Sun Oct 26 17:14:59 UTC 2025 I: starting to build pizzly/forky/arm64 on jenkins on '2025-10-26 17:14' Sun Oct 26 17:14:59 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_10/101616/console.log Sun Oct 26 17:14:59 UTC 2025 I: Downloading source for forky/pizzly=0.37.3+ds-11 --2025-10-26 17:14:59-- http://deb.debian.org/debian/pool/main/p/pizzly/pizzly_0.37.3%2bds-11.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2029 (2.0K) [text/prs.lines.tag] Saving to: ‘pizzly_0.37.3+ds-11.dsc’ 0K . 100% 238M=0s 2025-10-26 17:14:59 (238 MB/s) - ‘pizzly_0.37.3+ds-11.dsc’ saved [2029/2029] Sun Oct 26 17:14:59 UTC 2025 I: pizzly_0.37.3+ds-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pizzly Binary: pizzly Architecture: any Version: 0.37.3+ds-11 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Homepage: https://github.com/pmelsted/pizzly Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/pizzly Vcs-Git: https://salsa.debian.org/med-team/pizzly.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libseqan2-dev, help2man, cmake, kallisto, zlib1g-dev Package-List: pizzly deb science optional arch=any Checksums-Sha1: 3c134c7e66314d7c3fdb99d6f9aaa4347d12e713 262304 pizzly_0.37.3+ds.orig.tar.xz 90693bbb33ae31d9bbd7f18f9ade4d1ad1c7fa20 5540 pizzly_0.37.3+ds-11.debian.tar.xz Checksums-Sha256: 8dd0dfb08a9341d4eeb525679779d3afb641b198c88df646ffc7e72930039678 262304 pizzly_0.37.3+ds.orig.tar.xz 0ac7e3da2c3445d6a3ddc7a358571bb4e6e484a18a1d9c1e2f15aaf0f5909b59 5540 pizzly_0.37.3+ds-11.debian.tar.xz Files: cba5c09c8f5493378b068821029df3a5 262304 pizzly_0.37.3+ds.orig.tar.xz bac3535ead6e5120eaa7999c92dc8bd4 5540 pizzly_0.37.3+ds-11.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmj2hEIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEh4w/+IpqsMWw5LsVb88DDnqCRWtE3MT/Dkkhs xgomWv07dbjCDgTVnGTPq/8WUAJfSGEEbIvVvD9hYsIaSrOSpsXf7Yr22AdtcEzg iyoqcgie9mpaeCxF5BY7RHTKemJXE6qftEzxOXAUw8FV1OG9tt6OyWtLdFn9tYRm 17nDL1Z6CFJNwPRvVLF2awovrv/Vf7SJfrYmjwerzFFGkQ1DcDfHvHQGSWMBADLc 3PCAgtUS/utjqMzKs20kJrfN5fMob6fqK2Oz5OJEbqxJVi/12sSZnSZP1bwf6p4M +htQl5jvi0GxuTYOTMO9hhroXhQeB895mkqiS/J7s5ohliIJX8+qwPXot+3+6o43 8GNRI6B5+xe62YmkZ/YYrek6e4wVn2IwSNAdKaSWWgCvJrcCeZzr+GoesQIlvmR2 uiJmdR9xJsRZYz9q1oPsM3TvwI3x5+O2Yx8mppjv07HioUs/Fw3a/gbWAtbd5eMC 8FYNK5QuHX2yVmRNLx59b+2QuX6xmXiTRbR5d9bmDE5uaNCcBaW+kq0muJFWWTou FPgw9MK/U/+Zx/Edisf2PgqJ5CXdQBMBN4LxUXLT8EXQCsRHVFQUCP2Wyp7NmrHs q9QExs71Rrn9NSOUyusXKSO5l1fb3kpFfvR5NFcnolmbC8KUHG1gS1UFQiFiUFz6 mD6fAGDqouk= =e2L6 -----END PGP SIGNATURE----- Sun Oct 26 17:14:59 UTC 2025 I: Checking whether the package is not for us Sun Oct 26 17:14:59 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sun Oct 26 17:14:59 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sun Oct 26 17:16:20 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Oct 26 05:15:00 -12 2025 I: pbuilder-time-stamp: 1761498900 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 [pizzly_0.37.3+ds-11.dsc] I: copying [./pizzly_0.37.3+ds.orig.tar.xz] I: copying [./pizzly_0.37.3+ds-11.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./pizzly_0.37.3+ds-11.dsc: no acceptable signature found dpkg-source: info: extracting pizzly in pizzly-0.37.3+ds dpkg-source: info: unpacking pizzly_0.37.3+ds.orig.tar.xz dpkg-source: info: unpacking pizzly_0.37.3+ds-11.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying executable-not-elf-or-script.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/195030/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='f54edda08b8c44d29b2250857d8587f8' 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='195030' 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.3iO0LdxZ/pbuilderrc_Q0OK --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.3iO0LdxZ/b1 --logfile b1/build.log pizzly_0.37.3+ds-11.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/195030/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), libseqan2-dev, help2man, cmake, kallisto, 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 ... 