::setCapacity(int) [with OBJ = unsigned int]' at ./gclib/GVec.hh:109:18, inlined from 'void GVec::Grow() [with OBJ = unsigned int]' at ./gclib/GVec.hh:323:13, inlined from 'int GVec::Add(OBJ*) [with OBJ = unsigned int]' at ./gclib/GVec.hh:370:29, inlined from 'int GVec::Add(OBJ&) [with OBJ = unsigned int]' at ./gclib/GVec.hh:59:36, inlined from 'RC_Feature::RC_Feature(int, int, char, uint, uint)' at tablemaker.h:53:22, inlined from 'void RC_TData::addFeature(int, int, GPVec&, uint&, GList&, GPVec&, int&)' at tablemaker.cpp:309:73: /usr/include/c++/13/bits/stl_algobase.h:437:30: warning: 'void* __builtin_memcpy(void*, const void*, unsigned int)' forming offset 4 is out of the bounds [0, 4] [-Warray-bounds=] 437 | __builtin_memmove(__result, __first, sizeof(_Tp) * _Num); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gclib/gff.h:6: gclib/gff.cpp: In constructor 'BEDLine::BEDLine(GffReader*, const char*)': gclib/GBase.h:176:28: warning: 'blen' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/gff.cpp:243:11: note: in expansion of macro 'GMALLOC' 243 | GMALLOC(blen, numexons * sizeof(char*)); | ^~~~~~~ gclib/gff.cpp:241:18: note: 'blen' was declared here 241 | char** blen; | ^~~~ gclib/GBase.h:176:28: warning: 'bstart' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ gclib/gff.cpp:244:11: note: in expansion of macro 'GMALLOC' 244 | GMALLOC(bstart, numexons * sizeof(char*)); | ^~~~~~~ gclib/gff.cpp:242:18: note: 'bstart' was declared here 242 | char** bstart; | ^~~~~~ In file included from ./gclib/GStr.h:5, from rlink.h:4: In constructor 'GBitVec::GBitVec(uint, bool)', inlined from 'GBitVec::GBitVec(uint, bool)' at ./gclib/GBitVec.h:118:12, inlined from 'void process_transfrags(int, int, int, GPVec&, GPVec&, CTreePat*, GIntHash&, GVec&, GList&, GVec&)' at rlink.cpp:5826:29: ./gclib/GBase.h:176:28: warning: '*(void**)((char*)&trpat + offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ ./gclib/GBitVec.h:126:5: note: in expansion of macro 'GMALLOC' 126 | GMALLOC(fBits, Capacity * sizeof(BitWord)); | ^~~~~~~ rlink.cpp: In function 'void process_transfrags(int, int, int, GPVec&, GPVec&, CTreePat*, GIntHash&, GVec&, GList&, GVec&)': rlink.cpp:5826:41: note: '*(void**)((char*)&trpat + offsetof(GBitVec, GBitVec::fBits))' was declared here 5826 | GBitVec trpat(gno+edgeno); | ^~~~~ In copy constructor 'GBitVec::GBitVec(const GBitVec&)', inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:150:3, inlined from 'void process_refguides(int, int, GIntHash&, int&, GPVec&, GPVec&, int, GVec&, BundleData*)' at rlink.cpp:11677:44: ./gclib/GBase.h:176:28: warning: '*(void**)((char*)&trpattern + offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] 176 | #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ | ^~ ./gclib/GBitVec.h:158:5: note: in expansion of macro 'GMALLOC' 158 | GMALLOC(fBits, Capacity * sizeof(BitWord)); | ^~~~~~~ rlink.cpp: In function 'void process_refguides(int, int, GIntHash&, int&, GPVec&, GPVec&, int, GVec&, BundleData*)': rlink.cpp:11677:41: note: '*(void**)((char*)&trpattern + offsetof(GBitVec, GBitVec::fBits))' was declared here 11677 | GBitVec trpattern(transfrag[t]->pattern); | ^~~~~~~~~ In function 'bool GMalloc(void**, long unsigned int)', inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:158:5, inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:150:3, inlined from 'GBitVec traverse_dfs(int, int, CGraphnode*, CGraphnode*, GBitVec, int, GVec&, GPVec**, GPVec**, int&, GIntHash**, int&)' at rlink.cpp:2461:28: ./gclib/GBase.h:254:12: warning: '*(void**)((char*)&childparents + offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] 254 | return *ptr!=NULL; | ^~~~ rlink.cpp: In function 'GBitVec traverse_dfs(int, int, CGraphnode*, CGraphnode*, GBitVec, int, GVec&, GPVec**, GPVec**, int&, GIntHash**, int&)': rlink.cpp:2461:25: note: 'childparents' declared here 2461 | GBitVec childparents=parents; | ^~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -o stringtie gclib/GBase.o gclib/GArgs.o gclib/GStr.o gclib/GSam.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 -lbz2 -lz -lm WARNING: built DEBUG version [much slower], use "make clean release" for a faster, optimized version of the program. make[2]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+ds' make[1]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+ds' rm -f debian/stringtie.