Running as unit: rb-build-arm64_7-102558.service; invocation ID: cb47d842b8b549b0ad23b89f84ae9736 ==================================================================================== Fri Oct 31 05:12:13 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_7) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Fri Oct 31 05:12:13 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-samXAxor" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 05:12:13 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Oct 31 05:12:13 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-HZLAWD' Fri Oct 31 05:12:14 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Oct 31 05:12:14 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-tt9SV7' ok, let's check if lumpy-sv is building anywhere yet… ok, lumpy-sv is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of lumpy-sv in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Fri Oct 31 05:12:35 UTC 2025 I: starting to build lumpy-sv/unstable/arm64 on jenkins on '2025-10-31 05:12' Fri Oct 31 05:12:35 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/102558/console.log 1761887555 arm64 unstable lumpy-sv Fri Oct 31 05:12:35 UTC 2025 I: Downloading source for unstable/lumpy-sv=0.3.1+dfsg-8 --2025-10-31 05:12:35-- http://deb.debian.org/debian/pool/main/l/lumpy-sv/lumpy-sv_0.3.1%2bdfsg-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1594 (1.6K) [text/prs.lines.tag] Saving to: ‘lumpy-sv_0.3.1+dfsg-8.dsc’ 0K . 100% 207M=0s 2025-10-31 05:12:35 (207 MB/s) - ‘lumpy-sv_0.3.1+dfsg-8.dsc’ saved [1594/1594] --2025-10-31 05:12:35-- http://deb.debian.org/debian/pool/main/l/lumpy-sv/lumpy-sv_0.3.1%2bdfsg-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1594 (1.6K) [text/prs.lines.tag] Saving to: ‘lumpy-sv_0.3.1+dfsg-8.dsc’ 0K . 100% 207M=0s 2025-10-31 05:12:35 (207 MB/s) - ‘lumpy-sv_0.3.1+dfsg-8.dsc’ saved [1594/1594] Fri Oct 31 05:12:35 UTC 2025 I: lumpy-sv_0.3.1+dfsg-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: lumpy-sv Binary: lumpy-sv, lumpy-sv-examples Architecture: any all Version: 0.3.1+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/arq5x/lumpy-sv Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/lumpy-sv Vcs-Git: https://salsa.debian.org/med-team/lumpy-sv.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools Package-List: lumpy-sv deb science optional arch=any lumpy-sv-examples deb science optional arch=all Checksums-Sha1: b75a3ba46fb5197a96d8d5dccda356384c06bb77 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 4237faac649ff49f71fa9edac73689768ab3ad27 39265332 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz Checksums-Sha256: 78a6fe414739286d1f799bbdf3e34b9a1d6ed03b4c6dd17bfef1fcbba84bd35a 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 10a8ee20f04d1255322f09643940238685468d0f10e21cae7a046e834f2a4798 39265332 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz Files: 1167e4a94bceb29ac5b83cb170058e25 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz 5876c8eaebf4fc93883197da876153eb 39265332 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iIgEARYKADAWIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCaQPDMhIcbmlsZXNoQGRl Ymlhbi5vcmcACgkQKieQS9ckPtoUuAD/R0KPMsqdm9N4D9xaejuZx0ftADWl/KSm h/Ipw0wNjCkBAPOw9jQFwsfYCoKyq8D7whdRGE0xqfKdzh/aoNg90NMB =tEHJ -----END PGP SIGNATURE----- Fri Oct 31 05:12:35 UTC 2025 I: Checking whether the package is not for us Fri Oct 31 05:12:35 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Fri Oct 31 05:12:35 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Fri Oct 31 05:12:35 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Fri Oct 31 05:12:35 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-i5fZbL' ==================================================================================== Fri Oct 31 05:12:36 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 lumpy-sv unstable /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx 0.3.1+dfsg-8" as arguments. Fri Oct 31 05:12:36 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-xuAzWn7M" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 05:12:36 UTC 2025 I: Downloading source for unstable/lumpy-sv=0.3.1+dfsg-8 Reading package lists... NOTICE: 'lumpy-sv' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lumpy-sv.git Please use: git clone https://salsa.debian.org/med-team/lumpy-sv.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 39.4 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (dsc) [1594 B] Get:2 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (tar) [112 kB] Get:3 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (diff) [39.3 MB] Fetched 39.4 MB in 1s (42.3 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'lumpy-sv' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lumpy-sv.git Please use: git clone https://salsa.debian.org/med-team/lumpy-sv.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 39.4 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (dsc) [1594 B] Get:2 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (tar) [112 kB] Get:3 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (diff) [39.3 MB] Fetched 39.4 MB in 1s (42.3 MB/s) Download complete and in download only mode ============================================================================= Building lumpy-sv in unstable on arm64 on codethink04-arm64 now. Date: Fri Oct 31 05:12:37 GMT 2025 Date UTC: Fri Oct 31 05:12:37 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 30 17:12:37 -12 2025 I: pbuilder-time-stamp: 1761887557 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [lumpy-sv_0.3.1+dfsg-8.dsc] I: copying [./lumpy-sv_0.3.1+dfsg.orig.tar.xz] I: copying [./lumpy-sv_0.3.1+dfsg-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./lumpy-sv_0.3.1+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting lumpy-sv in lumpy-sv-0.3.1+dfsg dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying lumpyexpress.config.patch dpkg-source: info: applying fix_shebang.patch dpkg-source: info: applying do-not-override-dpkg-flags.patch dpkg-source: info: applying cleanup-bin.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3082459/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='e07ec7d0558a481ba4382837f8de28c3' 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='3082459' 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.MOdMJZyx/pbuilderrc_0AXc --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b1 --logfile b1/build.log lumpy-sv_0.3.1+dfsg-8.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/3082459/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), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 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 libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libfastahack-dev; however: Package libfastahack-dev is not installed. pbuilder-satisfydepends-dummy depends on libgzstream-dev; however: Package libgzstream-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libfastahack-dev{a} libfastahack0{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 102 newly installed, 0 to remove and 0 not upgraded. Need to get 33.1 MB of archives. After unpacking 123 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-3+b3 [56.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 24 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 35 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-5 [57.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-5 [41.1 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-5 [41.3 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-5 [53.0 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-5 [126 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libbamtools2.5.3 arm64 2.5.3+dfsg-1 [138 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libbamtools-dev arm64 2.5.3+dfsg-1 [207 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.17.0~rc3-1 [362 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.24.1-2 [560 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.10-3 [456 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.10-3 [455 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.8-4 [102 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.9-2 [220 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-5 [329 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-5 [621 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10.2-1 [1319 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.10-3 [1414 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-5 [16.1 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.10+dfsg-1 [305 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1.1+b1 [112 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.12.0-1 [91.6 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.16.0-1 [24.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.16.0-1 [183 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-3 [173 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.5.4-1 [3377 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.7+dfsg-2 [330 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.17.0~rc3-1 [498 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.23-2 [51.3 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libfastahack0 arm64 1.0.0+dfsg-11+b2 [23.6 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libfastahack-dev arm64 1.0.0+dfsg-11+b2 [26.1 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgzstream0 arm64 1.5+git20171107.9a20658-3 [7128 B] Get: 95 http://deb.debian.org/debian unstable/main arm64 libgzstream-dev arm64 1.5+git20171107.9a20658-3 [7452 B] Get: 96 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.8.1-2 [344 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.22.1+ds2-1 [1684 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libsqlite3-dev arm64 3.46.1-8 [1098 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.22.1-1 [666 kB] Fetched 33.1 MB in 0s (101 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19964 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. 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Preparing to unpack .../008-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../009-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../010-m4_1.4.20-2_arm64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../011-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../012-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../013-automake_1%3a1.18.1-2_all.deb ... Unpacking automake (1:1.18.1-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../014-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../015-libcom-err2_1.47.2-3+b3_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-3+b3) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../016-comerr-dev_2.1-1.47.2-3+b3_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.2-3+b3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../017-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../018-libtool_2.5.4-7_all.deb ... Unpacking libtool (2.5.4-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../019-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../020-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../021-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../022-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../023-libelf1t64_0.194-1_arm64.deb ... Unpacking libelf1t64:arm64 (0.194-1) ... Selecting previously unselected package dwz. Preparing to unpack .../024-dwz_0.16-2_arm64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../025-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../026-libxml2-16_2.15.1+dfsg-0.3_arm64.deb ... Unpacking libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Selecting previously unselected package gettext. Preparing to unpack .../027-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../028-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../029-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../030-debhelper_13.28_all.deb ... Unpacking debhelper (13.28) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../031-libkrb5support0_1.21.3-5_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../032-libk5crypto3_1.21.3-5_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../033-libkeyutils1_1.6.3-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../034-libkrb5-3_1.21.3-5_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../035-libgssapi-krb5-2_1.21.3-5_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-5) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../036-libgssrpc4t64_1.21.3-5_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-5) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../037-libkadm5clnt-mit12_1.21.3-5_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-5) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../038-libkdb5-10t64_1.21.3-5_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-5) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../039-libkadm5srv-mit12_1.21.3-5_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-5) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../040-krb5-multidev_1.21.3-5_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-5) ... Selecting previously unselected package libbamtools2.5.3:arm64. Preparing to unpack .../041-libbamtools2.5.3_2.5.3+dfsg-1_arm64.deb ... Unpacking libbamtools2.5.3:arm64 (2.5.3+dfsg-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../042-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libbamtools-dev:arm64. Preparing to unpack .../043-libbamtools-dev_2.5.3+dfsg-1_arm64.deb ... Unpacking libbamtools-dev:arm64 (2.5.3+dfsg-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../044-libbrotli1_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../045-libbrotli-dev_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../046-libbz2-dev_1.0.8-6_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-6) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../047-libnghttp3-9_1.12.