20002 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libseqan2-dev; however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on kallisto; however: Package kallisto 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} kallisto{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libngtcp2-crypto-ossl0{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 32.7 MB of archives. After unpacking 131 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 liblocale-gettext-perl arm64 1.07-7+b1 [15.2 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libproc2-0 arm64 2:4.0.4-9 [62.8 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 procps arm64 2:4.0.4-9 [871 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-1 [94.3 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 libarchive13t64 arm64 3.7.4-4+b1 [323 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 30 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-ossl0 arm64 1.16.0-1 [25.7 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 42 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.10-2 [1395 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 libcurl4t64 arm64 8.16.0-4 [368 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 libjsoncpp26 arm64 1.9.6-4 [73.2 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 librhash1 arm64 1.4.6-1 [131 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 libuv1t64 arm64 1.51.0-2 [150 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 cmake arm64 4.1.1+really3.31.6-2 [10.1 MB] Get: 51 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 57 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 help2man arm64 1.49.3+b1 [198 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get: 65 http://deb.debian.org/debian forky/main arm64 libcurl3t64-gnutls arm64 8.16.0-4 [362 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 kallisto arm64 0.48.0+dfsg-4+b2 [256 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libseqan2-dev all 2.4.0+dfsg-16 [1216 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Fetched 32.7 MB in 0s (137 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:arm64. (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 ... 20002 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-7+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../02-libproc2-0_2%3a4.0.4-9_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../03-procps_2%3a4.0.4-9_arm64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../04-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../05-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../06-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../07-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../08-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../09-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../10-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../11-bsdextrautils_2.41.2-1_arm64.deb ... Unpacking bsdextrautils (2.41.2-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../12-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../13-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../14-m4_1.4.20-2_arm64.deb ... 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Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/pizzly-0.37.3+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pizzly_0.37.3+ds-11_source.changes dpkg-buildpackage: info: source package pizzly dpkg-buildpackage: info: source version 0.37.3+ds-11 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/pizzly-0.37.3+ds' dh_auto_clean rm -f debian/pizzly.1 make[1]: Leaving directory '/build/reproducible-path/pizzly-0.37.3+ds' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/pizzly.substvars debian/files rm -fr -- debian/pizzly/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/pizzly-0.37.3+ds' dh_auto_configure -- -DCMAKE_POLICY_VERSION_MINIMUM=3.5 cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DCMAKE_POLICY_VERSION_MINIMUM=3.5 .. CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The CXX compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Configuring done (0.5s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR CMAKE_POLICY_VERSION_MINIMUM FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/pizzly-0.37.3+ds' dh_auto_build cd obj-aarch64-linux-gnu && make -j12 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/pizzly-0.37.3+ds -B/build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/pizzly.dir/build.make CMakeFiles/pizzly.dir/depend make[3]: Entering directory '/build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu' cd /build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/pizzly-0.37.3+ds /build/reproducible-path/pizzly-0.37.3+ds /build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu /build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu /build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu/CMakeFiles/pizzly.