Wed May 15 13:58:00 UTC 2024 I: starting to build subread/trixie/amd64 on jenkins on '2024-05-15 13:57' Wed May 15 13:58:00 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_26/6667/console.log Wed May 15 13:58:00 UTC 2024 I: Downloading source for trixie/subread=2.0.6+dfsg-3 --2024-05-15 13:58:01-- http://deb.debian.org/debian/pool/main/s/subread/subread_2.0.6%2bdfsg-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2185 (2.1K) [text/prs.lines.tag] Saving to: ‘subread_2.0.6+dfsg-3.dsc’ 0K .. 100% 301M=0s 2024-05-15 13:58:01 (301 MB/s) - ‘subread_2.0.6+dfsg-3.dsc’ saved [2185/2185] Wed May 15 13:58:01 UTC 2024 I: subread_2.0.6+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: subread Binary: subread, subread-data Architecture: any all Version: 2.0.6+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Alexandre Mestiashvili , Andreas Tille Homepage: http://sourceforge.net/projects/subread/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/subread Vcs-Git: https://salsa.debian.org/med-team/subread.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: bc , debhelper-compat (= 13), architecture-is-little-endian, python3 , zlib1g-dev Package-List: subread deb science optional arch=any subread-data deb science optional arch=all Checksums-Sha1: 7b8f9bcb1495dc417d8004cbadb799916885e2ff 16555528 subread_2.0.6+dfsg.orig.tar.xz e405e199da83f5223e77fe028b32fa7d29b020f0 19600 subread_2.0.6+dfsg-3.debian.tar.xz Checksums-Sha256: 55026879f4cb40f0eca223a017fb6790fbbeeec7c828f27cb61302defbdf9753 16555528 subread_2.0.6+dfsg.orig.tar.xz 2c0bcc064e2ceee01c53cdf91508f10931030580b33a4da9d4fcfc9ec8fd5519 19600 subread_2.0.6+dfsg-3.debian.tar.xz Files: c4512db7a4ffd29b1d7e371fa9c1e9b8 16555528 subread_2.0.6+dfsg.orig.tar.xz f4a898483ea601dda3f2334cfcd7be98 19600 subread_2.0.6+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYqMwoACgkQPCZ2P2xn 5uJk2Q//VW5f7tlCyJQhj90flZeb/lxRLOcuxBk7SFD3BfF7rT8Mf1vFsFSWQVS+ zIF16QfOu8F/WXgTIhiJT7OUTorol+dCx65NVNXe8Q/d1ixxLxcV/p1n17ks1j4X JPN8WJue+QRBYB3F7rM+KPJsH5ZmuvAZR3FXzHlEi6GlCOKpaZmUyrbYrYF10sdo uYCfNaMX6OeuswCOxC221sr9hKOOWY5hEJVcWneCrKCflUYFrfp60YggwDSJr+64 qfcNbR/hnuX5iU4VtnIBRtE9Q467KQaF/O7q+2bawfmJ7BBGKzvqwkl0zjj7IJQd GgEpdJWQoGYbmwpXt8gycfw/h+O+v56Q79j0ikXCyOHTL8791mPe+uTXfloQNJgJ 2QjeWnOnZDYyBhJ4nEtwjHiBF1QRMosNg/H03jPLX35yn4Qr/KpI0XbhQroSHJjc Gt5VMGZIqlaQ816WAtfgOCp0Fgw87eRGjGM+plxQuK+JyaKs7VA3cEZjRPSqXlEV lY/TML2nHKNLrGzoQXP+b/kdQkaAhBoMXgNb/VSeitY8VehKPFJvcUGlyWF9e2r+ qtoi3R8QIJA0IW6LiYGD9+5gqpBafIPueHSx8NN+CbMWXkpnxplkf5cZKZgglNcj IEyUV4d0X53Vi4Am6PsUjxRubWnSiE2MRZ1TTMe+r+qbX62GW8k= =7YAm -----END PGP SIGNATURE----- Wed May 15 13:58:01 UTC 2024 I: Checking whether the package is not for us Wed May 15 13:58:01 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Wed May 15 13:58:01 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Wed May 15 14:05:14 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 17 08:21:03 -12 2025 I: pbuilder-time-stamp: 1750191663 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: Copying source file I: copying [subread_2.0.6+dfsg-3.dsc] I: copying [./subread_2.0.6+dfsg.orig.tar.xz] I: copying [./subread_2.0.6+dfsg-3.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Apr 25 10:40:10 2024 gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./subread_2.0.6+dfsg-3.dsc: no acceptable signature found dpkg-source: info: extracting subread in subread-2.0.6+dfsg dpkg-source: info: unpacking subread_2.0.6+dfsg.orig.tar.xz dpkg-source: info: unpacking subread_2.0.6+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying typo.patch dpkg-source: info: applying fix_ftbfs_kfreebsd.patch dpkg-source: info: applying arch_specific_flags.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying 0001-src-Makefile.Linux-Do-not-set-CFLAGS-and-CXXFLAGS-to.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4030515/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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 parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='4e1e4ca5f6dd4757ab843b4ed18af450' 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='4030515' 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/r-b-build.lbv7B9T5/pbuilderrc_T07O --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.lbv7B9T5/b1 --logfile b1/build.log subread_2.0.6+dfsg-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 16 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4030515/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: bc, debhelper-compat (= 13), architecture-is-little-endian, python3, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19699 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 bc; however: Package bc is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on architecture-is-little-endian; however: Package architecture-is-little-endian is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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: architecture-properties{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 46 newly installed, 0 to remove and 0 not upgraded. Need to get 25.9 MB of archives. After unpacking 99.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 architecture-properties amd64 0.1.1+b1 [1888 B] Get: 25 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 bc amd64 1.07.1-4 [103 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 38 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Fetched 25.9 MB in 0s (107 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20015 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21007 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... 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%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/subread-2.0.6+dfsg/ && 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 > ../subread_2.0.6+dfsg-3_source.changes dpkg-buildpackage: info: source package subread dpkg-buildpackage: info: source version 2.0.6+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=makefile debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg' dh_auto_clean rm -f test/subread-align/data/test-err-mut-r1.fq.gz test/subread-align/data/test-err-mut-r2.fq.gz rm -rf bin src/longread-one/make.version find . -name "*.o" -delete dh_auto_clean --sourcedirectory=src -- -f Makefile.Linux cd src && make -j42 clean -f Makefile.Linux make[2]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src' rm -f core featureCounts exactSNP removeDup subread-buildindex core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o make[2]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg' dh_autoreconf_clean -O--buildsystem=makefile dh_clean -O--buildsystem=makefile rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/subread.substvars debian/subread-data.substvars debian/files rm -fr -- debian/subread/ debian/tmp/ debian/subread-data/ 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 --buildsystem=makefile dh_update_autotools_config -O--buildsystem=makefile dh_autoreconf -O--buildsystem=makefile dh_auto_configure -O--buildsystem=makefile debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg' dh_auto_build --sourcedirectory=src -- -f Makefile.Linux CC=x86_64-linux-gnu-gcc ; \ cd src && make -j42 "INSTALL=install --strip-program=true" -f Makefile.Linux CC=x86_64-linux-gnu-gcc make[2]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core.o core.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-junction.o core-junction.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-indel.o core-indel.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sambam-file.o sambam-file.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sublog.o sublog.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-algorithms.o gene-algorithms.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o hashtable.o hashtable.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-files.o input-files.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sorted-hashtable.o sorted-hashtable.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gene-value-index.o gene-value-index.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o exon-algorithms.o exon-algorithms.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o HelperFunctions.o HelperFunctions.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o interval_merge.o interval_merge.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o long-hashtable.o long-hashtable.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o core-bigtable.o core-bigtable.