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.12.0-1) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../048-libngtcp2-16_1.16.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.16.0-1) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../049-libidn2-0_2.3.8-4_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-4) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../050-libffi8_3.5.2-2_arm64.deb ... Unpacking libffi8:arm64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../051-libp11-kit0_0.25.9-2_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.9-2) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../052-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../053-libgnutls30t64_3.8.10-3_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.10-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../054-libsasl2-modules-db_2.1.28+dfsg1-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../055-libsasl2-2_2.1.28+dfsg1-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../056-libldap2_2.6.10+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../057-libnghttp2-14_1.64.0-1.1+b1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../058-libngtcp2-crypto-gnutls8_1.16.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../059-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../060-librtmp1_2.4+20151223.gitfa8646d.1-3_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../061-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../062-libcurl3t64-gnutls_8.17.0~rc3-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.17.0~rc3-1) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../063-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:arm64. Preparing to unpack .../064-libunbound8_1.24.1-2_arm64.deb ... Unpacking libunbound8:arm64 (1.24.1-2) ... Selecting previously unselected package libgnutls-dane0t64:arm64. Preparing to unpack .../065-libgnutls-dane0t64_3.8.10-3_arm64.deb ... Unpacking libgnutls-dane0t64:arm64 (3.8.10-3) ... Selecting previously unselected package libgnutls-openssl27t64:arm64. Preparing to unpack .../066-libgnutls-openssl27t64_3.8.10-3_arm64.deb ... Unpacking libgnutls-openssl27t64:arm64 (3.8.10-3) ... Selecting previously unselected package libidn2-dev:arm64. Preparing to unpack .../067-libidn2-dev_2.3.8-4_arm64.deb ... Unpacking libidn2-dev:arm64 (2.3.8-4) ... Selecting previously unselected package libp11-kit-dev:arm64. Preparing to unpack .../068-libp11-kit-dev_0.25.9-2_arm64.deb ... Unpacking libp11-kit-dev:arm64 (0.25.9-2) ... Selecting previously unselected package libtasn1-6-dev:arm64. Preparing to unpack .../069-libtasn1-6-dev_4.20.0-2_arm64.deb ... Unpacking libtasn1-6-dev:arm64 (4.20.0-2) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../070-libgmpxx4ldbl_2%3a6.3.0+dfsg-5_arm64.deb ... 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Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/lumpy-sv-0.3.1+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 > ../lumpy-sv_0.3.1+dfsg-8_source.changes dpkg-buildpackage: info: source package lumpy-sv dpkg-buildpackage: info: source version 0.3.1+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' Cleaning up. make --no-print-directory -C src/filter/ clean rm -vf lumpy_filter #rm -Rf /lib #rm -f /src/api/*.o #rm -f /src/api/internal/*.o #rm -Rf /include make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' [ -d bin ] || mkdir -p bin [ -d bin ] || mkdir -p bin [ -d obj ] || mkdir -p obj make --no-print-directory -C src/filter/ cp scripts/lumpyexpress bin/lumpyexpress [ -d bin ] || mkdir -p bin cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz -Wl,-z,relro -Wl,-z,now Building lumpy: > bin/lumpyexpress.config ========================================================= #make --no-print-directory --directory= api for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \ echo "- Building in $dir"; \ make --no-print-directory -C $dir; \ echo ""; \ done - Building in src/utils/bedFile * compiling bedFile.cpp cp src/filter/lumpy_filter bin In file included from bedFile.cpp:12: bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/version * compiling version.cpp - Building in src/utils/fileType * compiling fileType.cpp - Building in src/utils/bedFilePE * compiling bedFilePE.cpp In file included from bedFilePE.h:12, from bedFilePE.cpp:15: ../../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/genomeFile * compiling genomeFile.cpp genomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’: genomeFile.cpp:61:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 61 | long c2; | ^~ - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp * compiling BamAncillary.cpp In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp - Building in src/lumpy * compiling lumpy.cpp * compiling SV_Pair.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o * compiling SV_Evidence.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o * compiling SV_BreakPoint.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o * compiling SV_Bedpe.cpp * compiling SV_SplitRead.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o * compiling SV_SplitReadReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o * compiling SV_PairReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o * compiling SV_BedpeReader.cpp * compiling SV_BamReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o * compiling SV_InterChromBamReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o * compiling SV_EvidenceReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_PairReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_BreakPoint.cpp:16: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Evidence.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_EvidenceReader.h:20, from SV_EvidenceReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitReadReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_SplitRead.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Bedpe.cpp:14: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_InterChromBamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_BamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitRead.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from lumpy.cpp:20: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BedpeReader.h:21, from SV_Bedpe.cpp:17: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from lumpy.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Bedpe.h:18, from SV_BedpeReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 81 | for (j = 0; j < size; ++j) { | ~~^~~~~~ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_SplitReadReader.cpp:16: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BedpeReader.h:22: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ In file included from SV_Evidence.h:24: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ In file included from SV_Bedpe.h:19, from lumpy.cpp:27: SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); | ~~~~~~^~~~~~~~~~~~ SV_BreakPoint.cpp:1286:14: required from here 1286 | r_bin.add(interval_r.i.chr, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ 1287 | interval_r.i.start, | ~~~~~~~~~~~~~~~~~~~ 1288 | interval_r.i.end, | ~~~~~~~~~~~~~~~~~ 1289 | interval_r.i.strand, | ~~~~~~~~~~~~~~~~~~~~ 1290 | this); | ~~~~~ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_InterChromBamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_BedpeReader.h:23, from SV_Bedpe.h:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_Evidence.h:24: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_BamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ * compiling SV_Tools.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Pair.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long unsigned int’} [-Wsign-compare] 208 | ( bam.Position < pos ) ) { | ~~~~~~~~~~~~~^~~~~ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_Pair.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * compiling SV_VcfVariant.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o * compiling log_space.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o In file included from SV_Tools.h:19, from SV_Tools.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_VcfVariant.h:18, from SV_VcfVariant.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_Tools.cpp:27: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); | ~~~~~~^~~~~~~~~~~~ SV_Tools.cpp:541:32: required from here 541 | exclude_regions.add(bed.chrom, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 542 | bed.start, | ~~~~~~~~~~ 543 | bed.end, | ~~~~~~~~ 544 | '+', | ~~~~ 545 | 1); | ~~ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’: SV_BreakPoint.cpp:704:24: warning: ‘max_i’ may be used uninitialized [-Wmaybe-uninitialized] 704 | if ((l == r) && (l == max_i)) | ~~~^~~~~~~~~ SV_BreakPoint.cpp:667:21: note: ‘max_i’ was declared here 667 | unsigned int i, max_i; | ^~~~~ SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector&, CHR_POS*, CHR_POS*, CHR_POS*, CHR_POS*, log_space**, log_space**)’: SV_BreakPoint.cpp:1650:41: warning: ‘l_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1650 | CHR_POS abs_max_l = m_start_l + l_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:25: note: ‘l_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1662:41: warning: ‘r_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1662 | CHR_POS abs_max_r = m_start_r + r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ SV_BreakPoint.cpp: In member function ‘void SV_BreakPoint::get_mixture(breakpoint_interval**, breakpoint_interval**)’: SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/cstdlib:83, from /usr/include/c++/15/bits/stl_algo.h:71, from /usr/include/c++/15/algorithm:63, from ../utils//UCSCBins/ucsc_bins.hpp:4: /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 653 | free(new_split_read); | ~~~~^~~~~~~~~~~~~~~~ SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ 641 | _reader); | ^ SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] 156 | *end = last; | ~~~~~^~~~~~ SV_Tools.cpp:143:13: note: ‘last’ was declared here 143 | int last; | ^~~~ * linking lumpy g++ -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -o ../../bin//lumpy ../../obj//lumpy.o ../../obj//SV_Pair.o ../../obj//SV_Evidence.o ../../obj//SV_BreakPoint.o ../../obj//SV_Bedpe.o ../../obj//SV_SplitRead.o ../../obj//SV_SplitReadReader.o ../../obj//SV_PairReader.o ../../obj//SV_BedpeReader.o ../../obj//SV_BamReader.o ../../obj//SV_InterChromBamReader.o ../../obj//SV_EvidenceReader.o ../../obj//SV_Tools.o ../../obj//SV_VcfVariant.o ../../obj//log_space.o ../../obj//BamAncillary.o ../../obj//sequenceUtils.o ../../obj//bedFilePE.o ../../obj//bedFile.o ../../obj//genomeFile.o ../../obj//fileType.o \ -L../utils//BamTools/lib/ -lbamtools \ -lz -L /build/reproducible-path/lumpy-sv-0.3.1+dfsg/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \ -lgzstream -lz -lm -ldl -lpthread