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu' make -f CMakeFiles/pizzly.dir/build.make CMakeFiles/pizzly.dir/build make[3]: Entering directory '/build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu' [ 50%] Building CXX object CMakeFiles/pizzly.dir/main.cpp.o /usr/bin/c++ -I/build/reproducible-path/pizzly-0.37.3+ds/. -g -O2 -ffile-prefix-map=/build/reproducible-path/pizzly-0.37.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -DSEQAN_HAS_ZLIB=1 -MD -MT CMakeFiles/pizzly.dir/main.cpp.o -MF CMakeFiles/pizzly.dir/main.cpp.o.d -o CMakeFiles/pizzly.dir/main.cpp.o -c /build/reproducible-path/pizzly-0.37.3+ds/main.cpp In file included from /build/reproducible-path/pizzly-0.37.3+ds/main.cpp:6: /build/reproducible-path/pizzly-0.37.3+ds/common.h: In constructor 'ProgramOptions::ProgramOptions()': /build/reproducible-path/pizzly-0.37.3+ds/common.h:18:7: warning: 'ProgramOptions::kmerScore' will be initialized after [-Wreorder] 18 | int kmerScore; | ^~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/common.h:17:7: warning: 'int ProgramOptions::insertSize' [-Wreorder] 17 | int insertSize; | ^~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/common.h:19:3: warning: when initialized here [-Wreorder] 19 | ProgramOptions() : kmerScore(2), insertSize(400), ignoreProtein(false) {} | ^~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/common.h:17:7: warning: 'ProgramOptions::insertSize' will be initialized after [-Wreorder] 17 | int insertSize; | ^~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/common.h:14:8: warning: 'bool ProgramOptions::ignoreProtein' [-Wreorder] 14 | bool ignoreProtein; | ^~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/common.h:19:3: warning: when initialized here [-Wreorder] 19 | ProgramOptions() : kmerScore(2), insertSize(400), ignoreProtein(false) {} | ^~~~~~~~~~~~~~ In file included from /build/reproducible-path/pizzly-0.37.3+ds/main.cpp:8: /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp: In member function 'bool Transcriptome::translateTrPosition(const std::string&, int, std::string&, int&, std::string&)': /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp:117:10: warning: unused variable 'fw' [-Wunused-variable] 117 | bool fw = (trxmodel.strand == Strandedness::FORWARD); | ^~ /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp: In function 'void writeTranscriptome(Transcriptome&, std::ostream&)': /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp:146:17: warning: unused variable 'gene_id' [-Wunused-variable] 146 | const auto &gene_id = gene.first; | ^~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp:172:19: warning: unused variable 'tr_id' [-Wunused-variable] 172 | const auto &tr_id = trlist.first; | ^~~~~ /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp: In function 'void parseGTF(Transcriptome&, const std::string&, const ProgramOptions&)': /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp:282:25: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] 282 | for (int i = 0; i < length(record.tagNames); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp:329:25: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] 329 | for (int i = 0; i < length(record.tagNames); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp:392:25: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] 392 | for (int i = 0; i < length(record.tagNames); i++) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/pizzly-0.37.3+ds/main.cpp:9: /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp: In lambda function: /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:205:27: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 