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o seek-zlib.o seek-zlib.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o input-blc.o input-blc.c gene-value-index.c: In function 'is_offset_in_chro': gene-value-index.c:85:33: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding )) | ^~ In file included from gene-value-index.h:24, from gene-value-index.c:25: subread.h:143:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 143 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) | ^~~~~~~ gene-value-index.c:87:41: note: in expansion of macro 'SUBREADprintf' 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ input-blc.c: In function 'iCache_continuous_read_lanes': input-blc.c:579:59: warning: unused variable 'npos' [-Wunused-variable] 579 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); | ^~~~ input-blc.c: In function 'iCache_write_supIdx_result': input-blc.c:1123:24: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'void *' [-Wformat=] 1123 | fprintf(ofp, "%s\t%lld\n", ky, va-NULL); | ~^ ~~ | | | | char * void * | %p input-blc.c:1123:30: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] 1123 | fprintf(ofp, "%s\t%lld\n", ky, va-NULL); | ~~~^ | | | long long int | %ld core-junction.c: In function 'find_donor_receptor': core-junction.c:2099:25: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) | ^~ core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ input-blc.c: In function 'iCache_continuous_read_lanes': input-blc.c:489:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 489 | read(tfp -> cbcl_bin_fd,&btmp,1);// bits per call. | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-blc.c:491:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 491 | read(tfp -> cbcl_bin_fd,&tfp -> bits_per_bitscore,1);// bits per qscore. | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-blc.c:498:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 498 | read(tfp -> cbcl_bin_fd,&btmp,4);// Number of bins | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene-algorithms.c: In function 'miltime': input-blc.c:501:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 501 | read(tfp -> cbcl_bin_fd,&fromv,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-blc.c:502:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 502 | read(tfp -> cbcl_bin_fd,&tov,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene-algorithms.c:1395:17: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 1395 | ftime(&trp); | ^~~~~ In file included from gene-algorithms.c:33: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ input-blc.c:511:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 511 | read(tfp -> cbcl_bin_fd,&btmp,4);// Number of tiles (gzipped blocks) in this file | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-blc.c:515:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 515 | read(tfp -> cbcl_bin_fd,&tile_4digit,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-blc.c:516:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 516 | read(tfp -> cbcl_bin_fd,&reads_in_tile,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-blc.c:517:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 517 | read(tfp -> cbcl_bin_fd,&data_size,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-blc.c:518:57: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 518 | read(tfp -> cbcl_bin_fd,&compressed_size,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ input-blc.c:524:49: warning: ignoring return value of 'read' declared with attribute 'warn_unused_result' [-Wunused-result] 524 | read(tfp -> cbcl_bin_fd,&btmp,1); // excluding non-FP? | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o genRandomReads gen_rand_reads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o detectionCall detection-calls.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm echo " " > longread-one/make.version x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o repair read-repair.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o txUnique tx-unique.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o featureCounts readSummary.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm rm -f longread-one/*.o x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o removeDup removeDupReads.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o exactSNP SNPCalling.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-buildindex index-builder.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subindel SUBindel.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-align core-interface-aligner.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm cd longread-one && make x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subjunc core-interface-subjunc.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o qualityScores qualityScores.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o subread-fullscan fullscan.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o propmapped propmapped.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o flattenGTF flattenAnnotations.c core.o core-junction.o core-indel.o sambam-file.o sublog.o gene-algorithms.o hashtable.o input-files.o sorted-hashtable.o gene-value-index.o exon-algorithms.o HelperFunctions.o interval_merge.o long-hashtable.o core-bigtable.o seek-zlib.o input-blc.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm make[3]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg/src/longread-one' x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMsorted-hashtable.o -c LRMsorted-hashtable.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMbase-index.o -c LRMbase-index.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMchro-event.o -c LRMchro-event.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhelper.o -c LRMhelper.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMseek-zlib.o -c LRMseek-zlib.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMfile-io.o -c LRMfile-io.c x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRMhashtable.o -c LRMhashtable.c detection-calls.c: In function 'DTCwrite_annotations': detection-calls.c:155:9: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ detection-calls.c:155:109: warning: dangling pointer 'gc_2int' to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:66:31: warning: '.reads' directive writing 6 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 66 | sprintf(tmp_fname, "%s.reads", context->config.index_prefix); | ^~~~~~ In file included from /usr/include/stdio.h:964, from SUBindel.c:20: In function 'sprintf', inlined from 'load_global_context_forindel' at SUBindel.c:66:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 7 and 1006 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:77:39: warning: '.00.b.tab' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 77 | sprintf(tmp_fname, "%s.00.b.tab", context->config.index_prefix); | ^~~~~~~~~ In function 'sprintf', inlined from 'load_global_context_forindel' at SUBindel.c:77:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:75:39: warning: '.00.c.tab' directive writing 9 bytes into a region of size between 1 and 1000 [-Wformat-overflow=] 75 | sprintf(tmp_fname, "%s.00.c.tab", context->config.index_prefix); | ^~~~~~~~~ In function 'sprintf', inlined from 'load_global_context_forindel' at SUBindel.c:75:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1009 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:87:40: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ SUBindel.c:87:36: note: directive argument in the range [-2147483647, 2147483647] 87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'load_global_context_forindel' at SUBindel.c:87:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SUBindel.c: In function 'load_global_context_forindel': SUBindel.c:87:40: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ SUBindel.c:87:36: note: directive argument in the range [-2147483647, 2147483647] 87 | sprintf(tmp_fname, "%s.%02d.%c.tab", context->config.index_prefix, context->index_block_number, context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'load_global_context_forindel' at SUBindel.c:87:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 10 and 1018 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ SUBindel.c: In function 'load_indexes_forindel': SUBindel.c:110:40: warning: '%02d' directive writing between 2 and 10 bytes into a region of size between 0 and 999 [-Wformat-overflow=] 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~ SUBindel.c:110:36: note: directive argument in the range [0, 2147483646] 110 | sprintf(tmp_fname, "%s.