make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' cat debian/missing-sources/pe.pos_sorted.sam |samtools view -Sb - > data/pe.pos_sorted.bam cat debian/missing-sources/sr.pos_sorted.sam |samtools view -Sb - > data/sr.pos_sorted.bam dh_install rm -f debian/lumpy-sv*/usr/share/lumpy-sv/scripts/lumpyexpress.config rm -f data/pe.pos_sorted.bam data/sr.pos_sorted.bam make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/lumpy-sv/usr/bin/lumpy: DWARF compression not beneficial - old size 6412701 new size 6428429 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a 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 dh_gencontrol dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-8_all.deb'. dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb'. dpkg-deb: building package 'lumpy-sv' in '../lumpy-sv_0.3.1+dfsg-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo dpkg-genchanges --build=binary -O../lumpy-sv_0.3.1+dfsg-8_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/3082459 and its subdirectories I: Current time: Thu Oct 30 17:13:47 -12 2025 I: pbuilder-time-stamp: 1761887627 Fri Oct 31 05:13:47 UTC 2025 I: Signing ./b1/lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo as lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc Fri Oct 31 05:13:47 UTC 2025 I: Signed ./b1/lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo as ./b1/lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc Fri Oct 31 05:13:47 UTC 2025 - build #1 for lumpy-sv/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Fri Oct 31 05:13:47 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-xuAzWn7M, removing. /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 05:13 b1 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 05:12 b2 -rw-rw-r-- 1 jenkins jenkins 1594 Oct 30 20:06 lumpy-sv_0.3.1+dfsg-8.dsc -rw------- 1 jenkins jenkins 2738 Oct 31 05:12 rbuildlog.xSe0ha7 /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b1: total 95032 -rw-r--r-- 1 jenkins jenkins 80856 Oct 31 05:13 build.log -rw-r--r-- 1 jenkins jenkins 3184340 Oct 31 05:13 lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 54564224 Oct 31 05:13 lumpy-sv-examples_0.3.1+dfsg-8_all.deb -rw-r--r-- 1 jenkins jenkins 39265332 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1594 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8.dsc -rw-r--r-- 1 jenkins jenkins 7493 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 8375 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2284 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_arm64.changes -rw-r--r-- 1 jenkins jenkins 174924 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 1721 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b2: total 0 Fri Oct 31 05:13:51 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 30 17:12:37 -12 2025 I: pbuilder-time-stamp: 1761887557 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [lumpy-sv_0.3.1+dfsg-8.dsc] I: copying [./lumpy-sv_0.3.1+dfsg.orig.tar.xz] I: copying [./lumpy-sv_0.3.1+dfsg-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./lumpy-sv_0.3.1+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting lumpy-sv in lumpy-sv-0.3.1+dfsg dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying lumpyexpress.config.patch dpkg-source: info: applying fix_shebang.patch dpkg-source: info: applying do-not-override-dpkg-flags.patch dpkg-source: info: applying cleanup-bin.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3082459/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='e07ec7d0558a481ba4382837f8de28c3' 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='3082459' 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.MOdMJZyx/pbuilderrc_0AXc --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b1 --logfile b1/build.log lumpy-sv_0.3.1+dfsg-8.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/3082459/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), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 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 libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libfastahack-dev; however: Package libfastahack-dev is not installed. pbuilder-satisfydepends-dummy depends on libgzstream-dev; however: Package libgzstream-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libfastahack-dev{a} libfastahack0{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 102 newly installed, 0 to remove and 0 not upgraded. Need to get 33.1 MB of archives. After unpacking 123 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-3+b3 [56.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 24 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 35 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-5 [57.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-5 [41.1 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-5 [41.3 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-5 [53.0 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-5 [126 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libbamtools2.5.3 arm64 2.5.3+dfsg-1 [138 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libbamtools-dev arm64 2.5.3+dfsg-1 [207 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.17.0~rc3-1 [362 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.24.1-2 [560 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.10-3 [456 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.10-3 [455 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.8-4 [102 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.9-2 [220 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-5 [329 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-5 [621 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10.2-1 [1319 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.10-3 [1414 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-5 [16.1 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.10+dfsg-1 [305 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1.1+b1 [112 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.12.0-1 [91.6 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.16.0-1 [24.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.16.0-1 [183 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-3 [173 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.5.4-1 [3377 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.7+dfsg-2 [330 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.17.0~rc3-1 [498 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.23-2 [51.3 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libfastahack0 arm64 1.0.0+dfsg-11+b2 [23.6 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libfastahack-dev arm64 1.0.0+dfsg-11+b2 [26.1 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgzstream0 arm64 1.5+git20171107.9a20658-3 [7128 B] Get: 95 http://deb.debian.org/debian unstable/main arm64 libgzstream-dev arm64 1.5+git20171107.9a20658-3 [7452 B] Get: 96 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.8.1-2 [344 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.22.1+ds2-1 [1684 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libsqlite3-dev arm64 3.46.1-8 [1098 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.22.1-1 [666 kB] Fetched 33.1 MB in 0s (101 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19964 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../002-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../003-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../004-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 .../005-libuchardet0_0.0.8-2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../006-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../007-bsdextrautils_2.41.2-4_arm64.deb ... Unpacking bsdextrautils (2.41.2-4) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../008-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../009-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../010-m4_1.4.20-2_arm64.deb ... Unpacking m4 (1.4.20-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../011-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../012-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../013-automake_1%3a1.18.1-2_all.deb ... Unpacking automake (1:1.18.1-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../014-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../015-libcom-err2_1.47.2-3+b3_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2-3+b3) ... Selecting previously unselected package comerr-dev:arm64. Preparing to unpack .../016-comerr-dev_2.1-1.47.2-3+b3_arm64.deb ... Unpacking comerr-dev:arm64 (2.1-1.47.2-3+b3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../017-libdebhelper-perl_13.28_all.deb ... Unpacking libdebhelper-perl (13.28) ... Selecting previously unselected package libtool. Preparing to unpack .../018-libtool_2.5.4-7_all.deb ... Unpacking libtool (2.5.4-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../019-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../020-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../021-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../022-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../023-libelf1t64_0.194-1_arm64.deb ... Unpacking libelf1t64:arm64 (0.194-1) ... Selecting previously unselected package dwz. Preparing to unpack .../024-dwz_0.16-2_arm64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../025-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../026-libxml2-16_2.15.1+dfsg-0.3_arm64.deb ... Unpacking libxml2-16:arm64 (2.15.1+dfsg-0.3) ... Selecting previously unselected package gettext. Preparing to unpack .../027-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../028-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../029-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../030-debhelper_13.28_all.deb ... Unpacking debhelper (13.28) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../031-libkrb5support0_1.21.3-5_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-5) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../032-libk5crypto3_1.21.3-5_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../033-libkeyutils1_1.6.3-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../034-libkrb5-3_1.21.3-5_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../035-libgssapi-krb5-2_1.21.3-5_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-5) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../036-libgssrpc4t64_1.21.3-5_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-5) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../037-libkadm5clnt-mit12_1.21.3-5_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-5) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../038-libkdb5-10t64_1.21.3-5_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-5) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../039-libkadm5srv-mit12_1.21.3-5_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-5) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../040-krb5-multidev_1.21.3-5_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-5) ... Selecting previously unselected package libbamtools2.5.3:arm64. Preparing to unpack .../041-libbamtools2.5.3_2.5.3+dfsg-1_arm64.deb ... Unpacking libbamtools2.5.3:arm64 (2.5.3+dfsg-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../042-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libbamtools-dev:arm64. Preparing to unpack .../043-libbamtools-dev_2.5.3+dfsg-1_arm64.deb ... Unpacking libbamtools-dev:arm64 (2.5.3+dfsg-1) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../044-libbrotli1_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli1:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libbrotli-dev:arm64. Preparing to unpack .../045-libbrotli-dev_1.1.0-2+b7_arm64.deb ... Unpacking libbrotli-dev:arm64 (1.1.0-2+b7) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../046-libbz2-dev_1.0.8-6_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-6) ... Selecting previously unselected package libnghttp3-9:arm64. Preparing to unpack .../047-libnghttp3-9_1.12.0-1_arm64.deb ... Unpacking libnghttp3-9:arm64 (1.12.0-1) ... Selecting previously unselected package libngtcp2-16:arm64. Preparing to unpack .../048-libngtcp2-16_1.16.0-1_arm64.deb ... Unpacking libngtcp2-16:arm64 (1.16.0-1) ... Selecting previously unselected package libidn2-0:arm64. Preparing to unpack .../049-libidn2-0_2.3.8-4_arm64.deb ... Unpacking libidn2-0:arm64 (2.3.8-4) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../050-libffi8_3.5.2-2_arm64.deb ... Unpacking libffi8:arm64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:arm64. Preparing to unpack .../051-libp11-kit0_0.25.9-2_arm64.deb ... Unpacking libp11-kit0:arm64 (0.25.9-2) ... Selecting previously unselected package libtasn1-6:arm64. Preparing to unpack .../052-libtasn1-6_4.20.0-2_arm64.deb ... Unpacking libtasn1-6:arm64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:arm64. Preparing to unpack .../053-libgnutls30t64_3.8.10-3_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.10-3) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../054-libsasl2-modules-db_2.1.28+dfsg1-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../055-libsasl2-2_2.1.28+dfsg1-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-10) ... Selecting previously unselected package libldap2:arm64. Preparing to unpack .../056-libldap2_2.6.10+dfsg-1_arm64.deb ... Unpacking libldap2:arm64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../057-libnghttp2-14_1.64.0-1.1+b1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.64.0-1.1+b1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:arm64. Preparing to unpack .../058-libngtcp2-crypto-gnutls8_1.16.0-1_arm64.deb ... Unpacking libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... Selecting previously unselected package libpsl5t64:arm64. Preparing to unpack .../059-libpsl5t64_0.21.2-1.1+b1_arm64.deb ... Unpacking libpsl5t64:arm64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../060-librtmp1_2.4+20151223.gitfa8646d.1-3_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:arm64. Preparing to unpack .../061-libssh2-1t64_1.11.1-1_arm64.deb ... Unpacking libssh2-1t64:arm64 (1.11.1-1) ... Selecting previously unselected package libcurl3t64-gnutls:arm64. Preparing to unpack .../062-libcurl3t64-gnutls_8.17.0~rc3-1_arm64.deb ... Unpacking libcurl3t64-gnutls:arm64 (8.17.0~rc3-1) ... Selecting previously unselected package libevent-2.1-7t64:arm64. Preparing to unpack .../063-libevent-2.1-7t64_2.1.12-stable-10+b1_arm64.deb ... Unpacking libevent-2.1-7t64:arm64 (2.1.12-stable-10+b1) ... Selecting previously unselected package libunbound8:arm64. Preparing to unpack .../064-libunbound8_1.24.1-2_arm64.deb ... Unpacking libunbound8:arm64 (1.24.1-2) ... Selecting previously unselected package libgnutls-dane0t64:arm64. Preparing to unpack .../065-libgnutls-dane0t64_3.8.10-3_arm64.deb ... Unpacking libgnutls-dane0t64:arm64 (3.8.10-3) ... Selecting previously unselected package libgnutls-openssl27t64:arm64. Preparing to unpack .../066-libgnutls-openssl27t64_3.8.10-3_arm64.deb ... Unpacking libgnutls-openssl27t64:arm64 (3.8.10-3) ... Selecting previously unselected package libidn2-dev:arm64. Preparing to unpack .../067-libidn2-dev_2.3.8-4_arm64.deb ... Unpacking libidn2-dev:arm64 (2.3.8-4) ... Selecting previously unselected package libp11-kit-dev:arm64. Preparing to unpack .../068-libp11-kit-dev_0.25.9-2_arm64.deb ... Unpacking libp11-kit-dev:arm64 (0.25.9-2) ... Selecting previously unselected package libtasn1-6-dev:arm64. Preparing to unpack .../069-libtasn1-6-dev_4.20.0-2_arm64.deb ... Unpacking libtasn1-6-dev:arm64 (4.20.0-2) ... Selecting previously unselected package libgmpxx4ldbl:arm64. Preparing to unpack .../070-libgmpxx4ldbl_2%3a6.3.0+dfsg-5_arm64.deb ... Unpacking libgmpxx4ldbl:arm64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package libgmp-dev:arm64. Preparing to unpack .../071-libgmp-dev_2%3a6.3.0+dfsg-5_arm64.deb ... Unpacking libgmp-dev:arm64 (2:6.3.0+dfsg-5) ... Selecting previously unselected package nettle-dev:arm64. Preparing to unpack .../072-nettle-dev_3.10.2-1_arm64.deb ... Unpacking nettle-dev:arm64 (3.10.2-1) ... Selecting previously unselected package libgnutls28-dev:arm64. Preparing to unpack .../073-libgnutls28-dev_3.8.10-3_arm64.deb ... Unpacking libgnutls28-dev:arm64 (3.8.10-3) ... Selecting previously unselected package libkrb5-dev:arm64. Preparing to unpack .../074-libkrb5-dev_1.21.3-5_arm64.deb ... Unpacking libkrb5-dev:arm64 (1.21.3-5) ... Selecting previously unselected package libldap-dev:arm64. Preparing to unpack .../075-libldap-dev_2.6.10+dfsg-1_arm64.deb ... Unpacking libldap-dev:arm64 (2.6.10+dfsg-1) ... Selecting previously unselected package libpkgconf3:arm64. 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Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/lumpy-sv-0.3.1+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 > ../lumpy-sv_0.3.1+dfsg-8_source.changes dpkg-buildpackage: info: source package lumpy-sv dpkg-buildpackage: info: source version 0.3.1+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' Cleaning up. make --no-print-directory -C src/filter/ clean rm -vf lumpy_filter #rm -Rf /lib #rm -f /src/api/*.o #rm -f /src/api/internal/*.o #rm -Rf /include make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' [ -d bin ] || mkdir -p bin [ -d bin ] || mkdir -p bin [ -d obj ] || mkdir -p obj make --no-print-directory -C src/filter/ cp scripts/lumpyexpress bin/lumpyexpress [ -d bin ] || mkdir -p bin cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz -Wl,-z,relro -Wl,-z,now Building lumpy: > bin/lumpyexpress.config ========================================================= #make --no-print-directory --directory= api for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \ echo "- Building in $dir"; \ make --no-print-directory -C $dir; \ echo ""; \ done - Building in src/utils/bedFile * compiling bedFile.cpp cp src/filter/lumpy_filter bin In file included from bedFile.cpp:12: bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/version * compiling version.cpp - Building in src/utils/fileType * compiling fileType.cpp - Building in src/utils/bedFilePE * compiling bedFilePE.cpp In file included from bedFilePE.h:12, from bedFilePE.cpp:15: ../../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/genomeFile * compiling genomeFile.cpp genomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’: genomeFile.cpp:61:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 61 | long c2; | ^~ - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp * compiling BamAncillary.cpp In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp - Building in src/lumpy * compiling lumpy.cpp * compiling SV_Pair.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o * compiling SV_Evidence.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o * compiling SV_BreakPoint.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o * compiling SV_Bedpe.cpp * compiling SV_SplitRead.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o * compiling SV_SplitReadReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o * compiling SV_PairReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o * compiling SV_BedpeReader.cpp * compiling SV_BamReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o * compiling SV_InterChromBamReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o * compiling SV_EvidenceReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_PairReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_BreakPoint.cpp:16: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Evidence.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_EvidenceReader.h:20, from SV_EvidenceReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitReadReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_SplitRead.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Bedpe.cpp:14: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_InterChromBamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_BamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitRead.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from lumpy.cpp:20: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BedpeReader.h:21, from SV_Bedpe.cpp:17: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from lumpy.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Bedpe.h:18, from SV_BedpeReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 81 | for (j = 0; j < size; ++j) { | ~~^~~~~~ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_SplitReadReader.cpp:16: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BedpeReader.h:22: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ In file included from SV_Evidence.h:24: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ In file included from SV_Bedpe.h:19, from lumpy.cpp:27: SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); | ~~~~~~^~~~~~~~~~~~ SV_BreakPoint.cpp:1286:14: required from here 1286 | r_bin.add(interval_r.i.chr, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ 1287 | interval_r.i.start, | ~~~~~~~~~~~~~~~~~~~ 1288 | interval_r.i.end, | ~~~~~~~~~~~~~~~~~ 1289 | interval_r.i.strand, | ~~~~~~~~~~~~~~~~~~~~ 1290 | this); | ~~~~~ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_InterChromBamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_BedpeReader.h:23, from SV_Bedpe.h:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_Evidence.h:24: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_BamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ * compiling SV_Tools.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Pair.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long unsigned int’} [-Wsign-compare] 208 | ( bam.Position < pos ) ) { | ~~~~~~~~~~~~~^~~~~ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_Pair.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * compiling SV_VcfVariant.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o * compiling log_space.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o In file included from SV_Tools.h:19, from SV_Tools.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_VcfVariant.h:18, from SV_VcfVariant.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_Tools.cpp:27: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); | ~~~~~~^~~~~~~~~~~~ SV_Tools.cpp:541:32: required from here 541 | exclude_regions.add(bed.chrom, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 542 | bed.start, | ~~~~~~~~~~ 543 | bed.end, | ~~~~~~~~ 544 | '+', | ~~~~ 545 | 1); | ~~ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’: SV_BreakPoint.cpp:704:24: warning: ‘max_i’ may be used uninitialized [-Wmaybe-uninitialized] 704 | if ((l == r) && (l == max_i)) | ~~~^~~~~~~~~ SV_BreakPoint.cpp:667:21: note: ‘max_i’ was declared here 667 | unsigned int i, max_i; | ^~~~~ SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector&, CHR_POS*, CHR_POS*, CHR_POS*, CHR_POS*, log_space**, log_space**)’: SV_BreakPoint.cpp:1650:41: warning: ‘l_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1650 | CHR_POS abs_max_l = m_start_l + l_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:25: note: ‘l_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1662:41: warning: ‘r_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1662 | CHR_POS abs_max_r = m_start_r + r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ SV_BreakPoint.cpp: In member function ‘void SV_BreakPoint::get_mixture(breakpoint_interval**, breakpoint_interval**)’: SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/cstdlib:83, from /usr/include/c++/15/bits/stl_algo.h:71, from /usr/include/c++/15/algorithm:63, from ../utils//UCSCBins/ucsc_bins.hpp:4: /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 653 | free(new_split_read); | ~~~~^~~~~~~~~~~~~~~~ SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ 641 | _reader); | ^ SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] 156 | *end = last; | ~~~~~^~~~~~ SV_Tools.cpp:143:13: note: ‘last’ was declared here 143 | int last; | ^~~~ * linking lumpy g++ -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -o ../../bin//lumpy ../../obj//lumpy.o ../../obj//SV_Pair.o ../../obj//SV_Evidence.o ../../obj//SV_BreakPoint.o ../../obj//SV_Bedpe.o ../../obj//SV_SplitRead.o ../../obj//SV_SplitReadReader.o ../../obj//SV_PairReader.o ../../obj//SV_BedpeReader.o ../../obj//SV_BamReader.o ../../obj//SV_InterChromBamReader.o ../../obj//SV_EvidenceReader.o ../../obj//SV_Tools.o ../../obj//SV_VcfVariant.o ../../obj//log_space.o ../../obj//BamAncillary.o ../../obj//sequenceUtils.o ../../obj//bedFilePE.o ../../obj//bedFile.o ../../obj//genomeFile.o ../../obj//fileType.o \ -L../utils//BamTools/lib/ -lbamtools \ -lz -L /build/reproducible-path/lumpy-sv-0.3.1+dfsg/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \ -lgzstream -lz -lm -ldl -lpthread make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' cat