Sun Jan 16 19:33:29 UTC 2022 I: starting to build stringtie/bullseye/amd64 on jenkins on '2022-01-16 19:33' Sun Jan 16 19:33:29 UTC 2022 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_21/42006/console.log Sun Jan 16 19:33:29 UTC 2022 I: Downloading source for bullseye/stringtie=2.1.4+ds-4 --2022-01-16 19:33:30-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/stringtie/stringtie_2.1.4%2bds-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2413 (2.4K) Saving to: ‘stringtie_2.1.4+ds-4.dsc’ 0K .. 100% 153M=0s 2022-01-16 19:33:30 (153 MB/s) - ‘stringtie_2.1.4+ds-4.dsc’ saved [2413/2413] Sun Jan 16 19:33:30 UTC 2022 I: stringtie_2.1.4+ds-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: stringtie Binary: stringtie Architecture: any Version: 2.1.4+ds-4 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Nilesh Patra Homepage: https://ccb.jhu.edu/software/stringtie/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/stringtie Vcs-Git: https://salsa.debian.org/med-team/stringtie.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 13), libbam-dev, libhts-dev, help2man Package-List: stringtie deb science optional arch=any Checksums-Sha1: d10b773117f72f24088aeb8cb473cea800a4267a 789340 stringtie_2.1.4+ds.orig-debian-tests-data.tar.xz 63c07d48d1f55eab657b52d7ec3380a48ccb43a0 243788 stringtie_2.1.4+ds.orig.tar.xz 58abd6eaa91daca51ab2e59d0a350993bc6bad29 9076 stringtie_2.1.4+ds-4.debian.tar.xz Checksums-Sha256: 17efd2027d242890fd6828174508b63911f538cb83b2d2e87bcd3871e8a4f09b 789340 stringtie_2.1.4+ds.orig-debian-tests-data.tar.xz 3acc465f6549be6e0c6a1a5ce5cd9525caaa47e64fafc7fb3022d6f877c94fcd 243788 stringtie_2.1.4+ds.orig.tar.xz 361e5f4d868a66e6a2928e8a2f8bdc0dfe71b114bdea9b36c719368fd6c424f8 9076 stringtie_2.1.4+ds-4.debian.tar.xz Files: 6cd4731819c8630e1a6f7624a5b910da 789340 stringtie_2.1.4+ds.orig-debian-tests-data.tar.xz c08c2a5a6e16168575fb44900b7bc0ec 243788 stringtie_2.1.4+ds.orig.tar.xz a992b5d7b804c7b43951d2fc5619f37a 9076 stringtie_2.1.4+ds-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAl+vkaUUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafGBVQ/+LQxZWZxP/ZyDglVkpW6uDDX0aXYW Hkus7hAzuiCri1/KeuDWOTLeW4B+VZRTfEMoUT17v4v1ZkGgq/E6ThTeL9DQN7Dm mErI5TqspqLPe1IVi45CG85ktYxiccSgVbYeQnUuYDdg/9bFo0BHTR6gBm9XAeWR zmY8hKVasH0pKI9lk+uQWdHuOFne3aHABfhBSkpm5R7JQWIeprQXgWIvnaIMItwp ddOXtpSFEBV9ne294kLwCe9aHJECDs87NttstTQidkuDjWZGcnfPlqfMrP1snasJ To0yJxnzZeXB222KfNuis4ki1XVJ+6aPlVcqE6vqzrmnTrT6M5G5Vly5/sApcNlE NArTFrfd9AknqNYYGIQSI0RT/7Qj0X5Y7vRPTtyRWiGVS8qhN5zkO+csZg1QD1md KMFH7nqGQZhlU7oUuLcBdCMkYfIT3UKEO9e3fTg5cd2avLlzYocjQGAPnbz6o4Dr pwhclYUAbMHnd+o2XfilCG/f38TqqtjBI39aOPqxv6y8OqdyPpAR/sUfEVvGaBJC UZtyQE3S4M/GEeD3xqeL4XfzhFW3Au3jfkkuQOtnLqU9WVhbvkRkyofLxpBI5A20 yYweoDHbUodfuOkVqQYucnzHRX6jyGuCVRaFP84s9kp75Tw1c8v0FtkmsI9Z1B44 KyNQq6DAOQCjksk= =XPxT -----END PGP SIGNATURE----- Sun Jan 16 19:33:30 UTC 2022 I: Checking whether the package is not for us Sun Jan 16 19:33:30 UTC 2022 I: Starting 1st build on remote node ionos11-amd64.debian.net. Sun Jan 16 19:33:30 UTC 2022 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Sun Jan 16 19:34:49 UTC 2022 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 16 07:33:32 -12 2022 I: pbuilder-time-stamp: 1642361612 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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: Copying source file I: copying [stringtie_2.1.4+ds-4.dsc] I: copying [./stringtie_2.1.4+ds.orig-debian-tests-data.tar.xz] I: copying [./stringtie_2.1.4+ds.orig.tar.xz] I: copying [./stringtie_2.1.4+ds-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.CaE8Bka9/trustedkeys.kbx': General error gpgv: Signature made Fri Nov 13 20:13:25 2020 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./stringtie_2.1.4+ds-4.dsc dpkg-source: info: extracting stringtie in 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: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/913119/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='3e3b7ab45bbf4f96ad5d93c161219877' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='913119' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.zn3lyh4KqC/pbuilderrc_EjUp --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.zn3lyh4KqC/b1 --logfile b1/build.log stringtie_2.1.4+ds-4.