%02d.%c.array", global_context->config.index_prefix, block_no, global_context->config.space_type == GENE_SPACE_COLOR?'c':'b'); | ^~~~~~~~~~~~~~~~~~ In function 'sprintf', inlined from 'load_indexes_forindel' at SUBindel.c:110:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 12 and 1019 bytes into a destination of size 1000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ In file included from readSummary.c:41: readSummary.c: In function 'get_RG_tables': readSummary.c:2641:31: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 2641 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} subread.h:143:44: note: in definition of macro 'SUBREADprintf' 143 | #define SUBREADprintf(...) fprintf(stderr, __VA_ARGS__) | ^~~~~~~~~~~ readSummary.c:2641:64: note: format string is defined here 2641 | SUBREADprintf("cannot allocate memory for %s (%d)\n", rg_name, strlen(rg_name)); | ~^ | | | int | %ld x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/subread-2.0.6+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -mtune=generic -msse3 -O3 -fsigned-char -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D SUBREAD_VERSION=\""2.0.6"\" -D_FILE_OFFSET_BITS=64 -fmessage-length=0 -ggdb -O3 -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\""2.0.6"\" -fmessage-length=0 -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -o LRM longread-mapping.c LRMsorted-hashtable.o LRMbase-index.o LRMchro-event.o LRMhelper.o LRMseek-zlib.o LRMfile-io.o LRMhashtable.o -Wl,-z,relro -Wl,-z,now -pthread -lz -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE -lm -lpthread -lz -lm -O3 -DMAKE_FOR_EXON -D MAKE_STANDALONE longread-mapping.c: In function 'LRMmiltime': longread-mapping.c:234:9: warning: 'ftime' is deprecated: Use gettimeofday or clock_gettime instead [-Wdeprecated-declarations] 234 | ftime(&trp); | ^~~~~ In file included from longread-mapping.c:33: /usr/include/x86_64-linux-gnu/sys/timeb.h:29:12: note: declared here 29 | extern int ftime (struct timeb *__timebuf) | ^~~~~ make[3]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg/src/longread-one' readSummary.c: In function 'vote_and_add_count': readSummary.c:4923:66: warning: 'longest_overlap_score' may be used uninitialized [-Wmaybe-uninitialized] 4923 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:4691:51: note: 'longest_overlap_score' was declared here 4691 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ mkdir -p ../bin/utilities mv longread-one/LRM longread-one/sublong mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities ########################################################### # # # Installation successfully completed. # # # # Generated executables were copied to directory ../bin/ # # # ########################################################### make[2]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg/src' make[1]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg' rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg' debian/tests/subread-tests /build/reproducible-path/subread-2.0.6+dfsg  ************************************************** ************************************************** *** *** *** This script will test the major functions *** *** in our package, including the index build- *** *** er, subread-align, subjunc, featureCounts *** *** and exactSNP. *** *** *** *** Test will start in seconds. *** *** *** ************************************************** ************************************************** 9876543210[0,0Hrm: cannot remove 'test-tmp.log': No such file or directory ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Index name : small1 || || Index space : base space || || Index split : no-split || || Repeat threshold : 100 repeats || || Gapped index : no || || || || Free / total memory : 65.7GB / 78.5GB || || || || Input files : 1 file in total || || o chr901.fa || || || \\============================================================================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 52 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || || 8%, 0 mins elapsed, rate=598.8k bps/s || || 16%, 0 mins elapsed, rate=1110.4k bps/s || || 25%, 0 mins elapsed, rate=1552.4k bps/s || || 33%, 0 mins elapsed, rate=1949.6k bps/s || || 41%, 0 mins elapsed, rate=2290.5k bps/s || || 50%, 0 mins elapsed, rate=2592.7k bps/s || || 58%, 0 mins elapsed, rate=2862.6k bps/s || || 66%, 0 mins elapsed, rate=3133.9k bps/s || || 75%, 0 mins elapsed, rate=3368.3k bps/s || || 83%, 0 mins elapsed, rate=3582.6k bps/s || || 91%, 0 mins elapsed, rate=3810.5k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=53.4k bps/s || || 16%, 0 mins elapsed, rate=105.0k bps/s || || 25%, 0 mins elapsed, rate=155.1k bps/s || || 33%, 0 mins elapsed, rate=203.7k bps/s || || 41%, 0 mins elapsed, rate=250.8k bps/s || || 50%, 0 mins elapsed, rate=296.8k bps/s || || 58%, 0 mins elapsed, rate=341.4k bps/s || || 66%, 0 mins elapsed, rate=385.0k bps/s || || 75%, 0 mins elapsed, rate=427.5k bps/s || || 83%, 0 mins elapsed, rate=468.6k bps/s || || 91%, 0 mins elapsed, rate=509.8k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.1 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : test-noerror-r1.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || Min votes : 3 / 10 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (17-Jun-2025 08:22:07, pid=4041434) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 1.0 mins elapsed, rate=61.7k reads per second || || 74% completed, 1.0 mins elapsed, rate=0.3k reads per second || || 83% completed, 1.0 mins elapsed, rate=0.3k reads per second || || 91% completed, 1.0 mins elapsed, rate=0.3k reads per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total reads : 19998 || || Mapped : 18785 (93.9%) || || Uniquely mapped : 18785 || || Multi-mapping : 0 || || || || Unmapped : 1213 || || || || Indels : 0 || || || || Running time : 1.0 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file : test-noerror-r1.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || Min votes : 3 / 10 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (17-Jun-2025 08:23:04, pid=4048081) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 1.0 mins elapsed, rate=61.7k reads per second || || 74% completed, 1.0 mins elapsed, rate=0.3k reads per second || || 83% completed, 1.0 mins elapsed, rate=0.3k reads per second || || 91% completed, 1.0 mins elapsed, rate=0.3k reads per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total reads : 19998 || || Mapped : 18785 (93.9%) || || Uniquely mapped : 18785 || || Multi-mapping : 0 || || || || Unmapped : 1213 || || || || Indels : 0 || || || || Running time : 1.0 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-noerror-r1.fq || || Input file 2 : test-noerror-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (17-Jun-2025 08:24:03, pid=4056329) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 1.0 mins elapsed, rate=30.2k fragments per second || || Estimated fragment length : 495 bp || || 74% completed, 1.0 mins elapsed, rate=0.2k fragments per second || || 83% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || 91% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 19998 || || Mapped : 19491 (97.5%) || || Uniquely mapped : 19491 || || Multi-mapping : 0 || || || || Unmapped : 507 || || || || Properly paired : 19089 || || Not properly paired : 402 || || Singleton : 0 || || Chimeric : 0 || || Unexpected strandness : 0 || || Unexpected fragment length : 385 || || Unexpected read order : 17 || || || || Indels : 0 || || || || Running time : 1.0 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-noerror-r1.fq || || Input file 2 : test-noerror-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (17-Jun-2025 08:25:03, pid=4066135) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [9,9] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 1.0 mins elapsed, rate=29.2k fragments per second || || Estimated fragment length : 495 bp || || 74% completed, 1.1 mins elapsed, rate=0.2k fragments per second || || 83% completed, 1.1 mins elapsed, rate=0.3k fragments per second || || 91% completed, 1.1 mins elapsed, rate=0.3k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 19998 || || Mapped : 19491 (97.5%) || || Uniquely mapped : 19491 || || Multi-mapping : 0 || || || || Unmapped : 507 || || || || Properly paired : 19089 || || Not properly paired : 402 || || Singleton : 0 || || Chimeric : 