debian/missing-sources/pe.pos_sorted.sam |samtools view -Sb - > data/pe.pos_sorted.bam cat debian/missing-sources/sr.pos_sorted.sam |samtools view -Sb - > data/sr.pos_sorted.bam dh_install rm -f debian/lumpy-sv*/usr/share/lumpy-sv/scripts/lumpyexpress.config rm -f data/pe.pos_sorted.bam data/sr.pos_sorted.bam make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/lumpy-sv/usr/bin/lumpy: DWARF compression not beneficial - old size 6412701 new size 6428429 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a 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 dh_gencontrol dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-8_all.deb'. dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb'. dpkg-deb: building package 'lumpy-sv' in '../lumpy-sv_0.3.1+dfsg-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo dpkg-genchanges --build=binary -O../lumpy-sv_0.3.1+dfsg-8_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/3082459 and its subdirectories I: Current time: Thu Oct 30 17:13:47 -12 2025 I: pbuilder-time-stamp: 1761887627 Fri Oct 31 05:13:51 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Fri Oct 31 05:13:51 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Fri Oct 31 05:13:51 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Fri Oct 31 05:13:51 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-qlQMFJ' ==================================================================================== Fri Oct 31 05:13:52 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 lumpy-sv unstable /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx 0.3.1+dfsg-8" as arguments. Fri Oct 31 05:13:52 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-fhPCvIiv" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Oct 31 05:13:52 UTC 2025 I: Downloading source for unstable/lumpy-sv=0.3.1+dfsg-8 Reading package lists... NOTICE: 'lumpy-sv' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lumpy-sv.git Please use: git clone https://salsa.debian.org/med-team/lumpy-sv.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 39.4 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (dsc) [1594 B] Get:2 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (tar) [112 kB] Get:3 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (diff) [39.3 MB] Fetched 39.4 MB in 0s (129 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'lumpy-sv' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/lumpy-sv.git Please use: git clone https://salsa.debian.org/med-team/lumpy-sv.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 39.4 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (dsc) [1594 B] Get:2 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (tar) [112 kB] Get:3 http://deb.debian.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (diff) [39.3 MB] Fetched 39.4 MB in 0s (129 MB/s) Download complete and in download only mode ============================================================================= Re-Building lumpy-sv in unstable on arm64 on codethink03-arm64 now. Date: Fri Oct 31 05:13:52 GMT 2025 Date UTC: Fri Oct 31 05:13:52 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/pbuilderrc_MFBq + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' lumpy-sv = debian-installer -o lumpy-sv = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' lumpy-sv = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/pbuilderrc_MFBq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b2 --logfile b2/build.log lumpy-sv_0.3.1+dfsg-8.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Fri Oct 31 19:13:53 +14 2025 I: pbuilder-time-stamp: 1761887633 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] tar: ./build: time stamp 2026-11-30 04:05:37 is 34073503.56438751 s in the future tar: ./dev/ptmx: time stamp 2026-11-30 04:05:25 is 34073491.56429107 s in the future tar: ./dev/pts: time stamp 2026-11-30 04:05:25 is 34073491.56427975 s in the future tar: ./dev/console: time stamp 2026-11-30 04:05:25 is 34073491.56427151 s in the future tar: 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./usr/share/locale/zh_CN/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93271195 s in the future tar: ./usr/share/locale/zh_CN: time stamp 2026-11-30 04:05:23 is 34073477.93270587 s in the future tar: ./usr/share/locale/zh_TW/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93269859 s in the future tar: ./usr/share/locale/zh_TW: time stamp 2026-11-30 04:05:23 is 34073477.93269203 s in the future tar: ./usr/share/locale/be/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93268463 s in the future tar: ./usr/share/locale/eu/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93267343 s in the future tar: ./usr/share/locale/ia/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93266231 s in the future tar: ./usr/share/locale/kk/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93265075 s in the future tar: ./usr/share/locale/lg/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93263967 s in the future tar: ./usr/share/locale/ms/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93262831 s in the future tar: ./usr/share/locale/ta/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93261763 s in the future tar: ./usr/share/locale: time stamp 2026-11-30 04:05:42 is 34073496.93260731 s in the future tar: ./usr/share/aptitude: time stamp 2026-11-30 04:05:42 is 34073496.93260119 s in the future tar: ./usr/share: time stamp 2026-11-30 04:05:43 is 34073497.93259555 s in the future tar: ./usr: time stamp 2026-11-30 04:05:25 is 34073479.93258971 s in the future tar: ./etc/alternatives: time stamp 2026-11-30 04:05:44 is 34073498.93257867 s in the future tar: ./etc/systemd/system/timers.target.wants: time stamp 2026-11-30 04:05:37 is 34073491.93257095 s in the future tar: ./etc/systemd/system: time stamp 2026-11-30 04:05:25 is 34073479.93256523 s in the future 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 [lumpy-sv_0.3.1+dfsg-8.dsc] I: copying [./lumpy-sv_0.3.1+dfsg.orig.tar.xz] I: copying [./lumpy-sv_0.3.1+dfsg-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./lumpy-sv_0.3.1+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting lumpy-sv in lumpy-sv-0.3.1+dfsg dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg.orig.tar.xz dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying lumpyexpress.config.patch dpkg-source: info: applying fix_shebang.patch dpkg-source: info: applying do-not-override-dpkg-flags.patch dpkg-source: info: applying cleanup-bin.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/898656/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 31 05:14 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/898656/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/898656/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=2bcb1c83a7bc42b5b4e20543e98bf323 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=898656 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/pbuilderrc_MFBq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b2 --logfile b2/build.log lumpy-sv_0.3.1+dfsg-8.dsc' SUDO_GID=109 SUDO_HOME=/var/lib/jenkins SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 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/898656/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), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19964 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 libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libfastahack-dev; however: Package libfastahack-dev is not installed. pbuilder-satisfydepends-dummy depends on libgzstream-dev; however: Package libgzstream-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libfastahack-dev{a} libfastahack0{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libidn2-dev{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libxml2-16{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc lynx publicsuffix wget 0 packages upgraded, 102 newly installed, 0 to remove and 0 not upgraded. Need to get 33.1 MB of archives. After unpacking 123 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-3+b3 [56.9 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 24 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 35 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-5 [57.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-5 [41.1 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-5 [41.3 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-5 [53.0 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-5 [126 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libbamtools2.5.3 arm64 2.5.3+dfsg-1 [138 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libbamtools-dev arm64 2.5.3+dfsg-1 [207 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.10-3 [1384 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.17.0~rc3-1 [362 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.24.1-2 [560 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.10-3 [456 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.10-3 [455 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.8-4 [102 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.9-2 [220 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-5 [329 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-5 [621 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10.2-1 [1319 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.10-3 [1414 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-5 [16.1 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.10+dfsg-1 [305 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1.1+b1 [112 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.12.0-1 [91.6 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.16.0-1 [24.6 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.16.0-1 [183 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-3 [173 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.5.4-1 [3377 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.7+dfsg-2 [330 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.17.0~rc3-1 [498 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.23-2 [51.3 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libfastahack0 arm64 1.0.0+dfsg-11+b2 [23.6 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libfastahack-dev arm64 1.0.0+dfsg-11+b2 [26.1 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgzstream0 arm64 1.5+git20171107.9a20658-3 [7128 B] Get: 95 http://deb.debian.org/debian unstable/main arm64 libgzstream-dev arm64 1.5+git20171107.9a20658-3 [7452 B] Get: 96 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.8.1-2 [344 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.22.1+ds2-1 [1684 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libsqlite3-dev arm64 3.46.1-8 [1098 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.22.1-1 [666 kB] Fetched 33.1 MB in 0s (67.1 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19964 files and directories currently installed.) Preparing to unpack .../000-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../001-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. 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Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/898656/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/898656/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/lumpy-sv-0.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../lumpy-sv_0.3.1+dfsg-8_source.changes dpkg-buildpackage: info: source package lumpy-sv dpkg-buildpackage: info: source version 0.3.1+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' Cleaning up. make --no-print-directory -C src/filter/ clean rm -vf lumpy_filter #rm -Rf /lib #rm -f /src/api/*.o #rm -f /src/api/internal/*.o #rm -Rf /include make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' [ -d bin ] || mkdir -p bin make --no-print-directory -C src/filter/ [ -d bin ] || mkdir -p bin cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz -Wl,-z,relro -Wl,-z,now [ -d obj ] || mkdir -p obj cp scripts/lumpyexpress bin/lumpyexpress [ -d bin ] || mkdir -p bin Building lumpy: ========================================================= #make --no-print-directory --directory= api for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \ echo "- Building in $dir"; \ make --no-print-directory -C $dir; \ echo ""; \ done - Building in src/utils/bedFile > bin/lumpyexpress.config * compiling bedFile.cpp cp src/filter/lumpy_filter bin In file included from bedFile.cpp:12: bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/version * compiling version.cpp - Building in src/utils/fileType * compiling fileType.cpp - Building in src/utils/bedFilePE * compiling bedFilePE.cpp In file included from bedFilePE.h:12, from bedFilePE.cpp:15: ../../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/genomeFile * compiling genomeFile.cpp genomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’: genomeFile.cpp:61:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable] 61 | long c2; | ^~ - Building in src/utils/BamTools-Ancillary * compiling BamAncillary.cpp * compiling BamAncillary.cpp In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from BamAncillary.h:12, from BamAncillary.cpp:12: ..