205 | return std::move(m); | ~~~~~~~~~^~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:205:27: note: remove 'std::move' call /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:214:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 214 | return std::move(m); | ~~~~~~~~~^~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:214:21: note: remove 'std::move' call /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp: In lambda function: /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:251:9: warning: unused variable 'matchlen' [-Wunused-variable] 251 | int matchlen = seqan::length(krseq); | ^~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp: In lambda function: /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:311:19: warning: comparison of integer expressions of different signedness: 'int' and 'seqan::Size > >::Type' {aka 'long unsigned int'} [-Wsign-compare] 311 | if (tr_stop > seqan::length(trseq)) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:323:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 323 | return std::move(tlist); | ~~~~~~~~~^~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:323:21: note: remove 'std::move' call /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp: In lambda function: /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:709:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 709 | for (int i = 0; i < trm.exons.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp: In lambda function: /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:738:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 738 | for (int i = 0; i < trm.exons.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp: In lambda function: /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:765:11: warning: unused variable 'gap' [-Wunused-variable] 765 | int gap = d2 - d1; | ^~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:781:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move] 781 | return std::move(ret); | ~~~~~~~~~^~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:781:21: note: remove 'std::move' call /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp: In lambda function: /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:883:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 883 | for (int i = 0; i < v.size(); i++) { | ~~^~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:929:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 929 | for (int i = 0; i < readsInTr.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:867:17: warning: unused variable 'split_reads' [-Wunused-variable] 867 | int split_reads = spp.second; | ^~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:1033:29: warning: loop variable 'p' creates a copy from type 'const std::pair > >' [-Wrange-loop-construct] 1033 | for (const auto p : trfmap) { | ^ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:1033:29: note: use reference type to prevent copying 1033 | for (const auto p : trfmap) { | ^ | & /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:1091:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1091 | for (int i = 0; i < readsInTr.size(); i++) { | ~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:1115:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] 1115 | for (int i = 0; i < v.size(); i++) { | ~~^~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:1112:18: warning: unused variable 'firstJsonRead' [-Wunused-variable] 1112 | bool firstJsonRead = true; | ^~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/main.cpp: In function 'int main(int, const char**)': /build/reproducible-path/pizzly-0.37.3+ds/main.cpp:126:31: warning: comparison of integer expressions of different signedness: 'int' and 'std::unordered_map, seqan::String > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] 126 | } else if (numTxpSeqFound != trx.seqs.size()) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp: In function 'Strandedness operator~(const Strandedness&)': /build/reproducible-path/pizzly-0.37.3+ds/GeneModel.hpp:18:1: warning: control reaches end of non-void function [-Wreturn-type] 18 | } | ^ In file included from /usr/include/seqan/stream.h:119, from /usr/include/seqan/arg_parse.h:46, from /build/reproducible-path/pizzly-0.37.3+ds/main.cpp:2: In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = int; TSource = std::__cxx11::basic_string]', inlined from 'seqan::String seqan::_getNumbersFromString(const std::string&)' at /usr/include/seqan/arg_parse/arg_parse_version_check.h:356:46: /usr/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/seqan/stream/lexical_cast.h: In function 'seqan::String seqan::_getNumbersFromString(const std::string&)': /usr/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = int; TSource = std::__cxx11::basic_string]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /usr/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(GffRecord&, CharString&, TFwdIterator&) [with TFwdIterator = Iter >, StreamIterator > >]' at /usr/include/seqan/gff_io/gff_io_base.h:379:44: /usr/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(GffRecord&, CharString&, TFwdIterator&) [with TFwdIterator = Iter >, StreamIterator > >]': /usr/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /usr/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ In function 'TTarget seqan::lexicalCast(const TSource&) [with TTarget = unsigned int; TSource = String >]', inlined from 'void seqan::readRecord(GffRecord&, CharString&, TFwdIterator&) [with TFwdIterator = Iter >, StreamIterator > >]' at /usr/include/seqan/gff_io/gff_io_base.h:386:42: /usr/include/seqan/stream/lexical_cast.h:255:9: warning: 'target' may be used uninitialized [-Wmaybe-uninitialized] 255 | throw BadLexicalCast(target, source); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/seqan/stream/lexical_cast.h: In function 'void seqan::readRecord(GffRecord&, CharString&, TFwdIterator&) [with TFwdIterator = Iter >, StreamIterator > >]': /usr/include/seqan/stream/lexical_cast.h:72:5: note: by argument 2 of type 'const unsigned int&' to 'seqan::BadLexicalCast::BadLexicalCast(const TTarget&, const TSource&) [with TTarget = unsigned int; TSource = seqan::String >]' declared here 72 | BadLexicalCast(TTarget const & target, TSource const & source) : | ^~~~~~~~~~~~~~ /usr/include/seqan/stream/lexical_cast.h:253:13: note: 'target' declared here 253 | TTarget target; | ^~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp: In lambda function: /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:435:15: warning: 'splitStrand' may be used uninitialized [-Wmaybe-uninitialized] 435 | if (forwardRead) { | ^~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:389:22: note: 'splitStrand' was declared here 389 | Strandedness splitStrand, safeStrand; | ^~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp: In function 'bool filterFusionRecord(const Transcriptome&, ProgramOptions&, const FusionRecord&, SplitRecord&)': /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:602:25: warning: 'st1' may be used uninitialized [-Wmaybe-uninitialized] 602 | splitrec.dir1 = st1 == Strandedness::FORWARD; // check read 1 | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:554:18: note: 'st1' was declared here 554 | Strandedness st1,st2; | ^~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:603:25: warning: 'st2' may be used uninitialized [-Wmaybe-uninitialized] 603 | splitrec.dir2 = st2 == Strandedness::FORWARD; // check read 2 | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/pizzly-0.37.3+ds/FilterFusions.hpp:554:22: note: 'st2' was declared here 554 | Strandedness st1,st2; | ^~~ [100%] Linking CXX executable pizzly /usr/bin/cmake -E cmake_link_script CMakeFiles/pizzly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/pizzly-0.37.3+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++14 -DSEQAN_HAS_ZLIB=1 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/pizzly.dir/link.d CMakeFiles/pizzly.dir/main.cpp.o -o pizzly -lpthread -lz make[3]: Leaving directory '/build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu' [100%] Built target pizzly make[2]: Leaving directory '/build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/pizzly-0.37.3+ds/obj-aarch64-linux-gnu' dh_auto_test rm -fr -- /tmp/dh-xdg-rundir-Q6uuqq1S