0 || || Unexpected strandness : 0 || || Unexpected fragment length : 385 || || Unexpected read order : 17 || || || || Indels : 0 || || || || Running time : 1.1 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-error-r1.fq || || Input file 2 : test-error-r2.fq || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (17-Jun-2025 08:26:07, pid=4086647) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [-14,-14] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 33% completed, 1.0 mins elapsed, rate=31.6k fragments per second || || Estimated fragment length : 497 bp || || 74% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || 83% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || 91% completed, 1.0 mins elapsed, rate=0.3k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 20000 || || Mapped : 18937 (94.7%) || || Uniquely mapped : 18937 || || Multi-mapping : 0 || || || || Unmapped : 1063 || || || || Properly paired : 14143 || || Not properly paired : 4794 || || Singleton : 4504 || || Chimeric : 0 || || Unexpected strandness : 0 || || Unexpected fragment length : 274 || || Unexpected read order : 16 || || || || Indels : 15 || || || || Running time : 1.0 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Function : Read alignment (RNA-Seq) || || Input file 1 : test-err-mut-r1.fq.gz || || Input file 2 : test-err-mut-r2.fq.gz || || Output file : test-tmp.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 64 || || # of extracted subreads : 10 || || Min read1 vote : 3 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || Read group name : MyTestGroup || || || \\============================================================================// //=============== Running (17-Jun-2025 08:27:06, pid=4088556) ================\\ || || ERROR: unable to open file 'data/test-err-mut-r1.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. ERROR: unable to open file 'data/test-err-mut-r2.fq.gz'. File name might be incorrect, or you do not have the permission to read the file. 76f6c2a84c5097b13435bbeac4a8acd8 ../small1.00.b.array 39cd407b95c866d7db864ce69a7d08fb ../small1.00.b.tab ************************************************* *** SINGLE-END READS NO ERROR ****** ************************************************* unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.9393439343934393 paired_match= 0 ; paired= 0.0 ************************************************* *** SINGLE-END READS NO ERROR NO DUP ****** ************************************************* unmatched= 0 ; matched= 18785 ; unmapped= 1213 ; reads= 19998 ;NN= 0 accuracy= 1.0 ; sensitivity= 0.9393439343934393 paired_match= 0 ; paired= 0.0 ************************************************* *** READS WITH NO ERROR ****** ************************************************* unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 paired_match= 38926 ; paired= 1.0 ************************************************* *** READS NO ERROR, NO DUPLICATED REPORT ****** ************************************************* unmatched= 56 ; matched= 38926 ; unmapped= 1014 ; reads= 39996 ;NN= 0 accuracy= 0.9985634395361962 ; sensitivity= 0.9746474647464747 paired_match= 38926 ; paired= 1.0 ************************************************* *** READS WITH ONLY SEQUENCING ERROR ****** ************************************************* unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 accuracy= 0.9980221756068325 ; sensitivity= 0.83425 paired_match= 28800 ; paired= 0.8647609896709104 ************************************************* *** READS WITH SEQUENCING ERROR AND MUTATION *** *** SUBREAD IS RUN WITH LONG INDEL DETECTION *** ************************************************* unmatched= 66 ; matched= 33304 ; unmapped= 6630 ; reads= 40000 ;NN= 0 accuracy= 0.9980221756068325 ; sensitivity= 0.83425 paired_match= 28800 ; paired= 0.8647609896709104 ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Index name : small1 || || Index space : base space || || Memory : 8000 Mbytes || || Repeat threshold : 100 repeats || || Gapped index : yes || || || || Free / total memory : 65.6GB / 78.5GB || || || || Input files : 1 file in total || || o chr901.fa || || || \\============================================================================// //================================= Running ==================================\\ || || || Check the integrity of provided reference sequences ... || || There were 4 notes for reference sequences. || || The notes can be found in the log file, '../small1.log'. || || Scan uninformative subreads in reference sequences ... || || 2 uninformative subreads were found. || || These subreads were excluded from index building. || || Estimate the index size... || || 8%, 0 mins elapsed, rate=4412.2k bps/s || || 16%, 0 mins elapsed, rate=7289.7k bps/s || || 25%, 0 mins elapsed, rate=9314.6k bps/s || || 33%, 0 mins elapsed, rate=10817.0k bps/s || || 41%, 0 mins elapsed, rate=11976.0k bps/s || || 50%, 0 mins elapsed, rate=12897.2k bps/s || || 58%, 0 mins elapsed, rate=13972.0k bps/s || || 66%, 0 mins elapsed, rate=14579.5k bps/s || || 75%, 0 mins elapsed, rate=15089.7k bps/s || || 83%, 0 mins elapsed, rate=15524.4k bps/s || || 91%, 0 mins elapsed, rate=16178.1k bps/s || || 0.8 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=429.9k bps/s || || 16%, 0 mins elapsed, rate=821.9k bps/s || || 25%, 0 mins elapsed, rate=1186.3k bps/s || || 33%, 0 mins elapsed, rate=1524.2k bps/s || || 41%, 0 mins elapsed, rate=1838.4k bps/s || || 50%, 0 mins elapsed, rate=2131.3k bps/s || || 58%, 0 mins elapsed, rate=2405.0k bps/s || || 66%, 0 mins elapsed, rate=2661.3k bps/s || || 75%, 0 mins elapsed, rate=2901.9k bps/s || || 83%, 0 mins elapsed, rate=3128.1k bps/s || || 91%, 0 mins elapsed, rate=3341.1k bps/s || || Save current index block... || || [ 0.0% finished ] || || [ 10.0% finished ] || || [ 20.0% finished ] || || [ 30.0% finished ] || || [ 40.0% finished ] || || [ 50.0% finished ] || || [ 60.0% finished ] || || [ 70.0% finished ] || || [ 80.0% finished ] || || [ 90.0% finished ] || || [ 100.0% finished ] || || || || Total running time: 0.0 minutes. || || Index ../small1 was successfully built. || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Function : Read alignment + Junction detection (RNA-Seq) || || Input file 1 : junction-reads-A.fq || || Input file 2 : junction-reads-B.fq || || Output file : junctions.sam (SAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 14 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (17-Jun-2025 08:27:09, pid=4088626) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [2,41] || || Create the output SAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 41% completed, 0.1 mins elapsed, rate=20.8k fragments per second || || Estimated fragment length : 173 bp || || 77% completed, 0.1 mins elapsed, rate=1.5k fragments per second || || 87% completed, 0.1 mins elapsed, rate=1.7k fragments per second || || 97% completed, 0.1 mins elapsed, rate=1.9k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 16052 || || Mapped : 15291 (95.3%) || || Uniquely mapped : 15291 || || Multi-mapping : 0 || || || || Unmapped : 761 || || || || Properly paired : 13894 || || Not properly paired : 1397 || || Singleton : 962 || || Chimeric : 0 || || Unexpected strandness : 36 || || Unexpected fragment length : 335 || || Unexpected read order : 64 || || || || Junctions : 419 || || Indels : 177 || || || || Running time : 0.1 minutes || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //================================= setting ==================================\\ || || || Function : Read alignment + Junction/Fusion detection (RNA-Seq) || || Input file 1 : junction-reads-A.fq || || Input file 2 : junction-reads-B.fq || || Output file : junctionsNfusions.bam (BAM) || || Index name : small1 || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || # of extracted subreads : 28 || || Min read1 vote : 1 || || Min read2 vote : 1 || || Max fragment size : 600 || || Min fragment size : 50 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : no || || Max alignments per multi-mapping read : 1 || || || \\============================================================================// //=============== Running (17-Jun-2025 08:27:17, pid=4090013) ================\\ || || || Check the input reads. || || The input file contains base space reads. || || Initialise the memory objects. || || Estimate the mean read length. || || The range of Phred scores observed in the data is [2,41] || || Create the output BAM