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos11-amd64 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 08:25 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 07:09 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 07:09 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 07:09 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 07:09 more -rwsr-xr-x 1 root root 55528 Jul 28 07:09 mount -rwxr-xr-x 1 root root 18664 Jul 28 07:09 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 6 21:24 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 07:09 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 07:09 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 07:09 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/913119/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: amd64 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, 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 ... 19655 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 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} 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} libicu67{a} libldap-2.4-2{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} libsigsegv2{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: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 50 newly installed, 0 to remove and 0 not upgraded. Need to get 25.2 MB of archives. After unpacking 81.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libbam-dev amd64 0.1.19+dfsg-2 [118 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u1 [338 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libcurl4-gnutls-dev amd64 7.74.0-1.3+deb11u1 [429 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libdeflate-dev amd64 1.7-1 [46.9 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 liblzma-dev amd64 5.2.5-2 [229 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 libhts-dev amd64 1.11-4 [3858 kB] Fetched 25.2 MB in 2s (12.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../05-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../08-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../11-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-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 .../21-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../24-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../26-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.9.10+dfsg-6.7_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package help2man. Preparing to unpack .../32-help2man_1.48.1_amd64.deb ... Unpacking help2man (1.48.1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../33-zlib1g-dev_1%3a1.2.11.dfsg-2_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Selecting previously unselected package libbam-dev. Preparing to unpack .../34-libbam-dev_0.1.19+dfsg-2_amd64.deb ... Unpacking libbam-dev (0.1.19+dfsg-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../35-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../36-libsasl2-modules-db_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../37-libsasl2-2_2.1.27+dfsg-2.1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../38-libldap-2.4-2_2.4.57+dfsg-3_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../39-libnghttp2-14_1.43.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.43.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../40-libpsl5_0.21.0-1.2_amd64.deb ... Unpacking libpsl5:amd64 (0.21.0-1.2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../41-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../42-libssh2-1_1.9.0-2_amd64.deb ... Unpacking libssh2-1:amd64 (1.9.0-2) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../43-libcurl3-gnutls_7.74.0-1.3+deb11u1_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u1) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../44-libcurl4-gnutls-dev_7.74.0-1.3+deb11u1_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.74.0-1.3+deb11u1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../45-libdeflate0_1.7-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.7-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../46-libdeflate-dev_1.7-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.7-1) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../47-libhts3_1.11-4_amd64.deb ... Unpacking libhts3:amd64 (1.11-4) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../48-liblzma-dev_5.2.5-2_amd64.deb ... Unpacking liblzma-dev:amd64 (5.2.5-2) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../49-libhts-dev_1.11-4_amd64.deb ... Unpacking libhts-dev:amd64 (1.11-4) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Setting up liblzma-dev:amd64 (5.2.5-2) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libdeflate-dev:amd64 (1.7-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u1) ... Setting up libcurl4-gnutls-dev:amd64 (7.74.0-1.3+deb11u1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up libbam-dev (0.1.19+dfsg-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libhts3:amd64 (1.11-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:amd64 (1.11-4) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/stringtie-2.1.4+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../stringtie_2.1.4+ds-4_source.changes 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-2.1.4+ds' dh_auto_clean install -d /build/stringtie-2.1.4\+ds/debian/.debhelper/generated/_source/home make -j15 clean make[2]: Entering directory '/build/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-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-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 dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure install -d /build/stringtie-2.1.4\+ds/debian/.debhelper/generated/_source/home debian/rules override_dh_auto_build make[1]: Entering directory '/build/stringtie-2.1.4+ds' dh_auto_build -- 'LINKER=$(CXX)' make -j15 "INSTALL=install --strip-program=true" LINKER=\$\(CXX\) make[2]: Entering directory '/build/stringtie-2.1.4+ds' g++ -g -O2 -fdebug-prefix-map=/build/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-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-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-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 g++ -g -O2 -fdebug-prefix-map=/build/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-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-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 g++ -g -O2 -fdebug-prefix-map=/build/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-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 g++ -g -O2 -fdebug-prefix-map=/build/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-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-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-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 g++ -g -O2 -fdebug-prefix-map=/build/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 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/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 gclib/gff.h:1148:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1148 | struct { | ^ In file included from gclib/GBam.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 { | ^ 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: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 { | ^ ./gclib/gff.h:1148:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 1148 | struct { | ^ 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 { | ^ 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:327:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic] 327 | 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 { | ^ ./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 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 { | ^ ./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 tablemaker.cpp:2: ./gclib/GIntHash.hh:292:2: warning: extra ';' [-Wpedantic] 292 | }; | ^ In file included from rlink.h:10, from stringtie.cpp:2: ./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 rlink.cpp:1: ./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++ -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-2.1.4+ds' make[1]: Leaving directory '/build/stringtie-2.1.4+ds' rm -f debian/stringtie.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/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-2.1.4+ds' create-stamp debian/debhelper-build-stamp dh_prep 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-2.1.4+ds' help2man ./stringtie -n StringTie -s 1 -o debian/stringtie.1 dh_auto_install install -d /build/stringtie-2.1.4\+ds/debian/stringtie make[1]: Leaving directory '/build/stringtie-2.1.4+ds' dh_install install -d debian/stringtie/usr/bin cp --reflink=auto -a ./stringtie debian/stringtie/usr/bin/ install -d debian/.debhelper/generated/stringtie dh_installdocs install -d debian/stringtie/usr/share/doc/stringtie install -p -m0644 debian/copyright debian/stringtie/usr/share/doc/stringtie/copyright dh_installchangelogs install -p -m0644 debian/changelog debian/stringtie/usr/share/doc/stringtie/changelog.Debian dh_installman 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 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/stringtie-2.1.4+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 -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 -d debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/c7 objcopy --only-keep-debug --compress-debug-sections debian/stringtie/usr/bin/stringtie debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/c7/27e27d8397160c39c9a3ed5b56c39f1ef7234f.debug chmod 0644 -- debian/.debhelper/stringtie/dbgsym-root/usr/lib/debug/.build-id/c7/27e27d8397160c39c9a3ed5b56c39f1ef7234f.