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ - Building in src/utils/sequenceUtilities * compiling sequenceUtils.cpp - Building in src/lumpy * compiling lumpy.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o * compiling SV_Pair.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o * compiling SV_Evidence.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o * compiling SV_BreakPoint.cpp * compiling SV_Bedpe.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o * compiling SV_SplitRead.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o * compiling SV_SplitReadReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o * compiling SV_PairReader.cpp * compiling SV_BedpeReader.cpp * compiling SV_BamReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o * compiling SV_InterChromBamReader.cpp * compiling SV_EvidenceReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Bedpe.h:18, from SV_BedpeReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitReadReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_InterChromBamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_EvidenceReader.h:20, from SV_EvidenceReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_PairReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_BamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from lumpy.cpp:20: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from lumpy.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_Evidence.h:24: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ In file included from SV_Bedpe.h:19, from lumpy.cpp:27: SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, from SV_Evidence.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_BreakPoint.cpp:16: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_BedpeReader.h:23, from SV_Bedpe.h:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_SplitReadReader.cpp:16: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_Evidence.h:24: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_SplitRead.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Pair.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_Bedpe.cpp:14: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_InterChromBamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_SplitReadReader.h:22, from SV_SplitRead.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_Pair.cpp:19: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_BamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 81 | for (j = 0; j < size; ++j) { | ~~^~~~~~ In file included from SV_BedpeReader.h:21, from SV_Bedpe.cpp:17: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; | ^~~~~~~~~~~~~~ SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long unsigned int’} [-Wsign-compare] 208 | ( bam.Position < pos ) ) { | ~~~~~~~~~~~~~^~~~~ In file included from SV_BedpeReader.h:22: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling SV_Tools.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); | ~~~~~~^~~~~~~~~~~~ SV_BreakPoint.cpp:1286:14: required from here 1286 | r_bin.add(interval_r.i.chr, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ 1287 | interval_r.i.start, | ~~~~~~~~~~~~~~~~~~~ 1288 | interval_r.i.end, | ~~~~~~~~~~~~~~~~~ 1289 | interval_r.i.strand, | ~~~~~~~~~~~~~~~~~~~~ 1290 | this); | ~~~~~ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ * compiling SV_VcfVariant.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o * compiling log_space.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o In file included from SV_Tools.h:19, from SV_Tools.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_Tools.cpp:27: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, from SV_VcfVariant.h:18, from SV_VcfVariant.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); | ~~~~~~^~~~~~~~~~~~ SV_Tools.cpp:541:32: required from here 541 | exclude_regions.add(bed.chrom, | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 542 | bed.start, | ~~~~~~~~~~ 543 | bed.end, | ~~~~~~~~ 544 | '+', | ~~~~ 545 | 1); | ~~ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’: SV_BreakPoint.cpp:704:24: warning: ‘max_i’ may be used uninitialized [-Wmaybe-uninitialized] 704 | if ((l == r) && (l == max_i)) | ~~~^~~~~~~~~ SV_BreakPoint.cpp:667:21: note: ‘max_i’ was declared here 667 | unsigned int i, max_i; | ^~~~~ SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector&, CHR_POS*, CHR_POS*, CHR_POS*, CHR_POS*, log_space**, log_space**)’: SV_BreakPoint.cpp:1650:41: warning: ‘l_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1650 | CHR_POS abs_max_l = m_start_l + l_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:25: note: ‘l_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1662:41: warning: ‘r_max_i’ may be used uninitialized [-Wmaybe-uninitialized] 1662 | CHR_POS abs_max_r = m_start_r + r_max_i; | ^~~~~~~ SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 653 | free(new_split_read); | ~~~~^~~~~~~~~~~~~~~~ SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ 641 | _reader); | ^ SV_BreakPoint.cpp: In member function ‘void SV_BreakPoint::get_mixture(breakpoint_interval**, breakpoint_interval**)’: SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/cstdlib:83, from /usr/include/c++/15/bits/stl_algo.h:71, from /usr/include/c++/15/algorithm:63, from ../utils//UCSCBins/ucsc_bins.hpp:4: /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] 156 | *end = last; | ~~~~~^~~~~~ SV_Tools.cpp:143:13: note: ‘last’ was declared here 143 | int last; | ^~~~ * linking lumpy g++ -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -o ../../bin//lumpy ../../obj//lumpy.o ../../obj//SV_Pair.o ../../obj//SV_Evidence.o ../../obj//SV_BreakPoint.o ../../obj//SV_Bedpe.o ../../obj//SV_SplitRead.o ../../obj//SV_SplitReadReader.o ../../obj//SV_PairReader.o ../../obj//SV_BedpeReader.o ../../obj//SV_BamReader.o ../../obj//SV_InterChromBamReader.o ../../obj//SV_EvidenceReader.o ../../obj//SV_Tools.o ../../obj//SV_VcfVariant.o ../../obj//log_space.o ../../obj//BamAncillary.o ../../obj//sequenceUtils.o ../../obj//bedFilePE.o ../../obj//bedFile.o ../../obj//genomeFile.o ../../obj//fileType.o \ -L../utils//BamTools/lib/ -lbamtools \ -lz -L /build/reproducible-path/lumpy-sv-0.3.1+dfsg/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \ -lgzstream -lz -lm -ldl -lpthread make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' cat debian/missing-sources/pe.pos_sorted.sam |samtools view -Sb - > data/pe.pos_sorted.bam cat debian/missing-sources/sr.pos_sorted.sam |samtools view -Sb - > data/sr.pos_sorted.bam dh_install rm -f debian/lumpy-sv*/usr/share/lumpy-sv/scripts/lumpyexpress.config rm -f data/pe.pos_sorted.bam data/sr.pos_sorted.bam make[1]: Leaving directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dwz: debian/lumpy-sv/usr/bin/lumpy: DWARF compression not beneficial - old size 6412701 new size 6428429 dh_strip -a dh_makeshlibs -a dh_shlibdeps -a 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 dh_gencontrol dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package lumpy-sv: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-8_all.deb'. dpkg-deb: building package 'lumpy-sv' in '../lumpy-sv_0.3.1+dfsg-8_arm64.deb'. dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo dpkg-genchanges --build=binary -O../lumpy-sv_0.3.1+dfsg-8_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: user script /srv/workspace/pbuilder/898656/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/898656/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/898656 and its subdirectories I: Current time: Fri Oct 31 19:17:45 +14 2025 I: pbuilder-time-stamp: 1761887865 + false + set +x Fri Oct 31 05:17:45 UTC 2025 I: Signing ./b2/lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo as lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc Fri Oct 31 05:17:45 UTC 2025 I: Signed ./b2/lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo as ./b2/lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc Fri Oct 31 05:17:45 UTC 2025 - build #2 for lumpy-sv/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Fri Oct 31 05:17:45 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-fhPCvIiv, removing. /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx: total 100 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 05:13 b1 drwxrwxr-x 2 jenkins jenkins 4096 Oct 31 05:17 b2 -rw-rw-r-- 1 jenkins jenkins 1594 Oct 30 20:06 lumpy-sv_0.3.1+dfsg-8.dsc -rw------- 1 jenkins jenkins 83895 Oct 31 05:13 rbuildlog.xSe0ha7 /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b1: total 95144 -rw-r--r-- 1 jenkins jenkins 80856 Oct 31 05:13 build.log -rw-r--r-- 1 jenkins jenkins 3184340 Oct 31 05:13 lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 54564224 Oct 31 05:13 lumpy-sv-examples_0.3.1+dfsg-8_all.deb -rw-r--r-- 1 jenkins jenkins 39265332 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1594 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8.dsc -rw-r--r-- 1 jenkins jenkins 7493 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 8375 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 2284 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_arm64.changes -rw-r--r-- 1 jenkins jenkins 174924 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 1721 Oct 31 05:13 lumpy-sv_0.3.1+dfsg-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b2: total 95300 -rw-rw-r-- 1 jenkins jenkins 354527 Oct 31 05:17 build.log -rw-r--r-- 1 jenkins jenkins 3184340 Oct 31 05:17 lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb -rw-r--r-- 1 jenkins jenkins 54564224 Oct 31 05:17 lumpy-sv-examples_0.3.1+dfsg-8_all.deb -rw-r--r-- 1 jenkins jenkins 39265332 Oct 31 05:17 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 1594 Oct 31 05:17 lumpy-sv_0.3.1+dfsg-8.dsc -rw-rw-r-- 1 jenkins jenkins 7493 Oct 31 05:17 lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo -rw-rw-r-- 1 jenkins jenkins 8375 Oct 31 05:17 lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 2284 Oct 31 05:17 lumpy-sv_0.3.1+dfsg-8_arm64.changes -rw-r--r-- 1 jenkins jenkins 174924 Oct 31 05:17 lumpy-sv_0.3.1+dfsg-8_arm64.deb -rw-rw-r-- 1 jenkins jenkins 1721 Oct 31 05:17 lumpy-sv_0.3.1+dfsg-8_source.changes Fri Oct 31 05:17:49 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Fri Oct 31 05:17:49 UTC 2025 I: lumpy-sv_0.3.1+dfsg-8_arm64.changes: Format: 1.8 Date: Fri, 31 Oct 2025 00:58:42 +0530 Source: lumpy-sv Binary: lumpy-sv lumpy-sv-dbgsym lumpy-sv-examples Architecture: arm64 all Version: 0.3.1+dfsg-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: lumpy-sv - general probabilistic framework for structural variant discovery lumpy-sv-examples - general probabilistic framework for structural variant discovery Closes: 1047978 1119475 Changes: lumpy-sv (0.3.1+dfsg-8) unstable; urgency=medium . * Team Upload. * Add patch to not override dpkg provided c/cxxflags (Closes: #1119475) * Remove generated bam files post installation (Closes: #1047978) * Remove B-D on python3, dh-python and avoid using this debhelper. This works on makefile instead * Update shebang patch to fixup python3 shebangs * Bump Standards-Version to 4.7.2 (no changes needed) * Drop Redundant "Rules-Requires-Root: no" * Drop myself from uploaders * Drop python3:Depends Checksums-Sha1: 8a94aa2e92161b6dbf91c6b85c8d1828fe793105 3184340 lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb 7bedc0938ebbeb297e786bf12b27ea51729cdc2a 54564224 lumpy-sv-examples_0.3.1+dfsg-8_all.deb ec08c048d4f78cf7a59a93460c99daa070223cfd 7493 lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo ac7f43a4158d9829a5419bd714d776677386bd36 174924 lumpy-sv_0.3.1+dfsg-8_arm64.deb Checksums-Sha256: 261de35af5365596a15781b5325d8fd12b348b68d65518b18edd5581ef267634 3184340 lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb a5d0577b58d96fa7c00e8aeba74fffc8f481239c76c7e8aaf1b9d1d20265a920 54564224 lumpy-sv-examples_0.3.1+dfsg-8_all.deb b05d6be3408972ef49c4f5b517b91e4b9368fa576e484db250c511bc265262c0 7493 lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo 45bf2c1f8d2ff1ab01ca4cd98be7d453d6f69f7e4e31d396530be68b031f9ba1 174924 lumpy-sv_0.3.1+dfsg-8_arm64.deb Files: 59847ebd3a723991efdd7a4b74d6b980 3184340 debug optional lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb 1cde4a13adaa9c31b9a20cb1fd4aa95e 54564224 science optional lumpy-sv-examples_0.3.1+dfsg-8_all.deb d431919c1024295002150bc93613f48a 7493 science optional lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo 115a3c9cc2555cc24a1769cfd33370e6 174924 science optional lumpy-sv_0.3.1+dfsg-8_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/lumpy-sv_0.3.1+dfsg-7.