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' echo "Disabling tests, as they require network access." Disabling tests, as they require network access. make[1]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+ds' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/stringtie.substvars rm -fr -- debian/.debhelper/generated/stringtie/ debian/stringtie/ debian/tmp/ dh_auto_install --destdir=debian/stringtie/ install -m0755 -d /build/reproducible-path/stringtie-2.2.1\+ds/debian/stringtie debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_install prepDE.py3 usr/bin install -m0755 -d debian/stringtie/usr/bin cp --reflink=auto -a ./prepDE.py3 ./stringtie debian/stringtie/usr/bin/ mv debian/stringtie/usr/bin/prepDE.py3 debian/stringtie/usr/bin/prepDE.py make[1]: Leaving directory '/build/reproducible-path/stringtie-2.2.1+ds' dh_installdocs install -m0755 -d debian/stringtie/usr/share/doc/stringtie install -p -m0644 debian/copyright debian/stringtie/usr/share/doc/stringtie/copyright dh_installchangelogs install -m0755 -d debian/stringtie/usr/share/doc/stringtie install -p -m0644 debian/.debhelper/generated/stringtie/dh_installchangelogs.dch.trimmed debian/stringtie/usr/share/doc/stringtie/changelog.Debian dh_installman install -m0755 -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_lintian install -m0755 -d debian/stringtie/usr/share/lintian/overrides install -p -m0644 debian/lintian-overrides debian/stringtie/usr/share/lintian/overrides/stringtie dh_perl dh_link dh_strip_nondeterminism dh_compress 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/reproducible-path/stringtie-2.2.1+ds' dh_fixperms 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 debian/stringtie/usr/share/lintian/overrides -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 dh_dwz -a dwz -- debian/stringtie/usr/bin/stringtie dh_strip -a install -m0755 -d debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/81 objcopy --only-keep-debug --compress-debug-sections debian/stringtie/usr/bin/stringtie debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/81/b88177d126b846e675498541f523d1a8efa05c.debug chmod 0644 -- debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/81/b88177d126b846e675498541f523d1a8efa05c.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/81/b88177d126b846e675498541f523d1a8efa05c.debug debian/stringtie/usr/bin/stringtie install -m0755 -d debian/.debhelper/stringtie/dbgsym-root/usr/share/doc ln -s stringtie debian/.debhelper/stringtie/dbgsym-root/usr/share/doc/stringtie-dbgsym install -m0755 -d debian/.debhelper/stringtie dh_makeshlibs -a rm -f debian/stringtie/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/stringtie/DEBIAN dpkg-shlibdeps -Tdebian/stringtie.substvars debian/stringtie/usr/bin/stringtie dh_installdeb install -m0755 -d debian/stringtie/DEBIAN dh_gencontrol install -m0755 -d debian/stringtie/DEBIAN echo misc:Depends= >> debian/stringtie.substvars echo misc:Pre-Depends= >> debian/stringtie.substvars install -m0755 -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 -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=stringtie-dbgsym "-DDepends=stringtie (= \${binary:Version})" "-DDescription=debug symbols for stringtie" -DBuild-Ids=81b88177d126b846e675498541f523d1a8efa05c -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 install -m0755 -d debian/stringtie/DEBIAN cd debian/stringtie >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/stringtie/DEBIAN/md5sums install -m0755 -d debian/.debhelper/stringtie/dbgsym-root/DEBIAN 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 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_2.2.1+ds-3_i386.deb'. dpkg-deb: building package 'stringtie' in '../stringtie_2.2.1+ds-3_i386.deb'. dpkg-genbuildinfo --build=binary -O../stringtie_2.2.1+ds-3_i386.buildinfo dpkg-genchanges --build=binary -O../stringtie_2.2.1+ds-3_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2576/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2576/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2576 and its subdirectories I: Current time: Tue Mar 12 11:02:20 +14 2024 I: pbuilder-time-stamp: 1710190940