https://launchpad.net/ubuntu/+source/gatk-bwamem/1.0.4+dfsg2-3/+build/28283393 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-106 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu20.04.1 python3-lpbuildd_237~660~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 3 May 02:11:20 ntpdate[1840]: adjust time server 10.131.248.1 offset 0.000425 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28283393 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-28283393 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28283393 Starting target for build PACKAGEBUILD-28283393 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28283393 'deb http://ftpmaster.internal/ubuntu oracular main universe' 'deb http://ftpmaster.internal/ubuntu oracular-security main universe' 'deb http://ftpmaster.internal/ubuntu oracular-updates main universe' 'deb http://ftpmaster.internal/ubuntu oracular-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-28283393 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28283393 Updating target for build PACKAGEBUILD-28283393 Get:1 http://ftpmaster.internal/ubuntu oracular InRelease [64.6 kB] Get:2 http://ftpmaster.internal/ubuntu oracular-security InRelease [64.6 kB] Get:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease [64.6 kB] Get:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 Packages [1401 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main Translation-en [512 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 Packages [15.3 MB] Get:8 http://ftpmaster.internal/ubuntu oracular/universe Translation-en [5980 kB] Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [99.9 kB] Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/main Translation-en [34.1 kB] Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [242 kB] Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe Translation-en [81.6 kB] Fetched 23.9 MB in 2s (9797 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30* libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages will be upgraded: advancecomp apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10 libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libisl23 libitm1 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin liblockfile1 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libncursesw6 libnsl-dev libnsl2 libnss-nis libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng passwd patch perl perl-base pinentry-curses procps psmisc readline-common rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 177 upgraded, 23 newly installed, 14 to remove and 0 not upgraded. Need to get 121 MB of archives. After this operation, 78.3 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B] Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1build1 [193 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libnsl-dev amd64 1.3.0-3build3 [70.5 kB] Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libnsl2 amd64 1.3.0-3build3 [41.4 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1build1 [82.6 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libgssapi-krb5-2 amd64 1.20.1-6ubuntu2 [142 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libkrb5-3 amd64 1.20.1-6ubuntu2 [347 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 libk5crypto3 amd64 1.20.1-6ubuntu2 [81.7 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libkrb5support0 amd64 1.20.1-6ubuntu2 [33.5 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 libacl1 amd64 2.3.2-1build1 [16.8 kB] Get:11 http://ftpmaster.internal/ubuntu oracular/main amd64 libapparmor1 amd64 4.0.0-beta3-0ubuntu3 [49.5 kB] Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libaudit-common all 1:3.1.2-2.1build1 [5736 B] Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libcap-ng0 amd64 0.8.4-2build2 [15.2 kB] Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libaudit1 amd64 1:3.1.2-2.1build1 [46.9 kB] Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libblkid1 amd64 2.39.3-9ubuntu6 [123 kB] Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libcap2 amd64 1:2.66-5ubuntu2 [30.0 kB] Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 libcrypt-dev amd64 1:4.4.36-4build1 [112 kB] Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 libcrypt1 amd64 1:4.4.36-4build1 [82.3 kB] Get:19 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpg-error-l10n all 1.47-3build2 [8064 B] Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpg-error0 amd64 1.47-3build2 [70.0 kB] Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcrypt20 amd64 1.10.3-2build1 [532 kB] Get:22 http://ftpmaster.internal/ubuntu oracular/main amd64 liblzma5 amd64 5.6.1+really5.4.5-1 [127 kB] Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 libzstd1 amd64 1.5.5+dfsg2-2build1 [299 kB] Get:24 http://ftpmaster.internal/ubuntu oracular/main amd64 libkmod2 amd64 31+20240202-2ubuntu7 [51.7 kB] Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 liblz4-1 amd64 1.9.4-1build1 [63.0 kB] Get:26 http://ftpmaster.internal/ubuntu oracular/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu2 [227 kB] Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 libselinux1 amd64 3.5-2ubuntu2 [79.6 kB] Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libmount1 amd64 2.39.3-9ubuntu6 [134 kB] Get:29 http://ftpmaster.internal/ubuntu oracular/main amd64 perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB] Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-7 [734 kB] Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdbm6t64 amd64 1.23-5.1build1 [34.4 kB] Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libgdbm-compat4t64 amd64 1.23-5.1build1 [6710 B] Get:33 http://ftpmaster.internal/ubuntu oracular/main amd64 libperl5.38t64 amd64 5.38.2-3.2build2 [4873 kB] Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 perl amd64 5.38.2-3.2build2 [231 kB] Get:35 http://ftpmaster.internal/ubuntu oracular/main amd64 perl-base amd64 5.38.2-3.2build2 [1823 kB] Get:36 http://ftpmaster.internal/ubuntu oracular/main amd64 liblocale-gettext-perl amd64 1.07-6ubuntu5 [15.8 kB] Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 libtext-iconv-perl amd64 1.7-8build3 [13.5 kB] Get:38 http://ftpmaster.internal/ubuntu oracular/main amd64 libtext-charwidth-perl amd64 0.04-11build3 [9358 B] Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnss-nisplus amd64 1.3-5build1 [22.4 kB] Get:40 http://ftpmaster.internal/ubuntu oracular/universe amd64 libnss-nis amd64 3.1-0ubuntu7 [26.5 kB] Get:41 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-dev-bin amd64 2.39-0ubuntu8.1 [20.4 kB] Get:42 http://ftpmaster.internal/ubuntu oracular/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu7 [67.4 kB] Get:43 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6-dev amd64 2.39-0ubuntu8.1 [2124 kB] Get:44 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc6 amd64 2.39-0ubuntu8.1 [3265 kB] Get:45 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libc-bin amd64 2.39-0ubuntu8.1 [682 kB] Get:46 http://ftpmaster.internal/ubuntu oracular/main amd64 openssl amd64 3.0.13-0ubuntu3 [1002 kB] Get:47 http://ftpmaster.internal/ubuntu oracular/main amd64 libsystemd-shared amd64 255.4-1ubuntu8 [2067 kB] Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 libcryptsetup12 amd64 2:2.7.0-1ubuntu4 [266 kB] Get:49 http://ftpmaster.internal/ubuntu oracular/main amd64 libssl3t64 amd64 3.0.13-0ubuntu3 [1936 kB] Get:50 http://ftpmaster.internal/ubuntu oracular/main amd64 systemd-dev all 255.4-1ubuntu8 [104 kB] Get:51 http://ftpmaster.internal/ubuntu oracular/main amd64 systemd-sysv amd64 255.4-1ubuntu8 [11.9 kB] Get:52 http://ftpmaster.internal/ubuntu oracular/main amd64 systemd amd64 255.4-1ubuntu8 [3471 kB] Get:53 http://ftpmaster.internal/ubuntu oracular/main amd64 libsystemd0 amd64 255.4-1ubuntu8 [429 kB] Get:54 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libapt-pkg6.0t64 amd64 2.9.2 [987 kB] Get:55 http://ftpmaster.internal/ubuntu oracular/main amd64 libnettle8t64 amd64 3.9.1-2.2build1 [182 kB] Get:56 http://ftpmaster.internal/ubuntu oracular/main amd64 libhogweed6t64 amd64 3.9.1-2.2build1 [199 kB] Get:57 http://ftpmaster.internal/ubuntu oracular/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu2 [299 kB] Get:58 http://ftpmaster.internal/ubuntu oracular/main amd64 libunistring5 amd64 1.1-2build1 [535 kB] Get:59 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libgnutls30t64 amd64 3.8.3-1.1ubuntu3.1 [998 kB] Get:60 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 apt amd64 2.9.2 [1403 kB] Get:61 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 apt-utils amd64 2.9.2 [223 kB] Get:62 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu1 [51.9 kB] Get:63 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-modules amd64 1.5.3-7ubuntu1 [284 kB] Get:64 http://ftpmaster.internal/ubuntu oracular/main amd64 bzip2 amd64 1.0.8-5.1 [34.5 kB] Get:65 http://ftpmaster.internal/ubuntu oracular/main amd64 libbz2-1.0 amd64 1.0.8-5.1 [34.3 kB] Get:66 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-14-base amd64 14-20240412-0ubuntu1 [47.6 kB] Get:67 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcc-s1 amd64 14-20240412-0ubuntu1 [78.5 kB] Get:68 http://ftpmaster.internal/ubuntu oracular/main amd64 libstdc++6 amd64 14-20240412-0ubuntu1 [795 kB] Get:69 http://ftpmaster.internal/ubuntu oracular/main amd64 libudev1 amd64 255.4-1ubuntu8 [174 kB] Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 libxxhash0 amd64 0.8.2-2build1 [24.1 kB] Get:71 http://ftpmaster.internal/ubuntu oracular/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu2 [62.8 kB] Get:72 http://ftpmaster.internal/ubuntu oracular/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2ubuntu6 [253 kB] Get:73 http://ftpmaster.internal/ubuntu oracular/main amd64 libffi8 amd64 3.4.6-1build1 [24.7 kB] Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 libidn2-0 amd64 2.3.7-2build1 [66.2 kB] Get:75 http://ftpmaster.internal/ubuntu oracular/main amd64 libtasn1-6 amd64 4.19.0-3build1 [43.9 kB] Get:76 http://ftpmaster.internal/ubuntu oracular/main amd64 libdebconfclient0 amd64 0.271ubuntu3 [11.4 kB] Get:77 http://ftpmaster.internal/ubuntu oracular/main amd64 base-passwd amd64 3.6.3build1 [51.1 kB] Get:78 http://ftpmaster.internal/ubuntu oracular/main amd64 libassuan0 amd64 2.5.6-1build1 [37.3 kB] Get:79 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libsqlite3-0 amd64 3.45.3-1 [701 kB] Get:80 http://ftpmaster.internal/ubuntu oracular/main amd64 gpg amd64 2.4.4-2ubuntu17 [565 kB] Get:81 http://ftpmaster.internal/ubuntu oracular/main amd64 libreadline8t64 amd64 8.2-4build1 [153 kB] Get:82 http://ftpmaster.internal/ubuntu oracular/main