create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/pizzly.substvars rm -fr -- debian/.debhelper/generated/pizzly/ debian/pizzly/ debian/tmp/ dh_auto_install --destdir=debian/pizzly/ install -m0755 -d /build/reproducible-path/pizzly-0.37.3\+ds/debian/pizzly rm -f debian/pizzly.debhelper.log debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/pizzly-0.37.3+ds' help2man -N -n pizzly -s 1 obj-*/pizzly > debian/pizzly.1 dh_install install -m0755 -d debian/pizzly/usr/bin cp --reflink=auto -a ./obj-aarch64-linux-gnu/pizzly ./scripts/flatten_json.py ./scripts/get_fragment_length.py debian/pizzly/usr/bin/ make[1]: Leaving directory '/build/reproducible-path/pizzly-0.37.3+ds' dh_installdocs install -m0755 -d debian/pizzly/usr/share/doc/pizzly install -m0755 -d debian/pizzly/usr/share/doc/pizzly cp --reflink=auto -a ./README.md debian/pizzly/usr/share/doc/pizzly cp --reflink=auto -a ./debian/README.Debian debian/pizzly/usr/share/doc/pizzly chmod -R u\+rw,go=rX debian/pizzly/usr/share/doc install -p -m0644 debian/README.Debian debian/pizzly/usr/share/doc/pizzly/README.Debian install -p -m0644 debian/copyright debian/pizzly/usr/share/doc/pizzly/copyright dh_installchangelogs install -m0755 -d debian/pizzly/usr/share/doc/pizzly install -p -m0644 debian/.debhelper/generated/pizzly/dh_installchangelogs.dch.trimmed debian/pizzly/usr/share/doc/pizzly/changelog.Debian dh_installman install -m0755 -d debian/pizzly/usr/share/man/man1/ install -p -m0644 ./debian/pizzly.1 debian/pizzly/usr/share/man/man1/pizzly.1 man-recode --to-code UTF-8 --suffix .dh-new debian/pizzly/usr/share/man/man1/pizzly.1 mv debian/pizzly/usr/share/man/man1/pizzly.1.dh-new debian/pizzly/usr/share/man/man1/pizzly.1 chmod 0644 -- debian/pizzly/usr/share/man/man1/pizzly.1 dh_lintian install -m0755 -d debian/pizzly/usr/share/lintian/overrides install -p -m0644 debian/lintian-overrides debian/pizzly/usr/share/lintian/overrides/pizzly dh_perl dh_link install -m0755 -d debian/pizzly/usr/bin rm -f debian/pizzly/usr/bin/pizzly_flatten_json.py ln -s flatten_json.py debian/pizzly/usr/bin/pizzly_flatten_json.py dh_strip_nondeterminism dh_compress cd debian/pizzly chmod a-x usr/share/doc/pizzly/changelog.Debian usr/share/man/man1/pizzly.1 gzip -9nf usr/share/doc/pizzly/changelog.Debian usr/share/man/man1/pizzly.1 cd '/build/reproducible-path/pizzly-0.37.3+ds' dh_fixperms find debian/pizzly ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/pizzly/usr/share/doc -type f -a -true -a ! -regex 'debian/pizzly/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pizzly/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/pizzly/usr/share/man debian/pizzly/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/pizzly -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/pizzly/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_dwz -a dwz -- debian/pizzly/usr/bin/pizzly dh_strip -a install -m0755 -d debian/.debhelper/pizzly/dbgsym-root/usr/lib/debug/.build-id/08 objcopy --only-keep-debug --compress-debug-sections debian/pizzly/usr/bin/pizzly debian/.debhelper/pizzly/dbgsym-root/usr/lib/debug/.build-id/08/e94361d232cef1358000a651857af406ee189f.debug chmod 0644 -- debian/.debhelper/pizzly/dbgsym-root/usr/lib/debug/.build-id/08/e94361d232cef1358000a651857af406ee189f.debug strip --remove-section=.comment --remove-section=.note debian/pizzly/usr/bin/pizzly objcopy --add-gnu-debuglink debian/.debhelper/pizzly/dbgsym-root/usr/lib/debug/.build-id/08/e94361d232cef1358000a651857af406ee189f.debug debian/pizzly/usr/bin/pizzly install -m0755 -d debian/.debhelper/pizzly/dbgsym-root/usr/share/doc ln -s pizzly debian/.debhelper/pizzly/dbgsym-root/usr/share/doc/pizzly-dbgsym install -m0755 -d debian/.debhelper/pizzly dh_makeshlibs -a rm -f debian/pizzly/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/pizzly/DEBIAN dpkg-shlibdeps -Tdebian/pizzly.substvars debian/pizzly/usr/bin/pizzly dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb install -m0755 -d debian/pizzly/DEBIAN dh_gencontrol install -m0755 -d debian/pizzly/DEBIAN echo misc:Depends= >> debian/pizzly.substvars echo misc:Pre-Depends= >> debian/pizzly.substvars install -m0755 -d debian/.debhelper/pizzly/dbgsym-root/DEBIAN