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/lumpy-sv_0.3.1+dfsg-7.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/lumpy-sv_0.3.1+dfsg-7.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/lumpy-sv_0.3.1+dfsg-7.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/lumpy-sv_0.3.1+dfsg-7_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/lumpy-sv_0.3.1+dfsg-7.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-10-31 05:13:48.550626394 +0000 +++ b2/build.log 2025-10-31 05:17:46.798914682 +0000 @@ -1,8 +1,2548 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Oct 30 17:12:37 -12 2025 -I: pbuilder-time-stamp: 1761887557 +I: Current time: Fri Oct 31 19:13:53 +14 2025 +I: pbuilder-time-stamp: 1761887633 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] +tar: ./build: time stamp 2026-11-30 04:05:37 is 34073503.56438751 s in the future +tar: ./dev/ptmx: time stamp 2026-11-30 04:05:25 is 34073491.56429107 s in the future +tar: ./dev/pts: time stamp 2026-11-30 04:05:25 is 34073491.56427975 s in the future +tar: ./dev/console: time 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the future +tar: ./usr/share/locale/ru: time stamp 2026-11-30 04:05:23 is 34073477.93281507 s in the future +tar: ./usr/share/locale/sk/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93280683 s in the future +tar: ./usr/share/locale/sk: time stamp 2026-11-30 04:05:23 is 34073477.93280071 s in the future +tar: ./usr/share/locale/sl/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93279319 s in the future +tar: ./usr/share/locale/sl: time stamp 2026-11-30 04:05:23 is 34073477.93278715 s in the future +tar: ./usr/share/locale/sr/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93277879 s in the future +tar: ./usr/share/locale/sr: time stamp 2026-11-30 04:05:23 is 34073477.93277271 s in the future +tar: ./usr/share/locale/sv/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93276539 s in the future +tar: ./usr/share/locale/sv: time stamp 2026-11-30 04:05:23 is 34073477.93275927 s in the future +tar: ./usr/share/locale/tr/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93275239 s in the future +tar: ./usr/share/locale/tr: time stamp 2026-11-30 04:05:23 is 34073477.93274627 s in the future +tar: ./usr/share/locale/uk/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93273895 s in the future +tar: ./usr/share/locale/uk: time stamp 2026-11-30 04:05:23 is 34073477.93273251 s in the future +tar: ./usr/share/locale/vi/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93272567 s in the future +tar: ./usr/share/locale/vi: time stamp 2026-11-30 04:05:23 is 34073477.93271943 s in the future +tar: ./usr/share/locale/zh_CN/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93271195 s in the future +tar: ./usr/share/locale/zh_CN: time stamp 2026-11-30 04:05:23 is 34073477.93270587 s in the future +tar: ./usr/share/locale/zh_TW/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93269859 s in the future +tar: ./usr/share/locale/zh_TW: time stamp 2026-11-30 04:05:23 is 34073477.93269203 s in the future +tar: ./usr/share/locale/be/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93268463 s in the future +tar: ./usr/share/locale/eu/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93267343 s in the future +tar: ./usr/share/locale/ia/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93266231 s in the future +tar: ./usr/share/locale/kk/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93265075 s in the future +tar: ./usr/share/locale/lg/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93263967 s in the future +tar: ./usr/share/locale/ms/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93262831 s in the future +tar: ./usr/share/locale/ta/LC_TIME: time stamp 2026-11-30 04:05:26 is 34073480.93261763 s in the future +tar: ./usr/share/locale: time stamp 2026-11-30 04:05:42 is 34073496.93260731 s in the future +tar: ./usr/share/aptitude: time stamp 2026-11-30 04:05:42 is 34073496.93260119 s in the future +tar: ./usr/share: time stamp 2026-11-30 04:05:43 is 34073497.93259555 s in the future +tar: ./usr: time stamp 2026-11-30 04:05:25 is 34073479.93258971 s in the future +tar: ./etc/alternatives: time stamp 2026-11-30 04:05:44 is 34073498.93257867 s in the future +tar: ./etc/systemd/system/timers.target.wants: time stamp 2026-11-30 04:05:37 is 34073491.93257095 s in the future +tar: ./etc/systemd/system: time stamp 2026-11-30 04:05:25 is 34073479.93256523 s in the future I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem @@ -28,53 +2568,85 @@ dpkg-source: info: applying cleanup-bin.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3082459/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/898656/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 31 05:14 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/898656/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/898656/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='e07ec7d0558a481ba4382837f8de28c3' - 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='3082459' - PS1='# ' - PS2='> ' + INVOCATION_ID=2bcb1c83a7bc42b5b4e20543e98bf323 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=898656 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.MOdMJZyx/pbuilderrc_0AXc --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b1 --logfile b1/build.log lumpy-sv_0.3.1+dfsg-8.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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/pbuilderrc_MFBq --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b2 --logfile b2/build.log lumpy-sv_0.3.1+dfsg-8.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + 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 + Linux i-capture-the-hostname 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/3082459/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/898656/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -228,7 +2800,7 @@ Get: 100 http://deb.debian.org/debian unstable/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libsqlite3-dev arm64 3.46.1-8 [1098 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 samtools arm64 1.22.1-1 [666 kB] -Fetched 33.1 MB in 0s (101 MB/s) +Fetched 33.1 MB in 0s (67.1 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19964 files and directories currently installed.) @@ -657,7 +3229,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/lumpy-sv-0.3.1+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 > ../lumpy-sv_0.3.1+dfsg-8_source.changes +I: user script /srv/workspace/pbuilder/898656/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/898656/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/lumpy-sv-0.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../lumpy-sv_0.3.1+dfsg-8_source.changes dpkg-buildpackage: info: source package lumpy-sv dpkg-buildpackage: info: source version 0.3.1+dfsg-8 dpkg-buildpackage: info: source distribution unstable @@ -687,14 +3263,13 @@ make -j12 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' [ -d bin ] || mkdir -p bin +make --no-print-directory -C src/filter/ [ -d bin ] || mkdir -p bin +cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz -Wl,-z,relro -Wl,-z,now [ -d obj ] || mkdir -p obj -make --no-print-directory -C src/filter/ cp scripts/lumpyexpress bin/lumpyexpress [ -d bin ] || mkdir -p bin -cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz -Wl,-z,relro -Wl,-z,now Building lumpy: -> bin/lumpyexpress.config ========================================================= #make --no-print-directory --directory= api for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \ @@ -703,6 +3278,7 @@ echo ""; \ done - Building in src/utils/bedFile +> bin/lumpyexpress.config * compiling bedFile.cpp cp src/filter/lumpy_filter bin In file included from bedFile.cpp:12: @@ -754,45 +3330,47 @@ - Building in src/lumpy * compiling lumpy.cpp - * compiling SV_Pair.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o + * compiling SV_Pair.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o * compiling SV_Evidence.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o * compiling SV_BreakPoint.cpp -g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o * compiling SV_Bedpe.cpp +g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o * compiling SV_SplitRead.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o * compiling SV_SplitReadReader.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o * compiling SV_PairReader.cpp -g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o * compiling SV_BedpeReader.cpp * compiling SV_BamReader.cpp +g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o * compiling SV_InterChromBamReader.cpp -g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o * compiling SV_EvidenceReader.cpp +g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o In file included from SV_BreakPoint.h:19, - from SV_PairReader.h:22, - from SV_PairReader.cpp:15: + from SV_Evidence.h:22, + from SV_Bedpe.h:18, + from SV_BedpeReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, - from SV_BreakPoint.cpp:16: + from SV_SplitReadReader.h:22, + from SV_SplitReadReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, - from SV_Evidence.h:22, - from SV_Evidence.cpp:15: + from SV_PairReader.h:22, + from SV_InterChromBamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { @@ -804,27 +3382,8 @@ 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, - from SV_SplitReadReader.h:22, - from SV_SplitReadReader.cpp:15: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ -In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, - from SV_SplitRead.cpp:15: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ -In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, - from SV_Bedpe.cpp:14: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ -In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, - from SV_InterChromBamReader.cpp:15: + from SV_PairReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { @@ -836,51 +3395,55 @@ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: -SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] - 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; - | ^~~~~~~~~~~~~~ -SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] - 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; - | ^~~~~~~~~~~~~~ -In file included from SV_BreakPoint.h:19, - from SV_SplitReadReader.h:22, - from SV_SplitRead.cpp:19: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from lumpy.cpp:20: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ -In file included from SV_BedpeReader.h:21, - from SV_Bedpe.cpp:17: +In file included from SV_BreakPoint.h:19, + from SV_Evidence.h:22, + from lumpy.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ +In file included from SV_Evidence.h:24: +SV_EvidenceReader.h: At global scope: +SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] + 53 | virtual void process_input( BamAlignment &_bam, + | ^~~~~~~~~~~~~ +In file included from SV_Bedpe.h:19, + from lumpy.cpp:27: +SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ + 72 | void process_input( UCSCBins &r_bin); + | ^~~~~~~~~~~~~ +SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] + 57 | virtual void process_input( BamAlignment &_bam, + | ^~~~~~~~~~~~~ +SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ + 72 | void process_input( UCSCBins &r_bin); + | ^~~~~~~~~~~~~ In file included from SV_BreakPoint.h:19, from SV_Evidence.h:22, - from lumpy.cpp:24: + from SV_Evidence.