amd64 readline-common all 8.2-4build1 [56.5 kB] Get:83 http://ftpmaster.internal/ubuntu oracular/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu2 [148 kB] Get:84 http://ftpmaster.internal/ubuntu oracular/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu2 [108 kB] Get:85 http://ftpmaster.internal/ubuntu oracular/main amd64 gpg-agent amd64 2.4.4-2ubuntu17 [227 kB] Get:86 http://ftpmaster.internal/ubuntu oracular/main amd64 gpgconf amd64 2.4.4-2ubuntu17 [103 kB] Get:87 http://ftpmaster.internal/ubuntu oracular/main amd64 pinentry-curses amd64 1.2.1-3ubuntu5 [35.2 kB] Get:88 http://ftpmaster.internal/ubuntu oracular/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:89 http://ftpmaster.internal/ubuntu oracular/main amd64 libnpth0t64 amd64 1.6-3.1build1 [8378 B] Get:90 http://ftpmaster.internal/ubuntu oracular/main amd64 gpgv amd64 2.4.4-2ubuntu17 [157 kB] Get:91 http://ftpmaster.internal/ubuntu oracular/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:92 http://ftpmaster.internal/ubuntu oracular/main amd64 libseccomp2 amd64 2.5.5-1ubuntu3 [50.3 kB] Get:93 http://ftpmaster.internal/ubuntu oracular/main amd64 debconf-i18n all 1.5.86ubuntu1 [205 kB] Get:94 http://ftpmaster.internal/ubuntu oracular/main amd64 debconf all 1.5.86ubuntu1 [124 kB] Get:95 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam0g amd64 1.5.3-7ubuntu1 [67.8 kB] Get:96 http://ftpmaster.internal/ubuntu oracular/main amd64 libargon2-1 amd64 0~20190702+dfsg-4build1 [20.8 kB] Get:97 http://ftpmaster.internal/ubuntu oracular/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu3 [139 kB] Get:98 http://ftpmaster.internal/ubuntu oracular/main amd64 libjson-c5 amd64 0.17-1build1 [35.3 kB] Get:99 http://ftpmaster.internal/ubuntu oracular/main amd64 libuuid1 amd64 2.39.3-9ubuntu6 [35.2 kB] Get:100 http://ftpmaster.internal/ubuntu oracular/main amd64 libfdisk1 amd64 2.39.3-9ubuntu6 [146 kB] Get:101 http://ftpmaster.internal/ubuntu oracular/main amd64 mount amd64 2.39.3-9ubuntu6 [118 kB] Get:102 http://ftpmaster.internal/ubuntu oracular/main amd64 libcom-err2 amd64 1.47.0-2.4~exp1ubuntu4 [22.8 kB] Get:103 http://ftpmaster.internal/ubuntu oracular/main amd64 libkeyutils1 amd64 1.6.3-3build1 [9490 B] Get:104 http://ftpmaster.internal/ubuntu oracular/main amd64 linux-libc-dev amd64 6.8.0-31.31 [1598 kB] Get:105 http://ftpmaster.internal/ubuntu oracular/main amd64 base-files amd64 13.1ubuntu1 [73.8 kB] Get:106 http://ftpmaster.internal/ubuntu oracular/main amd64 debianutils amd64 5.17build1 [89.9 kB] Get:107 http://ftpmaster.internal/ubuntu oracular/main amd64 bash amd64 5.2.21-2ubuntu4 [794 kB] Get:108 http://ftpmaster.internal/ubuntu oracular/main amd64 bsdutils amd64 1:2.39.3-9ubuntu6 [95.0 kB] Get:109 http://ftpmaster.internal/ubuntu oracular/main amd64 coreutils amd64 9.4-3ubuntu6 [1412 kB] Get:110 http://ftpmaster.internal/ubuntu oracular/main amd64 tar amd64 1.35+dfsg-3build1 [253 kB] Get:111 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 dpkg amd64 1.22.6ubuntu10 [1283 kB] Get:112 http://ftpmaster.internal/ubuntu oracular/main amd64 dash amd64 0.5.12-6ubuntu5 [89.8 kB] Get:113 http://ftpmaster.internal/ubuntu oracular/main amd64 diffutils amd64 1:3.10-1build1 [177 kB] Get:114 http://ftpmaster.internal/ubuntu oracular/main amd64 findutils amd64 4.9.0-5build1 [298 kB] Get:115 http://ftpmaster.internal/ubuntu oracular/main amd64 grep amd64 3.11-4build1 [162 kB] Get:116 http://ftpmaster.internal/ubuntu oracular/main amd64 gzip amd64 1.12-1ubuntu3 [98.8 kB] Get:117 http://ftpmaster.internal/ubuntu oracular/main amd64 hostname amd64 3.23+nmu2ubuntu2 [11.1 kB] Get:118 http://ftpmaster.internal/ubuntu oracular/main amd64 login amd64 1:4.13+dfsg1-4ubuntu3 [202 kB] Get:119 http://ftpmaster.internal/ubuntu oracular/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu2 [188 kB] Get:120 http://ftpmaster.internal/ubuntu oracular/main amd64 sed amd64 4.9-2build1 [193 kB] Get:121 http://ftpmaster.internal/ubuntu oracular/main amd64 util-linux amd64 2.39.3-9ubuntu6 [1127 kB] Get:122 http://ftpmaster.internal/ubuntu oracular/main amd64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB] Get:123 http://ftpmaster.internal/ubuntu oracular/main amd64 sysvinit-utils amd64 3.08-6ubuntu3 [34.2 kB] Get:124 http://ftpmaster.internal/ubuntu oracular/main amd64 logsave amd64 1.47.0-2.4~exp1ubuntu4 [22.5 kB] Get:125 http://ftpmaster.internal/ubuntu oracular/main amd64 libext2fs2t64 amd64 1.47.0-2.4~exp1ubuntu4 [222 kB] Get:126 http://ftpmaster.internal/ubuntu oracular/main amd64 e2fsprogs amd64 1.47.0-2.4~exp1ubuntu4 [601 kB] Get:127 http://ftpmaster.internal/ubuntu oracular/main amd64 optipng amd64 0.7.8+ds-1build2 [110 kB] Get:128 http://ftpmaster.internal/ubuntu oracular/main amd64 libpng16-16t64 amd64 1.6.43-5build1 [187 kB] Get:129 http://ftpmaster.internal/ubuntu oracular/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:130 http://ftpmaster.internal/ubuntu oracular/main amd64 libsmartcols1 amd64 2.39.3-9ubuntu6 [64.8 kB] Get:131 http://ftpmaster.internal/ubuntu oracular/main amd64 uuid-runtime amd64 2.39.3-9ubuntu6 [33.1 kB] Get:132 http://ftpmaster.internal/ubuntu oracular/main amd64 libattr1 amd64 1:2.5.2-1build1 [11.3 kB] Get:133 http://ftpmaster.internal/ubuntu oracular/main amd64 libmd0 amd64 1.1.0-2build1 [27.0 kB] Get:134 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libpam-runtime all 1.5.3-7ubuntu1 [40.8 kB] Get:135 http://ftpmaster.internal/ubuntu oracular/main amd64 libsemanage-common all 3.5-1build5 [10.1 kB] Get:136 http://ftpmaster.internal/ubuntu oracular/main amd64 libsepol2 amd64 3.5-2build1 [303 kB] Get:137 http://ftpmaster.internal/ubuntu oracular/main amd64 libsemanage2 amd64 3.5-1build5 [93.2 kB] Get:138 http://ftpmaster.internal/ubuntu oracular/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu3 [845 kB] Get:139 http://ftpmaster.internal/ubuntu oracular/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu3 [59.1 kB] Get:140 http://ftpmaster.internal/ubuntu oracular/main amd64 libss2 amd64 1.47.0-2.4~exp1ubuntu4 [17.0 kB] Get:141 http://ftpmaster.internal/ubuntu oracular/main amd64 mawk amd64 1.3.4.20240123-1build1 [127 kB] Get:142 http://ftpmaster.internal/ubuntu oracular/main amd64 procps amd64 2:4.0.4-4ubuntu3 [708 kB] Get:143 http://ftpmaster.internal/ubuntu oracular/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:144 http://ftpmaster.internal/ubuntu oracular/main amd64 ca-certificates all 20240203 [159 kB] Get:145 http://ftpmaster.internal/ubuntu oracular/main amd64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB] Get:146 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 tzdata all 2024a-4ubuntu1 [274 kB] Get:147 http://ftpmaster.internal/ubuntu oracular/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:148 http://ftpmaster.internal/ubuntu oracular/main amd64 bsdextrautils amd64 2.39.3-9ubuntu6 [73.8 kB] Get:149 http://ftpmaster.internal/ubuntu oracular/main amd64 libgpm2 amd64 1.20.7-11 [14.1 kB] Get:150 http://ftpmaster.internal/ubuntu oracular/main amd64 libip4tc2 amd64 1.8.10-3ubuntu2 [23.3 kB] Get:151 http://ftpmaster.internal/ubuntu oracular/main amd64 libjansson4 amd64 2.14-2build2 [32.8 kB] Get:152 http://ftpmaster.internal/ubuntu oracular/main amd64 psmisc amd64 23.7-1build1 [179 kB] Get:153 http://ftpmaster.internal/ubuntu oracular/main amd64 xz-utils amd64 5.6.1+really5.4.5-1 [267 kB] Get:154 http://ftpmaster.internal/ubuntu oracular/main amd64 advancecomp amd64 2.5-1build1 [182 kB] Get:155 http://ftpmaster.internal/ubuntu oracular/main amd64 libgprofng0 amd64 2.42-4ubuntu2 [851 kB] Get:156 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf0 amd64 2.42-4ubuntu2 [94.5 kB] Get:157 http://ftpmaster.internal/ubuntu oracular/main amd64 libctf-nobfd0 amd64 2.42-4ubuntu2 [97.1 kB] Get:158 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-x86-64-linux-gnu amd64 2.42-4ubuntu2 [2469 kB] Get:159 http://ftpmaster.internal/ubuntu oracular/main amd64 libbinutils amd64 2.42-4ubuntu2 [572 kB] Get:160 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils amd64 2.42-4ubuntu2 [18.0 kB] Get:161 http://ftpmaster.internal/ubuntu oracular/main amd64 binutils-common amd64 2.42-4ubuntu2 [239 kB] Get:162 http://ftpmaster.internal/ubuntu oracular/main amd64 libsframe1 amd64 2.42-4ubuntu2 [14.8 kB] Get:163 http://ftpmaster.internal/ubuntu oracular/main amd64 libubsan1 amd64 14-20240412-0ubuntu1 [1175 kB] Get:164 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-13 amd64 13.2.0-23ubuntu4 [14.5 kB] Get:165 http://ftpmaster.internal/ubuntu oracular/main amd64 libstdc++-13-dev amd64 13.2.0-23ubuntu4 [2399 kB] Get:166 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14-20240412-0ubuntu1 [147 kB] Get:167 http://ftpmaster.internal/ubuntu oracular/main amd64 libitm1 amd64 14-20240412-0ubuntu1 [28.9 kB] Get:168 http://ftpmaster.internal/ubuntu oracular/main amd64 libatomic1 amd64 14-20240412-0ubuntu1 [10.4 kB] Get:169 http://ftpmaster.internal/ubuntu oracular/main amd64 libasan8 amd64 14-20240412-0ubuntu1 [3024 kB] Get:170 http://ftpmaster.internal/ubuntu oracular/main amd64 liblsan0 amd64 14-20240412-0ubuntu1 [1313 kB] Get:171 http://ftpmaster.internal/ubuntu oracular/main amd64 libhwasan0 amd64 14-20240412-0ubuntu1 [1632 kB] Get:172 http://ftpmaster.internal/ubuntu oracular/main amd64 libquadmath0 amd64 14-20240412-0ubuntu1 [153 kB] Get:173 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13 amd64 13.2.0-23ubuntu4 [482 kB] Get:174 http://ftpmaster.internal/ubuntu oracular/main amd64 libgcc-13-dev amd64 13.2.0-23ubuntu4 [2688 kB] Get:175 http://ftpmaster.internal/ubuntu oracular/main amd64 libtsan2 amd64 14-20240412-0ubuntu1 [2736 kB] Get:176 http://ftpmaster.internal/ubuntu oracular/main amd64 libcc1-0 amd64 14-20240412-0ubuntu1 [47.7 kB] Get:177 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-13 amd64 13.2.0-23ubuntu4 [1032 B] Get:178 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13-base amd64 13.2.0-23ubuntu4 [49.0 kB] Get:179 http://ftpmaster.internal/ubuntu oracular/main amd64 libisl23 amd64 0.26-3build1 [680 kB] Get:180 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpfr6 amd64 4.2.1-1build1 [355 kB] Get:181 http://ftpmaster.internal/ubuntu oracular/main amd64 libmpc3 amd64 1.3.1-1build1 [54.5 kB] Get:182 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [21.9 MB] Get:183 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [12.5 MB] Get:184 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-23ubuntu4 [11.2 MB] Get:185 http://ftpmaster.internal/ubuntu oracular/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:186 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:187 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:188 http://ftpmaster.internal/ubuntu oracular/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:189 http://ftpmaster.internal/ubuntu oracular/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:190 http://ftpmaster.internal/ubuntu oracular/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:191 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 dpkg-dev all 1.22.6ubuntu10 [1074 kB] Get:192 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 libdpkg-perl all 1.22.6ubuntu10 [269 kB] Get:193 http://ftpmaster.internal/ubuntu oracular/main amd64 patch amd64 2.7.6-7build3 [104 kB] Get:194 http://ftpmaster.internal/ubuntu oracular/main amd64 make amd64 4.3-4.1build2 [180 kB] Get:195 http://ftpmaster.internal/ubuntu oracular/main amd64 lto-disabled-list all 47 [12.4 kB] Get:196 http://ftpmaster.internal/ubuntu oracular/main amd64 libfakeroot amd64 1.34-1 [32.4 kB] Get:197 http://ftpmaster.internal/ubuntu oracular/main amd64 fakeroot amd64 1.34-1 [67.2 kB] Get:198 http://ftpmaster.internal/ubuntu oracular/main amd64 liblockfile-bin amd64 1.17-1build3 [11.2 kB] Get:199 http://ftpmaster.internal/ubuntu oracular/main amd64 liblockfile1 amd64 1.17-1build3 [6840 B] Get:200 http://ftpmaster.internal/ubuntu oracular/main amd64 lockfile-progs amd64 0.1.19build2 [8522 B] Preconfiguring packages ... 