file. || || Check the index. || || Init the voting space. || || Global environment is initialised. || || Load the 1-th index block... || || The index block has been loaded. || || Start read mapping in chunk. || || 41% completed, 0.1 mins elapsed, rate=11.9k fragments per second || || Estimated fragment length : 174 bp || || 77% completed, 0.1 mins elapsed, rate=1.5k fragments per second || || 87% completed, 0.1 mins elapsed, rate=1.6k fragments per second || || 97% completed, 0.2 mins elapsed, rate=1.7k fragments per second || || || || Completed successfully. || || || \\==================================== ====================================// //================================ Summary =================================\\ || || || Total fragments : 16052 || || Mapped : 15273 (95.1%) || || Uniquely mapped : 15273 || || Multi-mapping : 0 || || || || Unmapped : 779 || || || || Properly paired : 13793 || || Not properly paired : 1480 || || Singleton : 1013 || || Chimeric : 0 || || Unexpected strandness : 37 || || Unexpected fragment length : 368 || || Unexpected read order : 62 || || || || Junctions : 437 || || Fusions : 33 || || Indels : 180 || || || || Running time : 0.2 minutes || || || \\============================================================================// ================================================================================ FeatureCounts Basic Test http://subread.sourceforge.net/ ================================================================================ ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //========================== featureCounts setting ===========================\\ || || || Input files : 1 SAM file || || || || test-minimum.sam || || || || Output file : test-minimum.FC || || Summary : test-minimum.FC.summary || || Paired-end : yes || || Count read pairs : no || || Annotation : test-minimum.GTF (GTF) || || Dir for temp files : result || || || || Threads : 1 || || Level : meta-feature level || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || Min overlapping bases : 1 || || || \\============================================================================// //================================= Running ==================================\\ || || || Load annotation file test-minimum.GTF ... || || Features : 23 || || Meta-features : 7 || || Chromosomes/contigs : 3 || || || || Process SAM file test-minimum.sam... || || Paired-end reads are included. || || The reads are assigned on the single-end mode. || || Total alignments : 998 || || Successfully assigned alignments : 389 (39.0%) || || Running time : 0.00 minutes || || || || Write the final count table. || || Write the read assignment summary. || || || || Summary of counting results can be found in file "result/test-minimum.FC. || || summary" || || || \\============================================================================// ================================================================================ Basic Test finished. The results are in result/test-minimum.FC ================================================================================ ================================================================================ FeatureCounts Chromosome Name Aliases Tests http://subread.sourceforge.net/ ================================================================================ Testing chromosome aliases ... [PASS] ================================================================================ FeatureCounts Chromosome Name Inference Tests http://subread.sourceforge.net/ ================================================================================ Testing automatic inference of chromosome names ... [PASS] mkdir: unrecognized option '--countReadPairs' Try 'mkdir --help' for more information. ================================================================================ FeatureCounts Corner Case Tests http://subread.sourceforge.net/ ================================================================================ Testing indel reads ... [PASS] Testing junction reads ... [PASS] Testing paired-end reads (fragment counting) ... [PASS] Testing paired-end reads (fragment counting, both ends mapped) ... [PASS] Testing multi-overlapping reads ... [PASS] Testing feature-level summarization ... [PASS] Testing gene-level summarization ... [PASS] Testing multi-mapping reads ... [PASS] Testing multi-mapping reads (primary only) ... [PASS] Testing both ends mapped ... [PASS] Testing disallowing chimeric fragments ... [PASS] Testing Allowing multi-mapped reads ... [PASS] Testing not sorting input file ... [PASS] Testing minimum overlapping length ... [PASS] Testing minimum overlapping fraction ... [PASS] Testing Largest Overlapping ... [PASS] Testing paired-end distance ... [PASS] Testing Read to position (5' end) ... [PASS] Testing Read to position (3' end) ... [PASS] Testing Read extension to the 3' end ... [PASS] Testing Read extension to the 5' end ... [PASS] Testing Low maxOPs value ... [PASS] Testing minimum mapping quality ... [PASS] Testing Ignoring duplicated reads ... [PASS] Testing Fraction counting ... [PASS] Testing Advanced fractions ... [PASS] Testing Junction counting ... [PASS,PASS] Skipping Junction counting (with genome). Testing GTF format annotations ... [PASS] Testing SAF format annotations ... [PASS] Testing SAM format input ... [PASS] Testing BAM format input ... [PASS] Testing unstranded read summarization ... [PASS] Testing stranded read summarization ... [PASS] Testing reversely stranded read summarization ... [PASS] Testing Ignoring duplicate fragments ... [PASS] Testing Junction reads only ... [PASS] Testing Exonic reads only ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing intron_between ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_genes ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] Testing across_intron ... [PASS] ../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v2.0.6 //============================= exactSNP setting =============================\\ || || || Input file : test-in.BAM (BAM) || || Output file : test-out.VCF || || Reference genome : chr901.fa || || Temp path : || || || || Threads : 1 || || Min supporting reads : 1 || || Min pct. of supporting reads : 0.0% || || Min base quality score : 13 || || Number of trimmed bases : 3 || || || || Q value cutoff : 10E-12.0 || || P value upper bound : 0.00500 || || Flanking windows size : 5 || || || \\============================================================================// //====================== Running (17-Jun-2025 08:27:27) ======================\\ || || || Split BAM file into result/temp-snps-4092963-522AC0F4F503-* ... || || processed block chr901@999950 by thread 1/1 [block number=1/1] || || || || Completed successfully. || || || \\============================================================================// //================================= Summary ==================================\\ || || || Processed reads : 50204 || || Reported SNPs : 416 || || Reported indels : 22 || || || || Running time : 0.0 minutes || || || \\============================================================================//  ************************************************** ************************************************** *** *** *** Test finished. *** *** *** *** Should there be any error, please visit *** *** http://subread.sourceforge.net/ for more *** *** information. *** *** *** ************************************************** **************************************************  make[1]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=makefile dh_prep -O--buildsystem=makefile rm -f -- debian/subread.substvars debian/subread-data.substvars rm -fr -- debian/.debhelper/generated/subread/ debian/subread/ debian/tmp/ debian/.debhelper/generated/subread-data/ debian/subread-data/ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg' cp annotation/mm39_RefSeq_exon.txt.gz debian/mm39_RefSeq_exon.txt.gz.orig find /build/reproducible-path/subread-2.0.6+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \; dh_auto_install install -m0755 -d /build/reproducible-path/subread-2.0.6\+dfsg/debian/tmp mv debian/mm39_RefSeq_exon.txt.gz.orig annotation/mm39_RefSeq_exon.txt.gz make[1]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg' dh_install -O--buildsystem=makefile install -m0755 -d debian/subread/usr/bin cp --reflink=auto -a ./bin/exactSNP ./bin/featureCounts ./bin/subindel ./bin/subjunc ./bin/sublong ./bin/subread-align ./bin/subread-buildindex debian/subread/usr/bin/ install -m0755 -d debian/subread/usr/lib/subread cp --reflink=auto -a ./bin/utilities/flattenGTF ./bin/utilities/genRandomReads ./bin/utilities/propmapped ./bin/utilities/qualityScores ./bin/utilities/removeDup ./bin/utilities/repair ./bin/utilities/subread-fullscan ./bin/utilities/txUnique debian/subread/usr/lib/subread/ install -m0755 -d debian/subread-data/usr/share/doc/subread/examples cp --reflink=auto -a ./annotation debian/subread-data/usr/share/doc/subread/examples/ dh_installdocs -O--buildsystem=makefile install -m0755 -d debian/subread/usr/share/doc/subread install -m0755 -d debian/subread/usr/share/doc/subread cp --reflink=auto -a ./README.txt debian/subread/usr/share/doc/subread chmod -R u\+rw,go=rX debian/subread/usr/share/doc install -p -m0644 debian/README.Debian debian/subread/usr/share/doc/subread/README.Debian install -p -m0644 debian/copyright debian/subread/usr/share/doc/subread/copyright install -m0755 -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/copyright debian/subread-data/usr/share/doc/subread-data/copyright dh_installchangelogs -O--buildsystem=makefile install -m0755 -d debian/subread-data/usr/share/doc/subread-data install -p -m0644 debian/.debhelper/generated/subread-data/dh_installchangelogs.dch.trimmed debian/subread-data/usr/share/doc/subread-data/changelog.Debian install -m0755 -d debian/subread/usr/share/doc/subread install -p -m0644 debian/.debhelper/generated/subread/dh_installchangelogs.dch.trimmed debian/subread/usr/share/doc/subread/changelog.Debian rm -f debian/subread-data.debhelper.log debian/subread.debhelper.log debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/reproducible-path/subread-2.0.6+dfsg' tar --sort=name \ --mtime="@1714041519" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ -cJf /build/reproducible-path/subread-2.0.6+dfsg/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/ make[1]: Leaving directory '/build/reproducible-path/subread-2.0.6+dfsg' dh_installman -O--buildsystem=makefile install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/exactSNP.1 debian/subread/usr/share/man/man1/exactSNP.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/featureCounts.1 debian/subread/usr/share/man/man1/featureCounts.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/flattenGTF.1 debian/subread/usr/share/man/man1/flattenGTF.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/genRandomReads.1 debian/subread/usr/share/man/man1/genRandomReads.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/propmapped.1 debian/subread/usr/share/man/man1/propmapped.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/qualityScores.1 debian/subread/usr/share/man/man1/qualityScores.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/removeDup.1 debian/subread/usr/share/man/man1/removeDup.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/repair.1 debian/subread/usr/share/man/man1/repair.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/subindel.1 debian/subread/usr/share/man/man1/subindel.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/subjunc.1 debian/subread/usr/share/man/man1/subjunc.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/sublong.1 debian/subread/usr/share/man/man1/sublong.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/subread-align.1 debian/subread/usr/share/man/man1/subread-align.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/subread-buildindex.1 debian/subread/usr/share/man/man1/subread-buildindex.1 install -m0755 -d debian/subread/usr/share/man/man1/ install -p -m0644 ./debian/subread-fullscan.1 debian/subread/usr/share/man/man1/subread-fullscan.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/exactSNP.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/featureCounts.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/flattenGTF.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/genRandomReads.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/propmapped.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/qualityScores.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/removeDup.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/repair.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subindel.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subjunc.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/sublong.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-align.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 man-recode --to-code UTF-8 --suffix .dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 mv debian/subread/usr/share/man/man1/exactSNP.1.dh-new debian/subread/usr/share/man/man1/exactSNP.1 chmod 0644 -- debian/subread/usr/share/man/man1/exactSNP.1 mv debian/subread/usr/share/man/man1/featureCounts.1.dh-new debian/subread/usr/share/man/man1/featureCounts.1 chmod 0644 -- debian/subread/usr/share/man/man1/featureCounts.1 mv debian/subread/usr/share/man/man1/genRandomReads.1.dh-new debian/subread/usr/share/man/man1/genRandomReads.1 chmod 0644 -- debian/subread/usr/share/man/man1/genRandomReads.1 mv debian/subread/usr/share/man/man1/flattenGTF.1.dh-new debian/subread/usr/share/man/man1/flattenGTF.1 chmod 0644 -- debian/subread/usr/share/man/man1/flattenGTF.1 mv debian/subread/usr/share/man/man1/qualityScores.1.dh-new debian/subread/usr/share/man/man1/qualityScores.1 chmod 0644 -- debian/subread/usr/share/man/man1/qualityScores.1 mv debian/subread/usr/share/man/man1/removeDup.1.dh-new debian/subread/usr/share/man/man1/removeDup.1 chmod 0644 -- debian/subread/usr/share/man/man1/removeDup.1 mv debian/subread/usr/share/man/man1/propmapped.1.dh-new debian/subread/usr/share/man/man1/propmapped.1 chmod 0644 -- debian/subread/usr/share/man/man1/propmapped.1 mv debian/subread/usr/share/man/man1/repair.1.dh-new debian/subread/usr/share/man/man1/repair.1 chmod 0644 -- debian/subread/usr/share/man/man1/repair.1 mv debian/subread/usr/share/man/man1/subindel.1.dh-new debian/subread/usr/share/man/man1/subindel.1 chmod 0644 -- debian/subread/usr/share/man/man1/subindel.1 mv debian/subread/usr/share/man/man1/sublong.1.dh-new debian/subread/usr/share/man/man1/sublong.1 chmod 0644 -- debian/subread/usr/share/man/man1/sublong.1 mv debian/subread/usr/share/man/man1/subjunc.1.dh-new debian/subread/usr/share/man/man1/subjunc.1 chmod 0644 -- debian/subread/usr/share/man/man1/subjunc.1 mv debian/subread/usr/share/man/man1/subread-buildindex.1.dh-new debian/subread/usr/share/man/man1/subread-buildindex.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-buildindex.1 mv debian/subread/usr/share/man/man1/subread-align.1.dh-new debian/subread/usr/share/man/man1/subread-align.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-align.1 mv debian/subread/usr/share/man/man1/subread-fullscan.1.dh-new debian/subread/usr/share/man/man1/subread-fullscan.1 chmod 0644 -- debian/subread/usr/share/man/man1/subread-fullscan.1 dh_installsystemduser -O--buildsystem=makefile dh_perl -O--buildsystem=makefile dh_link -O--buildsystem=makefile dh_strip_nondeterminism -O--buildsystem=makefile Using 1714041519 as canonical time Normalizing debian/subread-data/usr/share/doc/subread/examples/annotation/mm39_RefSeq_exon.txt.gz using File::StripNondeterminism::handlers::gzip dh_compress -O--buildsystem=makefile cd debian/subread cd debian/subread-data chmod a-x usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 chmod a-x usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt gzip -9nf usr/share/doc/subread/changelog.Debian usr/share/man/man1/exactSNP.1 usr/share/man/man1/featureCounts.1 usr/share/man/man1/flattenGTF.1 usr/share/man/man1/genRandomReads.1 usr/share/man/man1/propmapped.1 usr/share/man/man1/qualityScores.1 usr/share/man/man1/removeDup.1 usr/share/man/man1/repair.1 usr/share/man/man1/subindel.1 usr/share/man/man1/subjunc.1 usr/share/man/man1/sublong.1 usr/share/man/man1/subread-align.1 usr/share/man/man1/subread-buildindex.1 usr/share/man/man1/subread-fullscan.1 gzip -9nf usr/share/doc/subread-data/changelog.Debian usr/share/doc/subread/examples/annotation/hg19_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/hg38_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm10_RefSeq_exon.txt usr/share/doc/subread/examples/annotation/mm9_RefSeq_exon.txt cd '/build/reproducible-path/subread-2.0.6+dfsg' cd '/build/reproducible-path/subread-2.0.6+dfsg' dh_fixperms -O--buildsystem=makefile find debian/subread ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/subread-data/usr/share/doc -type f -a -true -a ! -regex 