dpkg-gencontrol -ppizzly -ldebian/changelog -Tdebian/pizzly.substvars -cdebian/control -Pdebian/.debhelper/pizzly/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=pizzly-dbgsym -DDepends="pizzly (= \${binary:Version})" -DDescription="debug symbols for pizzly" -DBuild-Ids=08e94361d232cef1358000a651857af406ee189f -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/pizzly/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppizzly -ldebian/changelog -Tdebian/pizzly.substvars -cdebian/control -Pdebian/pizzly chmod 0644 -- debian/pizzly/DEBIAN/control dh_md5sums install -m0755 -d debian/pizzly/DEBIAN cd debian/pizzly >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/pizzly/DEBIAN/md5sums install -m0755 -d debian/.debhelper/pizzly/dbgsym-root/DEBIAN cd debian/.debhelper/pizzly/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/pizzly/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/pizzly .. dpkg-deb --root-owner-group --build debian/.debhelper/pizzly/dbgsym-root .. dpkg-deb: building package 'pizzly' in '../pizzly_0.37.3+ds-11_arm64.deb'. dpkg-deb: building package 'pizzly-dbgsym' in '../pizzly-dbgsym_0.37.3+ds-11_arm64.deb'. dpkg-genbuildinfo --build=binary -O../pizzly_0.37.3+ds-11_arm64.buildinfo dpkg-genchanges --build=binary -O../pizzly_0.37.3+ds-11_arm64.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/195030 and its subdirectories I: Current time: Sun Oct 26 05:16:20 -12 2025 I: pbuilder-time-stamp: 1761498980 Sun Oct 26 17:16:21 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sun Oct 26 17:16:21 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sun Oct 26 17:19:33 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sun Oct 26 17:19:34 UTC 2025 I: pizzly_0.37.3+ds-11_arm64.changes: Format: 1.8 Date: Sun, 19 Oct 2025 22:20:37 +0200 Source: pizzly Binary: pizzly pizzly-dbgsym Architecture: arm64 Version: 0.37.3+ds-11 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: pizzly - Identifies gene fusions in RNA sequencing data Closes: 1113407 Changes: pizzly (0.37.3+ds-11) unstable; urgency=medium . * Team upload. * Fix build with CMake 4 Closes: #1113407 * d/watch: version=5 * Standards-Version: 4.7.2 (routine-update) * debputy lint --auto-fix (routine-update) * Update lintian-override Checksums-Sha1: 8a8ebbc8ecdb84ca23f762956f8c54b35e1a793f 3751440 pizzly-dbgsym_0.37.3+ds-11_arm64.deb d26e3093dc0ef1d51a1951954022ccb9293dcef2 6240 pizzly_0.37.3+ds-11_arm64.buildinfo 49a9c88c7fb0840f42c9e00c4a8af756b14b953d 265284 pizzly_0.37.3+ds-11_arm64.deb Checksums-Sha256: a1554e6c3fd5dfae0f639a92e8d6df18cf50710ce7f71afbf2259f4ad797420f 3751440 pizzly-dbgsym_0.37.3+ds-11_arm64.deb 7cf9da6c47dca7524eded485be8f2533908a527344812e4e36bec2937b805e40 6240 pizzly_0.37.3+ds-11_arm64.buildinfo b6c79089c4170ad9b9ddcbeb32ec591b809b04a09c045ce029f79a901bfd15c1 265284 pizzly_0.37.3+ds-11_arm64.deb Files: 16489d4e3da0e97e7f9b7fee733a7b36 3751440 debug optional pizzly-dbgsym_0.37.3+ds-11_arm64.deb f91519d9fb3e9fbe11bca577f854fd38 6240 science optional pizzly_0.37.3+ds-11_arm64.buildinfo 1a8f7cec5dcd78bfa8375effa83ca9fa 265284 science optional pizzly_0.37.3+ds-11_arm64.deb Sun Oct 26 17:19:34 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_10-101616.service; invocation ID: 23094b94c6f943fd82f9c1dd1f6da865 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.3iO0LdxZ/pizzly_0.37.3+ds-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.3iO0LdxZ/pizzly_0.37.3+ds-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.3iO0LdxZ/pizzly_0.37.3+ds-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.3iO0LdxZ/b1/pizzly_0.37.3+ds-11_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.3iO0LdxZ/b2/pizzly_0.37.3+ds-11_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 195ms CPU time consumed: 168ms Memory peak: 17.7M (swap: 0B) Sun Oct 26 17:19:35 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Sun Oct 26 17:19:35 UTC 2025 I: pizzly from forky built successfully and reproducibly on arm64. Sun Oct 26 17:19:36 UTC 2025 I: Removing signed pizzly_0.37.3+ds-11_arm64.buildinfo.asc files: removed './b1/pizzly_0.37.3+ds-11_arm64.buildinfo.asc' removed './b2/pizzly_0.37.3+ds-11_arm64.buildinfo.asc'