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Setting up libctf0:amd64 (2.42-4ubuntu2) ... Setting up pinentry-curses (1.2.1-3ubuntu5) ... Setting up cpp-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... Setting up debconf-i18n (1.5.86ubuntu1) ... Setting up e2fsprogs (1.47.0-2.4~exp1ubuntu4) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 5 removed; done. Setting up perl (5.38.2-3.2build2) ... Setting up libgprofng0:amd64 (2.42-4ubuntu2) ... Setting up optipng (0.7.8+ds-1build2) ... Setting up lockfile-progs (0.1.19build2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6ubuntu2) ... Setting up libdpkg-perl (1.22.6ubuntu10) ... Setting up libreadline8t64:amd64 (8.2-4build1) ... Setting up libgcc-13-dev:amd64 (13.2.0-23ubuntu4) ... Setting up gpgconf (2.4.4-2ubuntu17) ... Setting up libc6-dev:amd64 (2.39-0ubuntu8.1) ... Setting up gpg (2.4.4-2ubuntu17) ... Setting up libstdc++-13-dev:amd64 (13.2.0-23ubuntu4) ... Setting up binutils-x86-64-linux-gnu (2.42-4ubuntu2) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up gpg-agent (2.4.4-2ubuntu17) ... Setting up cpp-13 (13.2.0-23ubuntu4) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.1build1) ... Setting up gcc-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... Setting up binutils (2.42-4ubuntu2) ... Setting up dpkg-dev (1.22.6ubuntu10) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.1build1) ... Setting up gcc-13 (13.2.0-23ubuntu4) ... Setting up cpp (4:13.2.0-7ubuntu1) ... Setting up libnsl2:amd64 (1.3.0-3build3) ... Setting up g++-13-x86-64-linux-gnu (13.2.0-23ubuntu4) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up libnss-nisplus:amd64 (1.3-5build1) ... Setting up gcc (4:13.2.0-7ubuntu1) ... Setting up libnss-nis:amd64 (3.1-0ubuntu7) ... Setting up libnsl-dev:amd64 (1.3.0-3build3) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... Setting up g++-13 (13.2.0-23ubuntu4) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for debianutils (5.17build1) ... (Reading database ... 15825 files and directories currently installed.) Purging configuration files for libssl3:amd64 (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28283393 amd64 oracular-proposed -c chroot:build-PACKAGEBUILD-28283393 --arch=amd64 --dist=oracular-proposed --nolog -A gatk-bwamem_1.0.4+dfsg2-3.dsc Initiating build PACKAGEBUILD-28283393 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-106.buildd +==============================================================================+ | gatk-bwamem 1.0.4+dfsg2-3 (amd64) Fri, 03 May 2024 02:11:52 +0000 | +==============================================================================+ Package: gatk-bwamem Version: 1.0.4+dfsg2-3 Source Version: 1.0.4+dfsg2-3 Distribution: oracular-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28283393/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/gatk-bwamem-vuD86M/resolver-BFCABY' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gatk-bwamem_1.0.4+dfsg2-3.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/gatk-bwamem-vuD86M/gatk-bwamem-1.0.4+dfsg2' with '<>' I: NOTICE: Log filtering will replace 'build/gatk-bwamem-vuD86M' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), default-jdk-headless, gradle-debian-helper, libsimde-dev, maven-repo-helper, testng, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), default-jdk-headless, gradle-debian-helper, libsimde-dev, maven-repo-helper, testng, zlib1g-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [431 B] Get:5 copy:/<>/apt_archive ./ Packages [503 B] Fetched 1891 B in 0s (181 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libgssapi-krb5-2 libip4tc2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: ant ant-optional antlr autoconf automake autopoint autotools-dev bnd ca-certificates-java debhelper debugedit default-jdk-headless default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gradle gradle-debian-helper groff-base groovy intltool-debian ivy java-common java-wrappers junit4 libantlr-java libaopalliance-java libapache-pom-java libarchive-zip-perl libasm-java libatinject-jsr330-api-java libbcel-java libbcpg-java libbcprov-java libbsf-java libbsh-java libcdi-api-java libcommons-cli-java libcommons-codec-java libcommons-collections3-java libcommons-compress-java libcommons-io-java libcommons-lang-java libcommons-lang3-java libcommons-logging-java libcommons-parent-java libdd-plist-java libdebhelper-perl libdom4j-java libdw1t64 libeclipse-jdt-annotation-java libel-api-java libelf1t64 liberror-prone-java libfelix-framework-java libfelix-gogo-runtime-java libfelix-resolver-java libfile-stripnondeterminism-perl libfindbugs-java libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgoogle-gson-java libgradle-core-java libgradle-plugins-java libguava-java libguice-java libhamcrest-java libhawtjni-runtime-java libhttpclient-java libhttpcore-java libicu74 libjansi-java libjansi-native-java libjansi1-java libjarjar-java libjatl-java libjavaewah-java libjaxen-java libjcifs-java libjcip-annotations-java libjcommander-java libjetty9-java libjformatstring-java libjgit-java libjline2-java libjna-java libjna-jni libjpeg-turbo8 libjpeg8 libjs-jquery libjsch-java libjsoup-java libjsp-api-java libjsr305-java libjzlib-java libkryo-java liblcms2-2 liblogback-java libmagic-mgc libmagic1t64 libmaven-parent-java libmaven-resolver-java libmaven-shared-utils-java libmaven3-core-java libminlog-java libnative-platform-java libnative-platform-jni libnekohtml-java libnspr4 libnss3 libobjenesis-java libosgi-annotation-java libosgi-compendium-java libosgi-core-java libpcsclite1 libpipeline1 libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-container-default-java libplexus-interpolation-java libplexus-sec-dispatcher-java libplexus-utils2-java libpolyglot-maven-java libqdox-java libreflectasm-java librhino-java libservlet-api-java libsimde-dev libsimple-http-java libsisu-inject-java libsisu-plexus-java libslf4j-java libsub-override-perl libtool libuchardet0 libwagon-file-java libwagon-http-java libwagon-provider-api-java libwebsocket-api-java libxbean-reflect-java libxerces2-java libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxpp3-java libxstream-java libxz-java libyaml-snake-java m4 man-db maven-repo-helper openjdk-21-jdk-headless openjdk-21-jre-headless po-debconf testng unzip zlib1g-dev Suggested packages: ant-doc javacc junit jython libactivation-java libcommons-net-java libmail-java libjaxp1.3-java libjdepend-java liblog4j1.2-java liboro-java libregexp-java libxalan2-java autoconf-archive gnu-standards autoconf-doc dh-make default-jre gettext-doc libasprintf-dev libgettextpo-dev gradle-doc groff groovy-doc default-jre | java2-runtime ivy-doc libjsch-agent-proxy-java libatinject-jsr330-api-java-doc libbcel-java-doc bsh rhino libcommons-collections3-java-doc libcommons-io-java-doc libcommons-lang-java-doc libavalon-framework-java libexcalibur-logkit-java libmsv-java libxpp2-java libfelix-framework-java-doc libfelix-gogo-runtime-java-doc libgoogle-gson-java-doc libcglib-java libjdom1-java libxom-java libjcifs-java-doc libjcommander-java-doc jetty9 libjsoup-java-doc libjsr305-java-doc liblcms2-utils libjanino-java libtomcat9-java libmaven-shared-utils-java-doc libnative-platform-java-doc libnekohtml-java-doc libosgi-annotation-java-doc libosgi-compendium-java-doc libosgi-core-java-doc pcscd libplexus-utils2-java-doc libpolyglot-maven-java-doc libqdox-java-doc libsimple-http-java-doc libtool-doc gfortran | fortran95-compiler gcj-jdk libxerces2-java-doc libxml-commons-resolver1.1-java-doc libcglib-nodep-java libjdom2-java libjettison-java libjoda-time-java libkxml2-java m4-doc apparmor less www-browser maven-debian-helper openjdk-21-demo openjdk-21-source libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic libmail-box-perl zip Recommended packages: libbindex-java curl | wget | lynx libgpars-groovy-java libarchive-cpio-perl javascript-common libreflectasm-java-doc libltdl-dev libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b libasound2t64 libmail-sendmail-perl The following NEW packages will be installed: ant ant-optional antlr autoconf automake autopoint autotools-dev bnd ca-certificates-java debhelper debugedit default-jdk-headless default-jre-headless dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base gradle gradle-debian-helper groff-base groovy intltool-debian ivy java-common java-wrappers junit4 libantlr-java libaopalliance-java libapache-pom-java libarchive-zip-perl libasm-java libatinject-jsr330-api-java libbcel-java libbcpg-java libbcprov-java libbsf-java libbsh-java libcdi-api-java libcommons-cli-java libcommons-codec-java libcommons-collections3-java libcommons-compress-java libcommons-io-java libcommons-lang-java libcommons-lang3-java libcommons-logging-java libcommons-parent-java libdd-plist-java libdebhelper-perl libdom4j-java libdw1t64 libeclipse-jdt-annotation-java libel-api-java libelf1t64 liberror-prone-java libfelix-framework-java libfelix-gogo-runtime-java libfelix-resolver-java libfile-stripnondeterminism-perl libfindbugs-java libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgoogle-gson-java libgradle-core-java libgradle-plugins-java libguava-java libguice-java libhamcrest-java libhawtjni-runtime-java libhttpclient-java libhttpcore-java libicu74 libjansi-java