'debian/subread-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread/usr/share/doc -type f -a -true -a ! -regex 'debian/subread/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/subread-data -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/subread/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/subread -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/subread/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian/subread/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w dh_missing -O--buildsystem=makefile dh_dwz -a -O--buildsystem=makefile install -m0755 -d debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu dwz -mdebian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug -- debian/subread/usr/bin/exactSNP debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/subjunc debian/subread/usr/bin/sublong debian/subread/usr/bin/subread-align debian/subread/usr/bin/subread-buildindex debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/repair debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/txUnique objcopy --compress-debug-sections debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug chmod 0644 -- debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu/subread.debug dh_strip -a -O--buildsystem=makefile install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-align debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/56c2b338ccd69e4227f70fc6144aad18a2c706.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/56c2b338ccd69e4227f70fc6144aad18a2c706.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-align objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f7/56c2b338ccd69e4227f70fc6144aad18a2c706.debug debian/subread/usr/bin/subread-align install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/featureCounts debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/66a0c855f65034b9c88c2604f64e2d8e24fc4e.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/66a0c855f65034b9c88c2604f64e2d8e24fc4e.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/featureCounts objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/4b/66a0c855f65034b9c88c2604f64e2d8e24fc4e.debug debian/subread/usr/bin/featureCounts install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/25 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subindel debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/25/4b4052f1e2ebcd9909b0ad8fb72d9fcfab759d.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/25/4b4052f1e2ebcd9909b0ad8fb72d9fcfab759d.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subindel objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/25/4b4052f1e2ebcd9909b0ad8fb72d9fcfab759d.debug debian/subread/usr/bin/subindel install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/sublong debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c/55ef4af20140aaf7fcb3560b08b4ad162fdd90.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c/55ef4af20140aaf7fcb3560b08b4ad162fdd90.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/sublong objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0c/55ef4af20140aaf7fcb3560b08b4ad162fdd90.debug debian/subread/usr/bin/sublong install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subjunc debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/d0cf3b544b5735c28db9cc7ad8e1bd5d748246.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/d0cf3b544b5735c28db9cc7ad8e1bd5d748246.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subjunc objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/0b/d0cf3b544b5735c28db9cc7ad8e1bd5d748246.debug debian/subread/usr/bin/subjunc install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/subread-buildindex debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/e2d3345f1d0afc84d44f1381918b1e6e5d9c34.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/e2d3345f1d0afc84d44f1381918b1e6e5d9c34.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/subread-buildindex objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/e2d3345f1d0afc84d44f1381918b1e6e5d9c34.debug debian/subread/usr/bin/subread-buildindex install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/bin/exactSNP debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d/476f0a481c5f537ae2e34f367ddc29edc84203.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d/476f0a481c5f537ae2e34f367ddc29edc84203.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/bin/exactSNP objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/2d/476f0a481c5f537ae2e34f367ddc29edc84203.debug debian/subread/usr/bin/exactSNP install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/genRandomReads debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/4fdc7167c4c9b6f1b051e85c3c12f38f1e855a.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/4fdc7167c4c9b6f1b051e85c3c12f38f1e855a.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/genRandomReads objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/6f/4fdc7167c4c9b6f1b051e85c3c12f38f1e855a.debug debian/subread/usr/lib/subread/genRandomReads install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/qualityScores debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc/86d036954c26bb2a4f5524a23d0b8a450432ff.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc/86d036954c26bb2a4f5524a23d0b8a450432ff.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/qualityScores objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bc/86d036954c26bb2a4f5524a23d0b8a450432ff.debug debian/subread/usr/lib/subread/qualityScores install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/txUnique debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf/8d32639f2d323f9de36c7e78821c915931e18c.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf/8d32639f2d323f9de36c7e78821c915931e18c.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/txUnique objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/bf/8d32639f2d323f9de36c7e78821c915931e18c.debug debian/subread/usr/lib/subread/txUnique install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/propmapped debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87/d4fe4204462f658b032c3b52322c1ed2b4343b.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87/d4fe4204462f658b032c3b52322c1ed2b4343b.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/propmapped objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/87/d4fe4204462f658b032c3b52322c1ed2b4343b.debug debian/subread/usr/lib/subread/propmapped install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/flattenGTF debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe/a9825a8fe565f69be8210e3f771792b4a6c616.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe/a9825a8fe565f69be8210e3f771792b4a6c616.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/flattenGTF objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/fe/a9825a8fe565f69be8210e3f771792b4a6c616.debug debian/subread/usr/lib/subread/flattenGTF install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/removeDup debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3/e6485c8d3af5cf50b4688a643c3fff3571a395.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3/e6485c8d3af5cf50b4688a643c3fff3571a395.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/removeDup objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/a3/e6485c8d3af5cf50b4688a643c3fff3571a395.debug debian/subread/usr/lib/subread/removeDup install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/subread-fullscan debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/35a71c76b73412c7a951bf2ad032f554bb838f.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/35a71c76b73412c7a951bf2ad032f554bb838f.