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, - from SV_Evidence.h:22, - from SV_Bedpe.h:18, - from SV_BedpeReader.cpp:15: + from SV_BreakPoint.cpp:16: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: -SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 81 | for (j = 0; j < size; ++j) { - | ~~^~~~~~ +In file included from ../utils//bedFilePE/bedFilePE.h:12, + from SV_BedpeReader.h:23, + from SV_Bedpe.h:19: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_SplitReadReader.cpp:16: @@ -888,27 +3451,11 @@ ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ -In file included from SV_BedpeReader.h:22: -SV_EvidenceReader.h: At global scope: -SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] - 53 | virtual void process_input( BamAlignment &_bam, - | ^~~~~~~~~~~~~ -SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ - 72 | void process_input( UCSCBins &r_bin); - | ^~~~~~~~~~~~~ -SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] - 57 | virtual void process_input( BamAlignment &_bam, - | ^~~~~~~~~~~~~ -SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ - 72 | void process_input( UCSCBins &r_bin); - | ^~~~~~~~~~~~~ In file included from SV_Evidence.h:24: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 53 | virtual void process_input( BamAlignment &_bam, | ^~~~~~~~~~~~~ -In file included from SV_Bedpe.h:19, - from lumpy.cpp:27: SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ @@ -918,28 +3465,24 @@ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ -SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: -SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long unsigned int]’: -../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ - 238 | BIN bin = getBin(start, end); - | ~~~~~~^~~~~~~~~~~~ -SV_BreakPoint.cpp:1286:14: required from here - 1286 | r_bin.add(interval_r.i.chr, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ - 1287 | interval_r.i.start, - | ~~~~~~~~~~~~~~~~~~~ - 1288 | interval_r.i.end, - | ~~~~~~~~~~~~~~~~~ - 1289 | interval_r.i.strand, - | ~~~~~~~~~~~~~~~~~~~~ - 1290 | this); - | ~~~~~ -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ +In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, + from SV_SplitRead.cpp:15: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ +In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, + from SV_Pair.cpp:15: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ +In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, + from SV_Bedpe.cpp:14: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_InterChromBamReader.cpp:19: @@ -947,14 +3490,49 @@ ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ +In file included from SV_BreakPoint.h:19, + from SV_SplitReadReader.h:22, + from SV_SplitRead.cpp:19: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ +In file included from SV_BreakPoint.h:19, + from SV_PairReader.h:22, + from SV_Pair.cpp:19: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, - from SV_BedpeReader.h:23, - from SV_Bedpe.h:19: + from SV_SplitRead.h:27, + from SV_BamReader.cpp:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ -In file included from SV_Evidence.h:24: +SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: +SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 81 | for (j = 0; j < size; ++j) { + | ~~^~~~~~ +In file included from SV_BedpeReader.h:21, + from SV_Bedpe.cpp:17: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ +SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: +SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] + 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; + | ^~~~~~~~~~~~~~ +SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] + 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; + | ^~~~~~~~~~~~~~ +SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: +SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long unsigned int’} [-Wsign-compare] + 208 | ( bam.Position < pos ) ) { + | ~~~~~~~~~~~~~^~~~~ +In file included from SV_BedpeReader.h:22: SV_EvidenceReader.h: At global scope: SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins&)’ was hidden [-Woverloaded-virtual=] 57 | virtual void process_input( BamAlignment &_bam, @@ -968,29 +3546,27 @@ SV_BedpeReader.h:72:14: note: by ‘void SV_BedpeReader::process_input(UCSCBins&)’ 72 | void process_input( UCSCBins &r_bin); | ^~~~~~~~~~~~~ -In file included from ../utils//bedFilePE/bedFilePE.h:12, - from SV_SplitRead.h:27, - from SV_BamReader.cpp:19: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ +SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: +SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * compiling SV_Tools.cpp g++ -g -c -g -O2 -ffile-prefix-map=/build/reproducible-path/lumpy-sv-0.3.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o -In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, - from SV_Pair.cpp:15: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ -SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: -SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long unsigned int’} [-Wsign-compare] - 208 | ( bam.Position < pos ) ) { - | ~~~~~~~~~~~~~^~~~~ -In file included from SV_BreakPoint.h:19, - from SV_PairReader.h:22, - from SV_Pair.cpp:19: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long unsigned int]’: +../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ + 238 | BIN bin = getBin(start, end); + | ~~~~~~^~~~~~~~~~~~ +SV_BreakPoint.cpp:1286:14: required from here + 1286 | r_bin.add(interval_r.i.chr, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~ + 1287 | interval_r.i.start, + | ~~~~~~~~~~~~~~~~~~~ + 1288 | interval_r.i.end, + | ~~~~~~~~~~~~~~~~~ + 1289 | interval_r.i.strand, + | ~~~~~~~~~~~~~~~~~~~~ + 1290 | this); + | ~~~~~ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ @@ -1004,6 +3580,11 @@ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ +In file included from SV_Tools.cpp:27: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ In file included from SV_BreakPoint.h:19, from SV_VcfVariant.h:18, from SV_VcfVariant.cpp:15: @@ -1011,11 +3592,6 @@ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -In file included from SV_Tools.cpp:27: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ ../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long unsigned int]’: ../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long unsigned int]’ 238 | BIN bin = getBin(start, end); @@ -1054,6 +3630,13 @@ SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ +SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: +SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] + 653 | free(new_split_read); + | ~~~~^~~~~~~~~~~~~~~~ +SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ + 641 | _reader); + | ^ SV_BreakPoint.cpp: In member function ‘void SV_BreakPoint::get_mixture(breakpoint_interval**, breakpoint_interval**)’: SV_BreakPoint.cpp:1379:39: warning: argument 1 value ‘18446744039349813264’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1379 | log_space *l = (log_space *)malloc((end_l-start_l+1)*sizeof(log_space)); @@ -1071,13 +3654,6 @@ /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘void* malloc(size_t)’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ -SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: -SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] - 653 | free(new_split_read); - | ~~~~^~~~~~~~~~~~~~~~ -SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ - 641 | _reader); - | ^ SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] 156 | *end = last; @@ -1129,8 +3705,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-8_all.deb'. -dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb'. dpkg-deb: building package 'lumpy-sv' in '../lumpy-sv_0.3.1+dfsg-8_arm64.deb'. +dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo dpkg-genchanges --build=binary -O../lumpy-sv_0.3.1+dfsg-8_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1138,12 +3714,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/898656/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/898656/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3082459 and its subdirectories -I: Current time: Thu Oct 30 17:13:47 -12 2025 -I: pbuilder-time-stamp: 1761887627 +I: removing directory /srv/workspace/pbuilder/898656 and its subdirectories +I: Current time: Fri Oct 31 19:17:45 +14 2025 +I: pbuilder-time-stamp: 1761887865 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/lumpy-sv_0.3.1+dfsg-8.diff: 89.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/lumpy-sv_0.3.1+dfsg-8.diff.gz b2/build.log: 88.8% -- replaced with stdout Compressing the 1st log... b1/build.log: 84.6% -- replaced with stdout Fri Oct 31 05:17:50 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_lumpy-sv_unstable_arm64_1761887870 + touch /var/log/reproducible-builds/diffoscope_stamp_lumpy-sv_unstable_arm64_1761887870 + RESULT=0 + systemd-run '--description=diffoscope on lumpy-sv/0.3.1+dfsg-8 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_7-102558 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx --run-session -c jenkins-reproducible-unstable-diffoscope-56a6ac01-6899-4c29-86f1-cddcfb9efaef -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/dbd-tmp-rg1rCAU ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/lumpy-sv_0.3.1+dfsg-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/lumpy-sv_0.3.1+dfsg-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/lumpy-sv_0.3.1+dfsg-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b1/lumpy-sv_0.3.1+dfsg-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b2/lumpy-sv_0.3.1+dfsg-8_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_7-102558.service; invocation ID: 5bc9321d184d41dfb889a10bdfc65542 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/lumpy-sv_0.3.1+dfsg-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/lumpy-sv_0.3.1+dfsg-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/lumpy-sv_0.3.1+dfsg-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b1/lumpy-sv_0.3.1+dfsg-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.MOdMJZyx/b2/lumpy-sv_0.3.1+dfsg-8_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: 218ms CPU time consumed: 172ms Memory peak: 17.1M (swap: 0B) _ | |_ _ _ __ ___ _ __ _ _ _____ __ | | | | | '_ ` _ \| '_ \| | | |_____/ __\ \ / / | | |_| | | | | | | |_) | |_| |_____\__ \\ V / |_|\__,_|_| |_| |_| .__/ \__, | |___/ \_/ |_| |___/ Fri Oct 31 05:17:51 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Fri Oct 31 05:17:51 UTC 2025 I: lumpy-sv from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-10-31 05:17:51] INFO: Starting at 2025-10-31 05:17:51.640584 [2025-10-31 05:17:51] INFO: Generating the pages of 1 package(s) [2025-10-31 05:17:51] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/lumpy-sv_0.3.1+dfsg-8_amd64.buildinfo [2025-10-31 05:17:51] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/lumpy-sv_0.3.1+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/lumpy-sv_0.3.1+dfsg-8.diff.gz is missing [2025-10-31 05:17:51] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/lumpy-sv didn't produce a buildlog, even though it has been built. [2025-10-31 05:17:51] INFO: Finished at 2025-10-31 05:17:51.876811, took: 0:00:00.236231 Fri Oct 31 05:17:51 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/lumpy-sv.html Fri Oct 31 05:17:51 UTC 2025 I: Removing signed lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc files: removed './b1/lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc' removed './b2/lumpy-sv_0.3.1+dfsg-8_arm64.buildinfo.asc' 1761887871 arm64 unstable lumpy-sv Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/lumpy-sv_0.3.1+dfsg-8.rbuild.log: 82.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/lumpy-sv_0.3.1+dfsg-8.rbuild.log.gz [2025-10-31 05:17:52] INFO: Starting at 2025-10-31 05:17:52.208660 [2025-10-31 05:17:52] INFO: Generating the pages of 1 package(s) [2025-10-31 05:17:52] CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/lumpy-sv_0.3.1+dfsg-8_amd64.buildinfo [2025-10-31 05:17:52] ERROR: Either /var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/lumpy-sv_0.3.1+dfsg-8.build2.log.gz or /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/lumpy-sv_0.3.1+dfsg-8.diff.gz is missing [2025-10-31 05:17:52] INFO: Finished at 2025-10-31 05:17:52.451332, took: 0:00:00.242678 All cleanup done. Fri Oct 31 05:17:52 UTC 2025 - total duration: 0h 5m 38s. Fri Oct 31 05:17:52 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-samXAxor, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 5min 38.964s CPU time consumed: 5.314s Memory peak: 228.1M (swap: 0B)