libjansi-native-java libjansi1-java libjarjar-java libjatl-java libjavaewah-java libjaxen-java libjcifs-java libjcip-annotations-java libjcommander-java libjetty9-java libjformatstring-java libjgit-java libjline2-java libjna-java libjna-jni libjpeg-turbo8 libjpeg8 libjs-jquery libjsch-java libjsoup-java libjsp-api-java libjsr305-java libjzlib-java libkryo-java liblcms2-2 liblogback-java libmagic-mgc libmagic1t64 libmaven-parent-java libmaven-resolver-java libmaven-shared-utils-java libmaven3-core-java libminlog-java libnative-platform-java libnative-platform-jni libnekohtml-java libnspr4 libnss3 libobjenesis-java libosgi-annotation-java libosgi-compendium-java libosgi-core-java libpcsclite1 libpipeline1 libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-container-default-java libplexus-interpolation-java libplexus-sec-dispatcher-java libplexus-utils2-java libpolyglot-maven-java libqdox-java libreflectasm-java librhino-java libservlet-api-java libsimde-dev libsimple-http-java libsisu-inject-java libsisu-plexus-java libslf4j-java libsub-override-perl libtool libuchardet0 libwagon-file-java libwagon-http-java libwagon-provider-api-java libwebsocket-api-java libxbean-reflect-java libxerces2-java libxml-commons-external-java libxml-commons-resolver1.1-java libxml2 libxpp3-java libxstream-java libxz-java libyaml-snake-java m4 man-db maven-repo-helper openjdk-21-jdk-headless openjdk-21-jre-headless po-debconf sbuild-build-depends-main-dummy testng unzip zlib1g-dev 0 upgraded, 162 newly installed, 0 to remove and 0 not upgraded. Need to get 227 MB of archives. After this operation, 498 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [718 B] Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libelf1t64 amd64 0.190-1.1build4 [57.6 kB] Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libicu74 amd64 74.2-1ubuntu3 [10.9 MB] Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libxml2 amd64 2.9.14+dfsg-1.3ubuntu3 [762 kB] Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libmagic-mgc amd64 1:5.45-3build1 [307 kB] Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libmagic1t64 amd64 1:5.45-3build1 [87.2 kB] Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 file amd64 1:5.45-3build1 [22.0 kB] Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 gettext-base amd64 0.21-14ubuntu2 [38.4 kB] Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 libuchardet0 amd64 0.0.8-1build1 [75.3 kB] Get:10 http://ftpmaster.internal/ubuntu oracular/main amd64 groff-base amd64 1.23.0-3build2 [1020 kB] Get:11 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http://ftpmaster.internal/ubuntu oracular/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1ubuntu2 [894 kB] Preconfiguring packages ... 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Setting up libplexus-utils2-java (3.4.2-1) ... Setting up libplexus-classworlds-java (2.7.0-1) ... Setting up libqdox-java (1.12.1-3) ... Setting up libjsr305-java (0.1~+svn49-11) ... Setting up libsimple-http-java (4.1.21-1.1fakesync1) ... Setting up java-common (0.75+exp1) ... Setting up libjcip-annotations-java (20060626-6) ... Setting up libobjenesis-java (3.3-3) ... Setting up libaopalliance-java (20070526-7) ... Setting up libcommons-cli-java (1.6.0-1) ... Setting up libmagic-mgc (1:5.45-3build1) ... Setting up liblogback-java (1:1.2.11-5) ... Setting up libminlog-java (1.3.0-1.1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libgoogle-gson-java (2.10.1-1) ... Setting up unzip (6.0-28ubuntu4) ... Setting up libdebhelper-perl (13.14.1ubuntu5) ... Setting up libmagic1t64:amd64 (1:5.45-3build1) ... Setting up libasm-java (9.7-1) ... Setting up libdd-plist-java (1.20-1.1) ... Setting up gettext-base (0.21-14ubuntu2) ... Setting up m4 (1.4.19-4build1) ... Setting up libel-api-java (3.0.0-3) ... Setting up libplexus-component-annotations-java (2.1.1-1) ... Setting up file (1:5.45-3build1) ... Setting up libpolyglot-maven-java (0.8~tobrien+git20120905-10) ... Setting up libfelix-gogo-runtime-java (0.16.2-1.1) ... Setting up libjzlib-java (1.1.3-3) ... Setting up libelf1t64:amd64 (0.190-1.1build4) ... Setting up libdw1t64:amd64 (0.190-1.1build4) ... Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... Setting up libgeronimo-interceptor-3.0-spec-java (1.0.1-4fakesync) ... Setting up libcommons-collections3-java (3.2.2-3) ... Setting up libjsch-java (0.1.55-1) ... Setting up libreflectasm-java (1.11.9+dfsg-4) ... Setting up librhino-java (1.7.14-2.1) ... Setting up autotools-dev (20220109.1) ... Setting up libbsf-java (1:2.4.0-8) ... Setting up libosgi-annotation-java (8.1.0-1) ... Setting up libjformatstring-java (0.10~20131207-2.1) ... Setting up libjavaewah-java (1.2.3-1) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libnspr4:amd64 (2:4.35-1.1build1) ... Setting up libeclipse-jdt-annotation-java (2.2.700+eclipse4.26-2) ... Setting up libjansi-java (2.4.1-2) ... Setting up libapache-pom-java (29-2) ... Setting up libxpp3-java (1.1.4c-3) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libwebsocket-api-java (1.1-2) ... Setting up libplexus-interpolation-java (1.26-1) ... Setting up libxml-commons-resolver1.1-java (1.2-11) ... Setting up libkryo-java (2.20-7) ... Setting up libxz-java (1.9-1) ... Setting up libjna-jni (5.14.0-1) ... Setting up autopoint (0.21-14ubuntu2) ... Setting up libfelix-framework-java (4.6.1-2.1) ... Setting up libpcsclite1:amd64 (2.0.3-1build1) ... Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu2) ... Setting up libhamcrest-java (2.2-2) ... Setting up libbsh-java (2.0b4-20) ... Setting up libjsp-api-java (2.3.4-3) ... Setting up autoconf (2.71-3) ... Setting up libicu74:amd64 (74.2-1ubuntu3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1ubuntu2) ... Setting up libjarjar-java (1.4+svn142-12) ... Setting up dwz (0.15-1build6) ... Setting up libjsoup-java (1.15.3-1) ... Setting up libuchardet0:amd64 (0.0.8-1build1) ... Setting up libxml-commons-external-java (1.4.01-6) ... Setting up libjna-java (5.14.0-1) ... Setting up libxbean-reflect-java (4.5-8) ... Setting up libservlet-api-java (4.0.1-2) ... Setting up debugedit (1:5.0-5build2) ... Setting up libsub-override-perl (0.10-1) ... Setting up libnative-platform-jni (0.14-6) ... Setting up libhttpcore-java (4.4.16-1) ... Setting up libbcpg-java (1.77-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libxerces2-java (2.12.2-1) ... Setting up libantlr-java (2.7.7+dfsg-13build1) ... Setting up libyaml-snake-java (1.33-2) ... Setting up libcdi-api-java (1.2-3) ... Setting up libhawtjni-runtime-java (1.18-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3ubuntu3) ... Setting up libjatl-java (0.2.3-1.1) ... Setting up libjpeg8:amd64 (8c-2ubuntu11) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libdom4j-java (2.1.4-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libwagon-provider-api-java (3.5.3-1) ... Setting up libnative-platform-java (0.14-6) ... Setting up libosgi-core-java (8.0.0-2) ... Setting up libxstream-java (1.4.20-1) ... Setting up libnekohtml-java (1.9.22.noko2-0.1) ... Setting up gettext (0.21-14ubuntu2) ... Setting up libjetty9-java (9.4.53-1) ... Setting up java-wrappers (0.4) ... Setting up libosgi-compendium-java (7.0.0-1) ... Setting up libtool (2.4.7-7build1) ... Setting up libmaven-parent-java (35-1) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.3.0-1ubuntu1) ... Setting up libsisu-inject-java (0.3.4-2) ... Setting up libnss3:amd64 (2:3.98-1build1) ... Setting up libcommons-lang-java (2.6-10) ... Setting up libplexus-cipher-java (2.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libsisu-plexus-java (0.3.4-3) ... Setting up libbcel-java (6.5.0-2) ... Setting up testng (6.9.12-4) ... Setting up libcommons-lang3-java (3.14.0-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libfelix-resolver-java (1.16.0-1) ... Setting up libjansi-native-java (1.8-2) ... Setting up groff-base (1.23.0-3build2) ... Setting up libjansi1-java (1.18-3ubuntu1) ... Setting up libplexus-sec-dispatcher-java (2.0-3) ... Setting up libwagon-file-java (3.5.3-1) ... Setting up libcommons-codec-java (1.16.0-1) ... Setting up libjline2-java (2.14.6-5) ... Setting up libfindbugs-java (3.1.0~preview2-3) ... Setting up openjdk-21-jre-headless:amd64 (21.0.3+9-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libcommons-compress-java (1.25.0-1) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-4build2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up libmaven-resolver-java (1.6.3-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up libwagon-http-java (3.5.3-1) ... Setting up libmaven-shared-utils-java (3.3.4-1) ... Setting up libjgit-java (4.11.9-2) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libplexus-container-default-java (2.1.1-1) ... Setting up libguice-java (4.2.3-2) ... Setting up libmaven3-core-java (3.8.7-2) ... Processing triggers for libc-bin (2.39-0ubuntu8.1) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up antlr (2.7.7+dfsg-13build1) ... Setting up ivy (2.5.2-1) ... Setting up ant (1.10.14-1) ... Setting up junit4 (4.13.2-4) ... Setting up groovy (2.4.21-10) ... update-alternatives: using /usr/share/groovy/bin/groovy to provide /usr/bin/groovy (groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyc to provide /usr/bin/groovyc (groovyc) in auto mode update-alternatives: using /usr/share/groovy/bin/grape to provide /usr/bin/grape (grape) in auto mode update-alternatives: using /usr/share/groovy/bin/startGroovy to provide /usr/bin/startGroovy (startGroovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovysh to provide /usr/bin/groovysh (groovysh) in auto mode update-alternatives: using /usr/share/groovy/bin/java2groovy to provide /usr/bin/java2groovy (java2groovy) in auto mode update-alternatives: using /usr/share/groovy/bin/groovyConsole to provide /usr/bin/groovyConsole (groovyConsole) in auto mode update-alternatives: using /usr/share/groovy/bin/groovydoc to provide /usr/bin/groovydoc (groovydoc) in auto mode Setting up openjdk-21-jdk-headless:amd64 (21.0.3+9-1ubuntu1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-75+exp1) ... Setting up maven-repo-helper (1.11) ... Setting up ant-optional (1.10.14-1) ... Setting up bnd (5.0.1-5) ... Setting up default-jdk-headless (2:1.21-75+exp1) ... Setting up libgradle-core-java (4.4.1-20) ... Setting up libgradle-plugins-java (4.4.1-20) ... Setting up gradle (4.4.1-20) ... Setting up gradle-debian-helper (2.4) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-177-generic #197-Ubuntu SMP Thu Mar 28 22:45:47 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu10 g++-13_13.2.0-23ubuntu4 gcc-13_13.2.0-23ubuntu4 libc6-dev_2.39-0ubuntu8.1 