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/subread-fullscan objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/f5/35a71c76b73412c7a951bf2ad032f554bb838f.debug debian/subread/usr/lib/subread/subread-fullscan install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14 objcopy --only-keep-debug --compress-debug-sections debian/subread/usr/lib/subread/repair debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14/8524a3f5d05379d4f5c899fd58b535d6fe7fa7.debug chmod 0644 -- debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14/8524a3f5d05379d4f5c899fd58b535d6fe7fa7.debug strip --remove-section=.comment --remove-section=.note debian/subread/usr/lib/subread/repair objcopy --add-gnu-debuglink debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.build-id/14/8524a3f5d05379d4f5c899fd58b535d6fe7fa7.debug debian/subread/usr/lib/subread/repair install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/subread/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/subread/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/subread/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/subread/usr/lib/debug install -m0755 -d debian/.debhelper/subread/dbgsym-root/usr/share/doc ln -s subread debian/.debhelper/subread/dbgsym-root/usr/share/doc/subread-dbgsym install -m0755 -d debian/.debhelper/subread dh_makeshlibs -a -O--buildsystem=makefile rm -f debian/subread/DEBIAN/shlibs dh_shlibdeps -a -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN dpkg-shlibdeps -Tdebian/subread.substvars debian/subread/usr/bin/subread-align debian/subread/usr/bin/featureCounts debian/subread/usr/bin/subindel debian/subread/usr/bin/sublong debian/subread/usr/bin/subjunc debian/subread/usr/bin/subread-buildindex debian/subread/usr/bin/exactSNP debian/subread/usr/lib/subread/genRandomReads debian/subread/usr/lib/subread/qualityScores debian/subread/usr/lib/subread/txUnique debian/subread/usr/lib/subread/propmapped debian/subread/usr/lib/subread/flattenGTF debian/subread/usr/lib/subread/removeDup debian/subread/usr/lib/subread/subread-fullscan debian/subread/usr/lib/subread/repair dh_installdeb -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN dh_gencontrol -O--buildsystem=makefile install -m0755 -d debian/subread-data/DEBIAN echo misc:Depends= >> debian/subread-data.substvars echo misc:Pre-Depends= >> debian/subread-data.substvars dpkg-gencontrol -psubread-data -ldebian/changelog -Tdebian/subread-data.substvars -cdebian/control -Pdebian/subread-data install -m0755 -d debian/subread/DEBIAN echo misc:Depends= >> debian/subread.substvars echo misc:Pre-Depends= >> debian/subread.substvars install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/.debhelper/subread/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=subread-dbgsym "-DDepends=subread (= \${binary:Version})" "-DDescription=debug symbols for subread" "-DBuild-Ids=0bd0cf3b544b5735c28db9cc7ad8e1bd5d748246 0c55ef4af20140aaf7fcb3560b08b4ad162fdd90 148524a3f5d05379d4f5c899fd58b535d6fe7fa7 254b4052f1e2ebcd9909b0ad8fb72d9fcfab759d 2d476f0a481c5f537ae2e34f367ddc29edc84203 4b66a0c855f65034b9c88c2604f64e2d8e24fc4e 6f4fdc7167c4c9b6f1b051e85c3c12f38f1e855a 87d4fe4204462f658b032c3b52322c1ed2b4343b a3e6485c8d3af5cf50b4688a643c3fff3571a395 bc86d036954c26bb2a4f5524a23d0b8a450432ff bf8d32639f2d323f9de36c7e78821c915931e18c f535a71c76b73412c7a951bf2ad032f554bb838f f5e2d3345f1d0afc84d44f1381918b1e6e5d9c34 f756c2b338ccd69e4227f70fc6144aad18a2c706 fea9825a8fe565f69be8210e3f771792b4a6c616" -DSection=debug -UMulti-Arch -UReplaces -UBreaks dpkg-gencontrol: warning: Depends field of package subread-data: substitution variable ${shlibs:Depends} used, but is not defined chmod 0644 -- debian/subread-data/DEBIAN/control chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/control dpkg-gencontrol -psubread -ldebian/changelog -Tdebian/subread.substvars -cdebian/control -Pdebian/subread chmod 0644 -- debian/subread/DEBIAN/control dh_md5sums -O--buildsystem=makefile install -m0755 -d debian/subread/DEBIAN install -m0755 -d debian/subread-data/DEBIAN cd debian/subread-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/subread >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread/DEBIAN/md5sums install -m0755 -d debian/.debhelper/subread/dbgsym-root/DEBIAN cd debian/.debhelper/subread/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/subread-data/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/subread/dbgsym-root/DEBIAN/md5sums dh_builddeb -O--buildsystem=makefile dpkg-deb --root-owner-group --build debian/subread .. dpkg-deb --root-owner-group --build debian/.debhelper/subread/dbgsym-root .. dpkg-deb --root-owner-group --build debian/subread-data .. dpkg-deb: building package 'subread' in '../subread_2.0.6+dfsg-3_amd64.deb'. dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_2.0.6+dfsg-3_amd64.deb'. dpkg-deb: building package 'subread-data' in '../subread-data_2.0.6+dfsg-3_all.deb'. dpkg-genbuildinfo --build=binary -O../subread_2.0.6+dfsg-3_amd64.buildinfo dpkg-genchanges --build=binary -O../subread_2.0.6+dfsg-3_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/4030515 and its subdirectories I: Current time: Tue Jun 17 08:28:13 -12 2025 I: pbuilder-time-stamp: 1750192093 Wed May 15 14:05:15 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Wed May 15 14:05:15 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Wed May 15 14:35:44 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Wed May 15 14:35:45 UTC 2024 I: subread_2.0.6+dfsg-3_amd64.changes: Format: 1.8 Date: Thu, 25 Apr 2024 13:38:39 +0300 Source: subread Binary: subread subread-data subread-dbgsym Architecture: all amd64 Version: 2.0.6+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: subread - toolkit for processing next-gen sequencing data subread-data - data files for subread package Closes: 1049300 1069030 Changes: subread (2.0.6+dfsg-3) unstable; urgency=medium . * Team upload. * d/control: simplify architecture specification by using the provisions from the architecture-properties package. * d/rules: preserve original mm39_RefSeq_exon.txt.gz to enable building twice. Closes: #1049300 * d/control: update description of subread-data to include the gene annotations for both the hh39 and mm39 genomes. * d/patches/arch_specific_flags.patch: since -D_FILE_OFFSET_BITS=64 is set, use fopen() even on 32-bit systems. Closes: #1069030 Thanks to blhc "E-pointer-trouble-at-implicit" for pointing this out. * d/patches/cross.patch: deleted, as it was unused and incorporated into arch_specific_flags.patch by Alexandre Mestiashvili. * d/upstream/metadata: add publications, bug info, changelog, link to user guide PDF. * d/test/control: python3 is needed Checksums-Sha1: bba1466c40027e6fc9052c3a98a6f69f1ed79902 19053272 subread-data_2.0.6+dfsg-3_all.deb a91cc1c4fe13235d5670758ee1878545630a3c09 11130980 subread-dbgsym_2.0.6+dfsg-3_amd64.deb ac170c171100221c7463fbd7210fa1f3ba4dff2b 6000 subread_2.0.6+dfsg-3_amd64.buildinfo 256fbb895be0eecf7c2ccfe3b59e91c7669cf4b4 829112 subread_2.0.6+dfsg-3_amd64.deb Checksums-Sha256: a1f5678f4dddbbbc0ed676e40409cc4ee47f1360a55b1617025d88982f1f30ab 19053272 subread-data_2.0.6+dfsg-3_all.deb 300451044a8018ec4b15797971a6fc9c449589431956db202272a4a3d6997fd9 11130980 subread-dbgsym_2.0.6+dfsg-3_amd64.deb e1474a16f72d9471027084723481dd5aed902bb7876ed1030d41a58ac66775a0 6000 subread_2.0.6+dfsg-3_amd64.buildinfo 5a359c2979292bee8424ab469743889e525dbc4ebe148de9f46c64801a240132 829112 subread_2.0.6+dfsg-3_amd64.deb Files: bc4d93656a9e8755bcecd0b8ba6da4df 19053272 science optional subread-data_2.0.6+dfsg-3_all.deb 7871336dcc33c66a28799471ebee5b45 11130980 debug optional subread-dbgsym_2.0.6+dfsg-3_amd64.deb e213e782aead6afb6dec596c18b4d741 6000 science optional subread_2.0.6+dfsg-3_amd64.buildinfo 0d593d8a7064947223d05b62c9b1bb20 829112 science optional subread_2.0.6+dfsg-3_amd64.deb Wed May 15 14:35:46 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_26-6667.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.lbv7B9T5/subread_2.0.6+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.lbv7B9T5/subread_2.0.6+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.lbv7B9T5/subread_2.0.6+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.lbv7B9T5/b1/subread_2.0.6+dfsg-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.lbv7B9T5/b2/subread_2.0.6+dfsg-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.676s) 0.676s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.333s) 0.333s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.008s CPU time consumed: 1.008s Wed May 15 14:35:47 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Wed May 15 14:35:47 UTC 2024 I: subread from trixie built successfully and reproducibly on amd64. Wed May 15 14:35:49 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 15 14:35:49 UTC 2024 I: Submitting 8.0K b1/subread_2.0.6+dfsg-3_amd64.buildinfo.asc Wed May 15 14:35:50 UTC 2024 I: Submitting 8.0K b2/subread_2.0.6+dfsg-3_amd64.buildinfo.asc Wed May 15 14:35:50 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 15 14:35:50 UTC 2024 I: Done submitting .buildinfo files. Wed May 15 14:35:50 UTC 2024 I: Removing signed subread_2.0.6+dfsg-3_amd64.buildinfo.asc files: removed './b1/subread_2.0.6+dfsg-3_amd64.buildinfo.asc' removed './b2/subread_2.0.6+dfsg-3_amd64.buildinfo.asc'