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/c7/27e27d8397160c39c9a3ed5b56c39f1ef7234f.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 rm -f debian/stringtie/DEBIAN/shlibs dh_shlibdeps -a install -d debian/stringtie/DEBIAN dpkg-shlibdeps -Tdebian/stringtie.substvars debian/stringtie/usr/bin/stringtie dh_installdeb dh_gencontrol 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 -UProtected -DPackage=stringtie-dbgsym "-DDepends=stringtie (= \${binary:Version})" "-DDescription=debug symbols for stringtie" -DBuild-Ids=c727e27d8397160c39c9a3ed5b56c39f1ef7234f -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 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 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=binary dpkg-genchanges --build=binary >../stringtie_2.1.4+ds-4_amd64.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: 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/913119 and its subdirectories I: Current time: Sun Jan 16 07:34:49 -12 2022 I: pbuilder-time-stamp: 1642361689 Sun Jan 16 19:34:49 UTC 2022 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Sun Jan 16 19:34:49 UTC 2022 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Sun Jan 16 19:35:48 UTC 2022 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Sun Jan 16 19:35:49 UTC 2022 I: stringtie_2.1.4+ds-4_amd64.changes: Format: 1.8 Date: Sat, 14 Nov 2020 13:38:57 +0530 Source: stringtie Binary: stringtie stringtie-dbgsym Architecture: amd64 Version: 2.1.4+ds-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: stringtie - assemble short RNAseq reads to transcripts Changes: stringtie (2.1.4+ds-4) unstable; urgency=medium . * Do not run on armhf Checksums-Sha1: fad7a491750dde42a8af27856a34d0a8524ed181 1688124 stringtie-dbgsym_2.1.4+ds-4_amd64.deb d1d82c924ab703a90bf332999a7003d29ba49a0f 5820 stringtie_2.1.4+ds-4_amd64.buildinfo ca62f9e22dd0256e041c9a28add05f4ede21b135 403840 stringtie_2.1.4+ds-4_amd64.deb Checksums-Sha256: 12b4ed9658b143624d596a0250cde5980b5c7a56d2db7d44a3a854fe8529b5a8 1688124 stringtie-dbgsym_2.1.4+ds-4_amd64.deb 48f7c9edc4b2640b796d114dc2becb719605d83e0e398c4365d52b08f7dd7795 5820 stringtie_2.1.4+ds-4_amd64.buildinfo 5bdbab823dd9c4fb8ee0db772a36ebb4eef9293c711eaa353308c4223191825e 403840 stringtie_2.1.4+ds-4_amd64.deb Files: ee9966420d64948a43f44575ad3be334 1688124 debug optional stringtie-dbgsym_2.1.4+ds-4_amd64.deb d0a128bc167f30fb8f9ce0ea134f4646 5820 science optional stringtie_2.1.4+ds-4_amd64.buildinfo a6040f2cf66b570d1f575d16b4610a5a 403840 science optional stringtie_2.1.4+ds-4_amd64.deb Sun Jan 16 19:35:52 UTC 2022 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.zn3lyh4KqC/stringtie_2.1.4+ds-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.zn3lyh4KqC/stringtie_2.1.4+ds-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.zn3lyh4KqC/stringtie_2.1.4+ds-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.zn3lyh4KqC/b1/stringtie_2.1.4+ds-4_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.zn3lyh4KqC/b2/stringtie_2.1.4+ds-4_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.001s) 0.001s 1 call abc.DotChangesFile ## main (total time: 0.713s) 0.713s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.343s) 0.343s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sun Jan 16 19:35:55 UTC 2022 I: found no differences in the changes files, and a .buildinfo file also exists. Sun Jan 16 19:35:55 UTC 2022 I: stringtie from bullseye built successfully and reproducibly on amd64. Sun Jan 16 19:35:57 UTC 2022 I: Submitting .buildinfo files to external archives: Sun Jan 16 19:35:57 UTC 2022 I: Submitting 8.0K b1/stringtie_2.1.4+ds-4_amd64.buildinfo.asc Sun Jan 16 19:36:00 UTC 2022 I: Submitting 8.0K b2/stringtie_2.1.4+ds-4_amd64.buildinfo.asc Sun Jan 16 19:36:01 UTC 2022 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Jan 16 19:36:01 UTC 2022 I: Done submitting .buildinfo files. Sun Jan 16 19:36:01 UTC 2022 I: Removing signed stringtie_2.1.4+ds-4_amd64.buildinfo.asc files: removed './b1/stringtie_2.1.4+ds-4_amd64.buildinfo.asc' removed './b2/stringtie_2.1.4+ds-4_amd64.buildinfo.asc'