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 linux-libc-dev_6.8.0-31.31 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 ant_1.10.14-1 ant-optional_1.10.14-1 antlr_2.7.7+dfsg-13build1 apt_2.9.2 apt-utils_2.9.2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13.1ubuntu1 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-x86-64-linux-gnu_2.42-4ubuntu2 bnd_5.0.1-5 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 ca-certificates-java_20240118 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu4 cpp-13-x86-64-linux-gnu_13.2.0-23ubuntu4 cpp-x86-64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 default-jdk-headless_2:1.21-75+exp1 default-jre-headless_2:1.21-75+exp1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu10 dpkg-dev_1.22.6ubuntu10 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.34-1 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xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2 zlib1g-dev_1:1.3.dfsg-3.1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gatk-bwamem Binary: libgatk-bwamem-java, libgatk-bwamem-jni Architecture: any all Version: 1.0.4+dfsg2-3 Maintainer: Debian Med Packaging Team Uploaders: Pierre Gruet Homepage: https://github.com/broadinstitute/gatk-bwamem-jni/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/gatk-bwamem Vcs-Git: https://salsa.debian.org/med-team/gatk-bwamem.git Build-Depends: debhelper-compat (= 13), default-jdk-headless, gradle-debian-helper, libsimde-dev, maven-repo-helper, testng , zlib1g-dev Package-List: libgatk-bwamem-java deb java optional arch=all libgatk-bwamem-jni deb java optional arch=any Checksums-Sha1: 514dfb2510d7c8d5d5f90707dc3f47dfeae7287b 144424 gatk-bwamem_1.0.4+dfsg2.orig-bwa-apache2.tar.xz c27d5ad7ee506407448891b75f3d155bd795dd47 21360 gatk-bwamem_1.0.4+dfsg2.orig.tar.xz afe41b692a607ca654338005ed13ef6f701c6aa4 10456 gatk-bwamem_1.0.4+dfsg2-3.debian.tar.xz Checksums-Sha256: 954d5d5aae624ce0faa4c9c3d30e91490dd93ce41b2205d84042c3391d35093a 144424 gatk-bwamem_1.0.4+dfsg2.orig-bwa-apache2.tar.xz 767c56d136ab24f1fc0511b4a5dcf927ba0028fa140c61e97da10dd57291d798 21360 gatk-bwamem_1.0.4+dfsg2.orig.tar.xz ce78146c4c6a08d9891e033c50bf88e60cda4d0ef7ea09f48fde28b97597fea0 10456 gatk-bwamem_1.0.4+dfsg2-3.debian.tar.xz Files: d0b90d3400ed4ccc469367c4dfbd9bca 144424 gatk-bwamem_1.0.4+dfsg2.orig-bwa-apache2.tar.xz ed2b395e5416b1bf2b6902acedd61c80 21360 gatk-bwamem_1.0.4+dfsg2.orig.tar.xz acf6ac69dcb09904bd5b12096e198075 10456 gatk-bwamem_1.0.4+dfsg2-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmYATxsACgkQPCZ2P2xn 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signature found dpkg-source: info: extracting gatk-bwamem in /<> dpkg-source: info: unpacking gatk-bwamem_1.0.4+dfsg2.orig.tar.xz dpkg-source: info: unpacking gatk-bwamem_1.0.4+dfsg2.orig-bwa-apache2.tar.xz dpkg-source: info: unpacking gatk-bwamem_1.0.4+dfsg2-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying build.patch dpkg-source: info: applying use_bwa_from_component.patch dpkg-source: info: applying fix_heap_block_overrun dpkg-source: info: applying fix_build_on_freebsd.patch dpkg-source: info: applying CVE-2019-10269.patch dpkg-source: info: applying simde dpkg-source: info: applying gcc10.patch dpkg-source: info: applying hurd dpkg-source: info: applying hardening.patch dpkg-source: info: applying missing_obj_files.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-28283393 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28283393 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-28283393 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package gatk-bwamem dpkg-buildpackage: info: source version 1.0.4+dfsg2-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with maven_repo_helper debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean sh -c "find . -wholename .*build/tmp | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" sh -c "find . -wholename .*build/debian | xargs echo | sed -e 's^build/tmp^build^g' | xargs rm -Rf" rm -Rf /<>/gatk-bwamem-1.0.4\+dfsg2/.gradle /<>/gatk-bwamem-1.0.4\+dfsg2/buildSrc/.gradle .m2 if [ -e src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c.save ]; then \ mv src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c.save src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c; \ fi rm src/test/resources/ref.fa.img rm: cannot remove 'src/test/resources/ref.fa.img': No such file or directory make[1]: [debian/rules:21: override_dh_auto_clean] Error 1 (ignored) # Cleaning the C part cd src/main/c/ && make clean make[2]: Entering directory '/<>/src/main/c' rm -rf bwaComponent *.o *.so make[2]: Leaving directory '/<>/src/main/c' rm -rf src/main/c/bwaComponent # Replacing the modified build.gradle file having a version number by the original one. if [ -e build.gradle.old ]; then mv build.gradle.old build.gradle; fi make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary --with maven_repo_helper dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' # Putting the version in the JNI file so that is can output version information. cp src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c.save sed -i "s/BWA_COMMIT/\"1.0.4+dfsg2-3\"/" src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c # Copying the component sources to src/main/c for the JNI build mkdir -p src/main/c/bwaComponent/ cp -a bwa-apache2/* src/main/c/bwaComponent/ # Adding a version number in the build.gradle file. cp build.gradle build.gradle.old sed -i "s/\(^group.*\)/\1\nversion = '1.0.4+dfsg2'/ ; s/\+dfsg[[:digit:]]*//" build.gradle dh_auto_configure make[1]: Leaving directory '/<>' dh_auto_build mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gatk-bwamem -Dfile.encoding=UTF-8 --parallel --max-workers=4 jar openjdk version "21.0.3" 2024-04-16 OpenJDK Runtime Environment (build 21.0.3+9-Ubuntu-1ubuntu1) OpenJDK 64-Bit Server VM (build 21.0.3+9-Ubuntu-1ubuntu1, mixed mode, sharing) Initialized native services in: /<>/.gradle/native To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /<>/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' An attempt to start the daemon took 0.542 secs. The client will now receive all logging from the daemon (pid: 12898). The daemon log file: /<>/.gradle/daemon/4.4.1/daemon-12898.out.log Daemon will be stopped at the end of the build stopping after processing Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Using 4 worker leases. Creating new cache for fileHashes, path /<>/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@7224dce2 Creating new cache for resourceHashesCache, path /<>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@7224dce2 Creating new cache for fileHashes, path /<>/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@2894dcd8 Starting Build Compiling initialization script '/<>/.gradle/init.d/init.gradle' using SubsetScriptTransformer. Creating new cache for metadata-1.1/results, path /<>/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@28d732ab Compiling initialization script '/<>/.gradle/init.d/init.gradle' using BuildScriptTransformer. Compiling settings file '/<>/settings.gradle' using SubsetScriptTransformer. Compiling settings file '/<>/settings.gradle' using BuildScriptTransformer. Settings evaluated using settings file '/<>/settings.gradle'. Projects loaded. Root project using build file '/<>/build.gradle'. Included projects: [root project 'gatk-bwamem-jni'] Keep-alive timer started Adding Debian repository to project 'gatk-bwamem-jni' Parallel execution is an incubating feature. Evaluating root project 'gatk-bwamem-jni' using build file '/<>/build.gradle'. Compiling build file '/<>/build.gradle' using SubsetScriptTransformer. Compiling build file '/<>/build.gradle' using BuildScriptTransformer. Adding Maven pom generation to project 'gatk-bwamem-jni' Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'jar' from project : Creating new cache for annotation-processors, path /<>/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@285a588b Tasks to be executed: [task ':compileJava', task ':buildBwaLib', task ':processResources', task ':classes', task ':debianMavenPom', task ':jar'] Creating new cache for resourceHashesCache, path /<>/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@2894dcd8 Creating new cache for taskHistory, path /<>/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@74254f0a Creating new cache for outputFiles, path /<>/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@33e33d9f :compileJava (Thread[#29,Daemon worker,5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.002 secs. Up-to-date check for task ':compileJava' took 0.015 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileJava'. Compiling with JDK Java compiler API. :compileJava (Thread[#29,Daemon worker,5,main]) completed. Took 0.745 secs. :buildBwaLib (Thread[#29,Daemon worker,5,main]) started. :buildBwaLib Putting task artifact state for task ':buildBwaLib' into context took 0.0 secs. Up-to-date check for task ':buildBwaLib' took 0.0 secs. It is not up-to-date because: No history is available. using /usr/lib/jvm/java-21-openjdk-amd64 -> /usr/lib/jvm/java-21-openjdk-amd64 as JAVA_HOME Starting process 'command 'make''. Working directory: /<>/src/main/c Command: make Successfully started process 'command 'make'' make[1]: Entering directory '/<>/src/main/c' gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -Wdate-time -D_FORTIFY_SOURCE=3 -c -o org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.o org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c gcc -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -Wdate-time -D_FORTIFY_SOURCE=3 -c -o jnibwa.o jnibwa.c make CFLAGS="-g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux" LDFLAGS="-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now" -C bwaComponent libbwa.a make[2]: Entering directory '/<>/src/main/c/bwaComponent' gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o rope.c: In function ‘rope_restore_node’: rope.c:282:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 282 | fread(&is_bottom, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:283:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 283 | fread(&n, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~~ rope.c:291:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 291 | fread(p[i].c, 8, 6, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c:292:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 292 | fread(q, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~ rope.c:293:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 293 | fread(q + 1, 1, *q, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c: In function ‘rope_restore’: rope.c:312:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 312 | fread(&r->max_nodes, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:313:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 313 | fread(&r->block_len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Wdate-time -D_FORTIFY_SOURCE=3 -c -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/gatk-bwamem-1.0.4+dfsg2-3 -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -ggdb -O2 -Wall -fPIC -I/usr/lib/jvm/java-21-openjdk-amd64/include -I/usr/lib/jvm/java-21-openjdk-amd64/include/linux -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o bwtindex.o is.o rope.o rle.o ar: `u' modifier ignored since `D' is the default (see `U') make[2]: Leaving directory '/<>/src/main/c/bwaComponent' gcc -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -ggdb -dynamiclib -shared -o libbwa.so org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.o jnibwa.o bwaComponent/libbwa.a -lm -lz -lpthread lto1: warning: unrecognized gcc debugging option: y lto1: warning: unrecognized gcc debugging option: n lto1: warning: unrecognized gcc debugging option: m lto1: warning: unrecognized gcc debugging option: i lto1: warning: unrecognized gcc debugging option: c lto1: warning: unrecognized gcc debugging option: l lto1: warning: unrecognized gcc debugging option: i lto1: warning: unrecognized gcc debugging option: b bwaComponent/bwamem.c:1204:21: warning: type of ‘kt_for’ does not match original declaration [-Wlto-type-mismatch] 1204 | extern void kt_for(int n_threads, void (*func)(void*,int,int), void *data, int n); | ^ bwaComponent/kthread.c:49:6: note: type mismatch in parameter 4 49 | void kt_for(int n_threads, void (*func)(void*,long,int), void *data, long n) | ^ bwaComponent/kthread.c:49:6: note: type ‘long int’ should match type ‘int’ bwaComponent/kthread.c:49:6: note: ‘kt_for’ was previously declared here bwaComponent/kthread.c:49:6: note: code may be misoptimized unless ‘-fno-strict-aliasing’ is used lto1: warning: unrecognized gcc debugging option: y lto1: warning: unrecognized gcc debugging option: n lto1: warning: unrecognized gcc debugging option: m lto1: warning: unrecognized gcc debugging option: i lto1: warning: unrecognized gcc debugging option: c lto1: warning: unrecognized gcc debugging option: l lto1: warning: unrecognized gcc debugging option: i lto1: warning: unrecognized gcc debugging option: b lto1: warning: unrecognized gcc debugging option: y lto1: warning: unrecognized gcc debugging option: n lto1: warning: unrecognized gcc debugging option: m lto1: warning: unrecognized gcc debugging option: i lto1: warning: unrecognized gcc debugging option: c lto1: warning: unrecognized gcc debugging option: l lto1: warning: unrecognized gcc debugging option: i lto1: warning: unrecognized gcc debugging option: b lto1: warning: unrecognized gcc debugging option: y lto1: warning: unrecognized gcc debugging option: n lto1: warning: unrecognized gcc debugging option: m lto1: warning: unrecognized gcc debugging option: i lto1: warning: unrecognized gcc debugging option: c lto1: warning: unrecognized gcc debugging option: l lto1: warning: unrecognized gcc debugging option: i lto1: warning: unrecognized gcc debugging option: b make[1]: Leaving directory '/<>/src/main/c' :buildBwaLib (Thread[#29,Daemon worker,5,main]) completed. Took 28.379 secs. :processResources (Thread[#29,Daemon worker,5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/<>/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE :processResources (Thread[#29,Daemon worker,5,main]) completed. Took 0.001 secs. :classes (Thread[#29,Daemon worker,5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes (Thread[#29,Daemon worker,5,main]) completed. Took 0.0 secs. :debianMavenPom (Thread[#29,Daemon worker,5,main]) started. :debianMavenPom Putting task artifact state for task ':debianMavenPom' into context took 0.0 secs. Up-to-date check for task ':debianMavenPom' took 0.0 secs. It is not up-to-date because: No history is available. Generating pom file /<>/build/debian/gatk-bwamem-jni.pom :debianMavenPom (Thread[#29,Daemon worker,5,main]) completed. Took 0.068 secs. :jar (Thread[#29,Daemon worker,5,main]) started. :jar Putting task artifact state for task ':jar' into context took 0.0 secs. Up-to-date check for task ':jar' took 0.005 secs. It is not up-to-date because: No history is available. :jar (Thread[#29,Daemon worker,5,main]) completed. Took 0.035 secs. BUILD SUCCESSFUL in 32s 4 actionable tasks: 4 executed debian/rules override_dh_auto_test make[1]: Entering directory '/<>' # The shared lib should be looked for in its build directory. LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$(readlink -f src/main/c)" dh_auto_test mkdir -p .gradle/init.d cp /usr/share/gradle-debian-helper/init.gradle .gradle/init.d/ gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=gatk-bwamem -Dfile.encoding=UTF-8 --parallel --max-workers=4 test openjdk version "21.0.3" 2024-04-16 OpenJDK Runtime Environment (build 21.0.3+9-Ubuntu-1ubuntu1) OpenJDK 64-Bit Server VM (build 21.0.3+9-Ubuntu-1ubuntu1, mixed mode, sharing) Initialized native services in: /<>/.gradle/native To honour the JVM settings for this build a new JVM will be forked. Please consider using the daemon: https://docs.gradle.org/4.4.1/userguide/gradle_daemon.html. Starting process 'Gradle build daemon'. Working directory: /<>/.gradle/daemon/4.4.1 Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java --add-opens java.base/java.lang=ALL-UNNAMED -Xbootclasspath/a:/usr/share/java/gradle-helper-hook.jar:/usr/share/java/maven-repo-helper.jar -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -cp /usr/share/gradle/lib/gradle-launcher-4.4.1.jar org.gradle.launcher.daemon.bootstrap.GradleDaemon 4.4.1 Successfully started process 'Gradle build daemon' An attempt to start the daemon took 0.6 secs. The client will now receive all logging from the daemon (pid: 13203). The daemon log file: /<>/.gradle/daemon/4.4.1/daemon-13203.out.log Closing daemon's stdin at end of input. The daemon will no longer process any standard input. Daemon will be stopped at the end of the build stopping after processing Using 4 worker leases. Creating new cache for fileHashes, path /<>/.gradle/caches/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@64b9565d Creating new cache for resourceHashesCache, path /<>/.gradle/caches/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@64b9565d Creating new cache for fileHashes, path /<>/.gradle/4.4.1/fileHashes/fileHashes.bin, access org.gradle.cache.internal.DefaultCacheAccess@6510ca76 Starting Build Creating new cache for metadata-1.1/results, path /<>/.gradle/caches/transforms-1/metadata-1.1/results.bin, access org.gradle.cache.internal.DefaultCacheAccess@62300bb9 Settings evaluated using settings file '/<>/settings.gradle'. Projects loaded. Root project using build file '/<>/build.gradle'. Included projects: [root project 'gatk-bwamem-jni'] Keep-alive timer started Adding Debian repository to project 'gatk-bwamem-jni' Parallel execution is an incubating feature. Evaluating root project 'gatk-bwamem-jni' using build file '/<>/build.gradle'. Adding Maven pom generation to project 'gatk-bwamem-jni' Linking the generated javadoc to the system JDK API documentation All projects evaluated. Selected primary task 'test' from project : Creating new cache for annotation-processors, path /<>/.gradle/4.4.1/fileContent/annotation-processors.bin, access org.gradle.cache.internal.DefaultCacheAccess@19d1b713 Tasks to be executed: [task ':compileJava', task ':buildBwaLib', task ':processResources', task ':classes', task ':compileTestJava', task ':processTestResources', task ':testClasses', task ':test'] Creating new cache for resourceHashesCache, path /<>/.gradle/4.4.1/fileHashes/resourceHashesCache.bin, access org.gradle.cache.internal.DefaultCacheAccess@6510ca76 Creating new cache for taskHistory, path /<>/.gradle/4.4.1/taskHistory/taskHistory.bin, access org.gradle.cache.internal.DefaultCacheAccess@4ead9807 Creating new cache for outputFiles, path /<>/.gradle/buildOutputCleanup/outputFiles.bin, access org.gradle.cache.internal.DefaultCacheAccess@70e18c21 :compileJava (Thread[#41,Task worker for ':',5,main]) started. :compileJava Putting task artifact state for task ':compileJava' into context took 0.003 secs. Skipping task ':compileJava' as it is up-to-date (took 0.02 secs). :compileJava UP-TO-DATE :compileJava (Thread[#41,Task worker for ':',5,main]) completed. Took 0.089 secs. :buildBwaLib (Thread[#41,Task worker for ':',5,main]) started. :buildBwaLib Putting task artifact state for task ':buildBwaLib' into context took 0.0 secs. Skipping task ':buildBwaLib' as it is up-to-date (took 0.001 secs). :buildBwaLib UP-TO-DATE :buildBwaLib (Thread[#41,Task worker for ':',5,main]) completed. Took 0.004 secs. :processResources (Thread[#41,Task worker for ':',5,main]) started. :processResources Putting task artifact state for task ':processResources' into context took 0.0 secs. file or directory '/<>/src/main/resources', not found Skipping task ':processResources' as it has no source files and no previous output files. :processResources NO-SOURCE :processResources (Thread[#41,Task worker for ':',5,main]) completed. Took 0.001 secs. :classes (Thread[#41,Task worker for ':',5,main]) started. :classes Skipping task ':classes' as it has no actions. :classes UP-TO-DATE :classes (Thread[#41,Task worker for ':',5,main]) completed. Took 0.0 secs. :compileTestJava (Thread[#41,Task worker for ':',5,main]) started. :compileTestJava Putting task artifact state for task ':compileTestJava' into context took 0.0 secs. Creating new cache for metadata-2.36/module-metadata, path /<>/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@a6ea3ef Loading the Maven rules... Replacing org.testng:testng:jar:6.9.6 -> org.testng:testng:jar:debian Passing through org.beanshell:bsh:jar:debian Passing through com.beust:jcommander:jar:debian Up-to-date check for task ':compileTestJava' took 0.329 secs. It is not up-to-date because: No history is available. All input files are considered out-of-date for incremental task ':compileTestJava'. Compiling with JDK Java compiler API. :compileTestJava (Thread[#41,Task worker for ':',5,main]) completed. Took 0.937 secs. :processTestResources (Thread[#41,Task worker for ':',5,main]) started. :processTestResources Putting task artifact state for task ':processTestResources' into context took 0.0 secs. Up-to-date check for task ':processTestResources' took 0.003 secs. It is not up-to-date because: No history is available. :processTestResources (Thread[#41,Task worker for ':',5,main]) completed. Took 0.02 secs. :testClasses (Thread[#41,Task worker for ':',5,main]) started. :testClasses Skipping task ':testClasses' as it has no actions. :testClasses (Thread[#41,Task worker for ':',5,main]) completed. Took 0.0 secs. :test (Thread[#41,Task worker for ':',5,main]) started. :test Putting task artifact state for task ':test' into context took 0.0 secs. Up-to-date check for task ':test' took 0.062 secs. It is not up-to-date because: No history is available. Starting process 'Gradle Test Executor 1'. Working directory: /<> Command: /usr/lib/jvm/java-21-openjdk-amd64/bin/java -Dorg.gradle.native=false @/tmp/gradle-worker-classpath6345873372412108290txt -Dfile.encoding=UTF-8 -Duser.country -Duser.language=en -Duser.variant -ea worker.org.gradle.process.internal.worker.GradleWorkerMain 'Gradle Test Executor 1' Successfully started process 'Gradle Test Executor 1' Gradle Test Executor 1 started executing tests. [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] skip orientation FR as there are not enough pairs [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs Gradle Test Executor 1 finished executing tests. Results: SUCCESS (7 tests, 7 successes, 0 failures, 0 skipped) Finished generating test XML results (0.019 secs) into: /<>/build/test-results/test Generating HTML test report... Finished generating test html results (0.012 secs) into: /<>/build/reports/tests/test :test (Thread[#41,Task worker for ':',5,main]) completed. Took 0.802 secs. BUILD SUCCESSFUL in 4s 5 actionable tasks: 3 executed, 2 up-to-date make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install dh_install mh_install dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a 01ef64e52808d7ce7f6beac4aa919e079e42dec5 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libgatk-bwamem-java: substitution variable ${java:Depends} used, but is not defined dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libgatk-bwamem-jni (in debian/libgatk-bwamem-jni); do_strip: , oemstrip: pkgstriptranslations: processing libgatk-bwamem-jni-dbgsym (in debian/.debhelper/libgatk-bwamem-jni/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing libgatk-bwamem-java (in debian/libgatk-bwamem-java); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/libgatk-bwamem-jni/DEBIAN/control, package libgatk-bwamem-jni, directory debian/libgatk-bwamem-jni INFO: pkgstripfiles: waiting for lock (libgatk-bwamem-jni) ... pkgstripfiles: processing control file: debian/.debhelper/libgatk-bwamem-jni/dbgsym-root/DEBIAN/control, package libgatk-bwamem-jni-dbgsym, directory debian/.debhelper/libgatk-bwamem-jni/dbgsym-root pkgstripfiles: processing control file: debian/libgatk-bwamem-java/DEBIAN/control, package libgatk-bwamem-java, directory debian/libgatk-bwamem-java dpkg-deb: building package 'libgatk-bwamem-jni-dbgsym' in 'debian/.debhelper/scratch-space/build-libgatk-bwamem-jni/libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.deb'. Searching for duplicated docs in dependency libgatk-bwamem-jni... symlinking changelog.Debian.gz in libgatk-bwamem-java to file in libgatk-bwamem-jni Searching for duplicated docs in dependency libgatk-bwamem-jni... pkgstripfiles: Running PNG optimization (using 4 cpus) for package libgatk-bwamem-java ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libgatk-bwamem-java' in '../libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb'. Renaming libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.deb to libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.ddeb pkgstripfiles: Running PNG optimization (using 4 cpus) for package libgatk-bwamem-jni ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libgatk-bwamem-jni' in '../libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../gatk-bwamem_1.0.4+dfsg2-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-05-03T02:12:58Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gatk-bwamem_1.0.4+dfsg2-3_amd64.changes: ---------------------------------------- Format: 1.8 Date: Sun, 24 Mar 2024 17:03:31 +0100 Source: gatk-bwamem Binary: libgatk-bwamem-java libgatk-bwamem-jni Built-For-Profiles: noudeb Architecture: all amd64 Version: 1.0.4+dfsg2-3 Distribution: oracular-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Michael R. Crusoe Description: libgatk-bwamem-java - interface to call Heng Li's bwa mem aligner from Java code libgatk-bwamem-jni - interface to call Heng Li's bwa mem aligner from Java code (jni) Changes: gatk-bwamem (1.0.4+dfsg2-3) unstable; urgency=medium . * Team upload. * d/rules: make sure the openmp-simd compiler flag is used. * d/patches/hardening: improve with the help of blhc. * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 5b2bf97070bb003c2352abce90b288287a291cbe 11002 gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo 8a98be512caddd38d98e67113360ddf3c21f4086 23438 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 44ee8269f3110fa662aaa7feba05cb6edee3021e 240586 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.ddeb 1b9a75ab5716d9ea307305102bf310bd5a18e9c6 99648 libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb Checksums-Sha256: 944008bc37843bea913be2def8197227771b74a9c1d38beef95376adbc20810d 11002 gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo 879ccd7cf1d706c7b57510b78e1a3ed2916a4133882d585f386864b53bd94a7b 23438 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 3c05738fdb324fce246033c43d7e2f95d6fb5c0f23f424619bbf6c86a51f77d4 240586 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.ddeb 5eb58e90a29b0f1cc5c33d2c04645050ab315ed8ed3b48849badc61424d407f1 99648 libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb Files: 326988813340e38d397d3c94ab39d9c3 11002 java optional gatk-bwamem_1.0.4+dfsg2-3_amd64.buildinfo 9e2e73263144bc05751a93249e4721b6 23438 java optional libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 2398047bd2e4f286906b45d5e3cf1c90 240586 debug optional libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.ddeb 7546b4e08a5b8a05c783f2b765a57bbf 99648 java optional libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb /<>/gatk-bwamem_1.0.4+dfsg2-3_amd64.changes.new could not be renamed to /<>/gatk-bwamem_1.0.4+dfsg2-3_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: gatk-bwamem Binary: libgatk-bwamem-java libgatk-bwamem-jni libgatk-bwamem-jni-dbgsym Architecture: all amd64 Version: 1.0.4+dfsg2-3 Checksums-Md5: 9e2e73263144bc05751a93249e4721b6 23438 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 2398047bd2e4f286906b45d5e3cf1c90 240586 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.ddeb 7546b4e08a5b8a05c783f2b765a57bbf 99648 libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb Checksums-Sha1: 8a98be512caddd38d98e67113360ddf3c21f4086 23438 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 44ee8269f3110fa662aaa7feba05cb6edee3021e 240586 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.ddeb 1b9a75ab5716d9ea307305102bf310bd5a18e9c6 99648 libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb Checksums-Sha256: 879ccd7cf1d706c7b57510b78e1a3ed2916a4133882d585f386864b53bd94a7b 23438 libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb 3c05738fdb324fce246033c43d7e2f95d6fb5c0f23f424619bbf6c86a51f77d4 240586 libgatk-bwamem-jni-dbgsym_1.0.4+dfsg2-3_amd64.ddeb 5eb58e90a29b0f1cc5c33d2c04645050ab315ed8ed3b48849badc61424d407f1 99648 libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Fri, 03 May 2024 02:12:58 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: ant (= 1.10.14-1), ant-optional (= 1.10.14-1), antlr (= 2.7.7+dfsg-13build1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu2), autotools-dev (= 20220109.1), base-files (= 13.1ubuntu1), base-passwd (= 3.6.3build1), bash (= 5.2.21-2ubuntu4), binutils (= 2.42-4ubuntu2), binutils-common (= 2.42-4ubuntu2), binutils-x86-64-linux-gnu (= 2.42-4ubuntu2), bnd (= 5.0.1-5), bsdextrautils (= 2.39.3-9ubuntu6), bsdutils (= 1:2.39.3-9ubuntu6), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5.1), ca-certificates (= 20240203), ca-certificates-java (= 20240118), coreutils (= 9.4-3ubuntu6), cpp (= 4:13.2.0-7ubuntu1), cpp-13 (= 13.2.0-23ubuntu4), cpp-13-x86-64-linux-gnu (= 13.2.0-23ubuntu4), cpp-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), dash (= 0.5.12-6ubuntu5), debconf (= 1.5.86ubuntu1), debhelper (= 13.14.1ubuntu5), debianutils (= 5.17build1), debugedit (= 1:5.0-5build2), default-jdk-headless (= 2:1.21-75+exp1), default-jre-headless (= 2:1.21-75+exp1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1build1), dpkg (= 1.22.6ubuntu10), dpkg-dev (= 1.22.6ubuntu10), dwz (= 0.15-1build6), file (= 1:5.45-3build1), findutils (= 4.9.0-5build1), g++ (= 4:13.2.0-7ubuntu1), g++-13 (= 13.2.0-23ubuntu4), g++-13-x86-64-linux-gnu (= 13.2.0-23ubuntu4), g++-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gcc (= 4:13.2.0-7ubuntu1), gcc-13 (= 13.2.0-23ubuntu4), gcc-13-base (= 13.2.0-23ubuntu4), gcc-13-x86-64-linux-gnu (= 13.2.0-23ubuntu4), gcc-14-base (= 14-20240412-0ubuntu1), gcc-x86-64-linux-gnu (= 4:13.2.0-7ubuntu1), gettext (= 0.21-14ubuntu2), gettext-base (= 0.21-14ubuntu2), gradle (= 4.4.1-20), gradle-debian-helper (= 2.4), grep (= 3.11-4build1), groff-base (= 1.23.0-3build2), groovy (= 2.4.21-10), gzip (= 1.12-1ubuntu3), hostname (= 3.23+nmu2ubuntu2), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), ivy (= 2.5.2-1), java-common (= 0.75+exp1), java-wrappers (= 0.4), junit4 (= 4.13.2-4), libacl1 (= 2.3.2-1build1), libantlr-java (= 2.7.7+dfsg-13build1), libaopalliance-java (= 20070526-7), libapache-pom-java (= 29-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240412-0ubuntu1), libasm-java (= 9.7-1), libatinject-jsr330-api-java (= 1.0+ds1-5), libatomic1 (= 14-20240412-0ubuntu1), libattr1 (= 1:2.5.2-1build1), libaudit-common (= 1:3.1.2-2.1build1), libaudit1 (= 1:3.1.2-2.1build1), libbcel-java (= 6.5.0-2), libbcpg-java (= 1.77-1), libbcprov-java (= 1.77-1), libbinutils (= 2.42-4ubuntu2), libblkid1 (= 2.39.3-9ubuntu6), libbsf-java (= 1:2.4.0-8), libbsh-java (= 2.0b4-20), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-0ubuntu8.1), libc-dev-bin (= 2.39-0ubuntu8.1), libc6 (= 2.39-0ubuntu8.1), libc6-dev (= 2.39-0ubuntu8.1), libcap-ng0 (= 0.8.4-2build2), libcap2 (= 1:2.66-5ubuntu2), libcc1-0 (= 14-20240412-0ubuntu1), libcdi-api-java (= 1.2-3), libcommons-cli-java (= 1.6.0-1), libcommons-codec-java (= 1.16.0-1), libcommons-collections3-java (= 3.2.2-3), libcommons-compress-java (= 1.25.0-1), libcommons-io-java (= 2.11.0-2), libcommons-lang-java (= 2.6-10), libcommons-lang3-java (= 3.14.0-1), libcommons-logging-java (= 1.3.0-1ubuntu1), libcommons-parent-java (= 56-1), libcrypt-dev (= 1:4.4.36-4build1), libcrypt1 (= 1:4.4.36-4build1), libctf-nobfd0 (= 2.42-4ubuntu2), libctf0 (= 2.42-4ubuntu2), libdb5.3t64 (= 5.3.28+dfsg2-7), libdd-plist-java (= 1.20-1.1), libdebconfclient0 (= 0.271ubuntu3), libdebhelper-perl (= 13.14.1ubuntu5), libdom4j-java (= 2.1.4-1), libdpkg-perl (= 1.22.6ubuntu10), libdw1t64 (= 0.190-1.1build4), libeclipse-jdt-annotation-java (= 2.2.700+eclipse4.26-2), libel-api-java (= 3.0.0-3), libelf1t64 (= 0.190-1.1build4), liberror-prone-java (= 2.18.0-1), libfelix-framework-java (= 4.6.1-2.1), libfelix-gogo-runtime-java (= 0.16.2-1.1), libfelix-resolver-java (= 1.16.0-1), libffi8 (= 3.4.6-1build1), libfile-stripnondeterminism-perl (= 1.13.1-1), libfindbugs-java (= 3.1.0~preview2-3), libgcc-13-dev (= 13.2.0-23ubuntu4), libgcc-s1 (= 14-20240412-0ubuntu1), libgcrypt20 (= 1.10.3-2build1), libgdbm-compat4t64 (= 1.23-5.1build1), libgdbm6t64 (= 1.23-5.1build1), libgeronimo-annotation-1.3-spec-java (= 1.3-1), libgeronimo-interceptor-3.0-spec-java (= 1.0.1-4fakesync), libgmp10 (= 2:6.3.0+dfsg-2ubuntu6), libgomp1 (= 14-20240412-0ubuntu1), libgoogle-gson-java (= 2.10.1-1), libgpg-error0 (= 1.47-3build2), libgprofng0 (= 2.42-4ubuntu2), libgradle-core-java (= 4.4.1-20), libgradle-plugins-java (= 4.4.1-20), libguava-java (= 32.0.1-1), libguice-java (= 4.2.3-2), libhamcrest-java (= 2.2-2), libhawtjni-runtime-java (= 1.18-1), libhttpclient-java (= 4.5.14-1), libhttpcore-java (= 4.4.16-1), libhwasan0 (= 14-20240412-0ubuntu1), libicu74 (= 74.2-1ubuntu3), libisl23 (= 0.26-3build1), libitm1 (= 14-20240412-0ubuntu1), libjansi-java (= 2.4.1-2), libjansi-native-java (= 1.8-2), libjansi1-java (= 1.18-3ubuntu1), libjansson4 (= 2.14-2build2), libjarjar-java (= 1.4+svn142-12), libjatl-java (= 0.2.3-1.1), libjavaewah-java (= 1.2.3-1), libjaxen-java (= 1.1.6-4), libjcifs-java (= 1.3.19-2), libjcip-annotations-java (= 20060626-6), libjcommander-java (= 1.71-4), libjetty9-java (= 9.4.53-1), libjformatstring-java (= 0.10~20131207-2.1), libjgit-java (= 4.11.9-2), libjline2-java (= 2.14.6-5), libjna-java (= 5.14.0-1), libjna-jni (= 5.14.0-1), libjpeg-turbo8 (= 2.1.5-2ubuntu2), libjpeg8 (= 8c-2ubuntu11), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libjsch-java (= 0.1.55-1), libjsoup-java (= 1.15.3-1), libjsp-api-java (= 2.3.4-3), libjsr305-java (= 0.1~+svn49-11), libjzlib-java (= 1.1.3-3), libkryo-java (= 2.20-7), liblcms2-2 (= 2.14-2build1), liblogback-java (= 1:1.2.11-5), liblsan0 (= 14-20240412-0ubuntu1), liblz4-1 (= 1.9.4-1build1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3build1), libmagic1t64 (= 1:5.45-3build1), libmaven-parent-java (= 35-1), libmaven-resolver-java (= 1.6.3-1), libmaven-shared-utils-java (= 3.3.4-1), libmaven3-core-java (= 3.8.7-2), libmd0 (= 1.1.0-2build1), libminlog-java (= 1.3.0-1.1), libmount1 (= 2.39.3-9ubuntu6), libmpc3 (= 1.3.1-1build1), libmpfr6 (= 4.2.1-1build1), libnative-platform-java (= 0.14-6), libnative-platform-jni (= 0.14-6), libnekohtml-java (= 1.9.22.noko2-0.1), libnspr4 (= 2:4.35-1.1build1), libnss3 (= 2:3.98-1build1), libobjenesis-java (= 3.3-3), libosgi-annotation-java (= 8.1.0-1), libosgi-compendium-java (= 7.0.0-1), libosgi-core-java (= 8.0.0-2), libpam-modules (= 1.5.3-7ubuntu1), libpam-modules-bin (= 1.5.3-7ubuntu1), libpam-runtime (= 1.5.3-7ubuntu1), libpam0g (= 1.5.3-7ubuntu1), libpcre2-8-0 (= 10.42-4ubuntu2), libpcsclite1 (= 2.0.3-1build1), libperl5.38t64 (= 5.38.2-3.2build2), libpipeline1 (= 1.5.7-2), libplexus-cipher-java (= 2.0-1), libplexus-classworlds-java (= 2.7.0-1), libplexus-component-annotations-java (= 2.1.1-1), libplexus-container-default-java (= 2.1.1-1), libplexus-interpolation-java (= 1.26-1), libplexus-sec-dispatcher-java (= 2.0-3), libplexus-utils2-java (= 3.4.2-1), libpolyglot-maven-java (= 0.8~tobrien+git20120905-10), libqdox-java (= 1.12.1-3), libquadmath0 (= 14-20240412-0ubuntu1), libreflectasm-java (= 1.11.9+dfsg-4), librhino-java (= 1.7.14-2.1), libseccomp2 (= 2.5.5-1ubuntu3), libselinux1 (= 3.5-2ubuntu2), libservlet-api-java (= 4.0.1-2), libsframe1 (= 2.42-4ubuntu2), libsimde-dev (= 0.7.6-1), libsimple-http-java (= 4.1.21-1.1fakesync1), libsisu-inject-java (= 0.3.4-2), libsisu-plexus-java (= 0.3.4-3), libslf4j-java (= 1.7.32-1), libsmartcols1 (= 2.39.3-9ubuntu6), libsqlite3-0 (= 3.45.3-1), libssl3t64 (= 3.0.13-0ubuntu3), libstdc++-13-dev (= 13.2.0-23ubuntu4), libstdc++6 (= 14-20240412-0ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.4-1ubuntu8), libtinfo6 (= 6.4+20240113-1ubuntu2), libtool (= 2.4.7-7build1), libtsan2 (= 14-20240412-0ubuntu1), libubsan1 (= 14-20240412-0ubuntu1), libuchardet0 (= 0.0.8-1build1), libudev1 (= 255.4-1ubuntu8), libunistring5 (= 1.1-2build1), libuuid1 (= 2.39.3-9ubuntu6), libwagon-file-java (= 3.5.3-1), libwagon-http-java (= 3.5.3-1), libwagon-provider-api-java (= 3.5.3-1), libwebsocket-api-java (= 1.1-2), libxbean-reflect-java (= 4.5-8), libxerces2-java (= 2.12.2-1), libxml-commons-external-java (= 1.4.01-6), libxml-commons-resolver1.1-java (= 1.2-11), libxml2 (= 2.9.14+dfsg-1.3ubuntu3), libxpp3-java (= 1.1.4c-3), libxstream-java (= 1.4.20-1), libxz-java (= 1.9-1), libyaml-snake-java (= 1.33-2), libzstd1 (= 1.5.5+dfsg2-2build1), linux-libc-dev (= 6.8.0-31.31), login (= 1:4.13+dfsg1-4ubuntu3), lto-disabled-list (= 47), m4 (= 1.4.19-4build1), make (= 4.3-4.1build2), man-db (= 2.12.0-4build2), maven-repo-helper (= 1.11), mawk (= 1.3.4.20240123-1build1), ncurses-base (= 6.4+20240113-1ubuntu2), ncurses-bin (= 6.4+20240113-1ubuntu2), openjdk-21-jdk-headless (= 21.0.3+9-1ubuntu1), openjdk-21-jre-headless (= 21.0.3+9-1ubuntu1), openssl (= 3.0.13-0ubuntu3), patch (= 2.7.6-7build3), perl (= 5.38.2-3.2build2), perl-base (= 5.38.2-3.2build2), perl-modules-5.38 (= 5.38.2-3.2build2), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu7), sed (= 4.9-2build1), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu3), tar (= 1.35+dfsg-3build1), testng (= 6.9.12-4), unzip (= 6.0-28ubuntu4), util-linux (= 2.39.3-9ubuntu6), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg-3.1ubuntu2), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu2) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1711296211" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libgatk-bwamem-java_1.0.4+dfsg2-3_all.deb ----------------------------------------- new Debian package, version 2.0. size 23438 bytes: control archive=803 bytes. 859 bytes, 21 lines control 395 bytes, 4 lines md5sums Package: libgatk-bwamem-java Source: gatk-bwamem Version: 1.0.4+dfsg2-3 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 47 Depends: libgatk-bwamem-jni (>= 1.0.4+dfsg2-3), libgatk-bwamem-jni (<< 1.0.4+dfsg2-3.1~) Suggests: bwa Section: java Priority: optional Homepage: https://github.com/broadinstitute/gatk-bwamem-jni/ Description: interface to call Heng Li's bwa mem aligner from Java code BWA (Burrows-Wheeler Aligner) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It is written in C. . gatk-bwamem provides a Java library and a shared library to allow one to use BWA from Java code. . This package contains the Java library. drwxr-xr-x root/root 0 2024-03-24 16:03 ./ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/doc/libgatk-bwamem-java/ lrwxrwxrwx root/root 0 2024-03-24 16:03 ./usr/share/doc/libgatk-bwamem-java/changelog.Debian.gz -> ../libgatk-bwamem-jni/changelog.Debian.gz -rw-r--r-- root/root 5395 2024-03-24 16:02 ./usr/share/doc/libgatk-bwamem-java/copyright drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/java/ -rw-r--r-- root/root 22184 2024-03-24 16:03 ./usr/share/java/gatk-bwamem-1.0.4.jar lrwxrwxrwx root/root 0 2024-03-24 16:03 ./usr/share/java/gatk-bwamem.jar -> gatk-bwamem-1.0.4.jar drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/maven-repo/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/maven-repo/org/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/maven-repo/org/broadinstitute/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/maven-repo/org/broadinstitute/gatk-bwamem-jni/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/maven-repo/org/broadinstitute/gatk-bwamem-jni/1.0.4/ lrwxrwxrwx root/root 0 2024-03-24 16:03 ./usr/share/maven-repo/org/broadinstitute/gatk-bwamem-jni/1.0.4/gatk-bwamem-jni-1.0.4.jar -> ../../../../../java/gatk-bwamem-1.0.4.jar -rw-r--r-- root/root 705 2024-03-24 16:03 ./usr/share/maven-repo/org/broadinstitute/gatk-bwamem-jni/1.0.4/gatk-bwamem-jni-1.0.4.pom drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/maven-repo/org/broadinstitute/gatk-bwamem-jni/debian/ lrwxrwxrwx root/root 0 2024-03-24 16:03 ./usr/share/maven-repo/org/broadinstitute/gatk-bwamem-jni/debian/gatk-bwamem-jni-debian.jar -> ../../../../../java/gatk-bwamem-1.0.4.jar -rw-r--r-- root/root 706 2024-03-24 16:03 ./usr/share/maven-repo/org/broadinstitute/gatk-bwamem-jni/debian/gatk-bwamem-jni-debian.pom libgatk-bwamem-jni_1.0.4+dfsg2-3_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 99648 bytes: control archive=764 bytes. 812 bytes, 20 lines control 220 bytes, 3 lines md5sums Package: libgatk-bwamem-jni Source: gatk-bwamem Version: 1.0.4+dfsg2-3 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 222 Depends: libc6 (>= 2.34), zlib1g (>= 1:1.1.4) Section: java Priority: optional Homepage: https://github.com/broadinstitute/gatk-bwamem-jni/ Description: interface to call Heng Li's bwa mem aligner from Java code (jni) BWA (Burrows-Wheeler Aligner) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It is written in C. . gatk-bwamem provides a Java library and a shared library to allow one to use BWA from Java code. . This package contains the native library. drwxr-xr-x root/root 0 2024-03-24 16:03 ./ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/lib/jni/ -rw-r--r-- root/root 211216 2024-03-24 16:03 ./usr/lib/jni/libbwa.so drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-24 16:03 ./usr/share/doc/libgatk-bwamem-jni/ -rw-r--r-- root/root 364 2024-03-24 16:03 ./usr/share/doc/libgatk-bwamem-jni/changelog.Debian.gz -rw-r--r-- root/root 5395 2024-03-24 16:02 ./usr/share/doc/libgatk-bwamem-jni/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 2838708 Build-Time: 50 Distribution: oracular-proposed Host Architecture: amd64 Install-Time: 15 Job: gatk-bwamem_1.0.4+dfsg2-3.dsc Machine Architecture: amd64 Package: gatk-bwamem Package-Time: 66 Source-Version: 1.0.4+dfsg2-3 Space: 2838708 Status: successful Version: 1.0.4+dfsg2-3 -------------------------------------------------------------------------------- Finished at 2024-05-03T02:12:58Z Build needed 00:01:06, 2838708k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=oracular --arch=amd64 PACKAGEBUILD-28283393 Scanning for processes to kill in build PACKAGEBUILD-28283393