https://launchpad.net/ubuntu/+source/samtools-legacy/0.1.19+dfsg-6ubuntu1/+build/27012353 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos03-amd64-012 5.4.0-164-generic #181-Ubuntu SMP Fri Sep 1 13:41:22 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~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... 21 Nov 23:08:41 ntpdate[1928]: adjust time server 10.211.37.1 offset 0.007392 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27012353 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-27012353 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27012353 Starting target for build PACKAGEBUILD-27012353 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27012353 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27012353 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27012353 Updating target for build PACKAGEBUILD-27012353 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [240 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [102 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1407 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [517 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.0 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6023 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [94.1 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [34.4 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [1298 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [400 kB] Fetched 25.2 MB in 3s (8521 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libunistring2 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libunistring5 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils cpp-13 debianutils diffutils dpkg dpkg-dev fakeroot g++-13 gcc-13 gcc-13-base grep krb5-locales libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libfakeroot libfdisk1 libgcc-13-dev libgcc-s1 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmount1 libncursesw6 libnsl-dev libnsl2 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpng16-16 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng pinentry-curses procps systemd systemd-dev systemd-sysv sysvinit-utils util-linux uuid-runtime xz-utils 109 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 95.2 MB of archives. After this operation, 1976 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.38-3ubuntu1 [2114 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.38-3ubuntu1 [20.3 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-common all 1.3.4+ds-1 [7920 B] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1 [193 kB] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgssapi-krb5-2 amd64 1.20.1-5 [142 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkrb5-3 amd64 1.20.1-5 [346 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libk5crypto3 amd64 1.20.1-5 [81.3 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkrb5support0 amd64 1.20.1-5 [33.2 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libssl3 amd64 3.0.10-1ubuntu3 [1910 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc3 amd64 1.3.4+ds-1 [81.4 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl2 amd64 1.3.0-3 [41.3 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 13.2.0-6ubuntu1 [48.1 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-base amd64 13.2.0-6ubuntu1 [44.3 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-s1 amd64 13.2.0-6ubuntu1 [62.4 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 13.2.0-6ubuntu1 [142 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 13.2.0-6ubuntu1 [29.3 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 13.2.0-6ubuntu1 [10.4 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 13.2.0-6ubuntu1 [2835 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 13.2.0-6ubuntu1 [1203 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 13.2.0-6ubuntu1 [2606 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 13.2.0-6ubuntu1 [1105 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 13.2.0-6ubuntu1 [1262 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 13.2.0-6ubuntu1 [153 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-6ubuntu1 [12.1 MB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-6ubuntu1 [2351 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-6ubuntu1 [2686 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-6ubuntu1 [21.5 MB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-6ubuntu1 [10.7 MB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++6 amd64 13.2.0-6ubuntu1 [771 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.41-6ubuntu1 [847 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.41-6ubuntu1 [94.1 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.41-6ubuntu1 [96.4 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.41-6ubuntu1 [14.6 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.41-6ubuntu1 [563 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.41-6ubuntu1 [248 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.41-6ubuntu1 [17.9 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.41-6ubuntu1 [2468 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libc6 amd64 2.38-3ubuntu1 [3248 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu4 [73.7 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.14 [89.0 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bash amd64 5.2.15-2ubuntu2 [795 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bsdutils amd64 1:2.39.2-6ubuntu1 [93.9 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma5 amd64 5.4.4-0.1 [127 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libapparmor1 amd64 4.0.0~alpha2-0ubuntu6 [47.6 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit-common all 1:3.1.1-1build1 [5510 B] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libcap-ng0 amd64 0.8.3-1build3 [15.3 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit1 amd64 1:3.1.1-1build1 [46.5 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libblkid1 amd64 2.39.2-6ubuntu1 [122 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libselinux1 amd64 3.5-1build1 [78.4 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmount1 amd64 2.39.2-6ubuntu1 [132 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam0g amd64 1.5.2-9.1ubuntu1 [65.1 kB] Get:55 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libseccomp2 amd64 2.5.4-2ubuntu1 [49.3 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 systemd-sysv amd64 253.5-1ubuntu7 [11.5 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 systemd-dev all 253.5-1ubuntu7 [78.5 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 systemd amd64 253.5-1ubuntu7 [3060 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libsystemd-shared amd64 253.5-1ubuntu7 [1871 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libuuid1 amd64 2.39.2-6ubuntu1 [34.1 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcryptsetup12 amd64 2:2.6.1-5ubuntu1 [242 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfdisk1 amd64 2.39.2-6ubuntu1 [145 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 mount amd64 2.39.2-6ubuntu1 [118 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libsystemd0 amd64 253.5-1ubuntu7 [407 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libudev1 amd64 253.5-1ubuntu7 [159 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libapt-pkg6.0 amd64 2.7.6 [948 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg amd64 1.22.1ubuntu2 [1385 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-3 [161 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ncurses-bin amd64 6.4+20231118-1 [186 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 util-linux amd64 2.39.2-6ubuntu1 [1120 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.2 [51.2 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libc-bin amd64 2.38-3ubuntu1 [680 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ncurses-base all 6.4+20231118-1 [25.0 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 sysvinit-utils amd64 3.08-3ubuntu1 [33.7 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4 [736 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 apt amd64 2.7.6 [1373 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 apt-utils amd64 2.7.6 [216 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.4-1build1 [64.3 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgnutls30 amd64 3.8.1-4ubuntu4 [988 kB] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules-bin amd64 1.5.2-9.1ubuntu1 [47.6 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules amd64 1.5.2-9.1ubuntu1 [284 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsmartcols1 amd64 2.39.2-6ubuntu1 [63.3 kB] Get:86 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 uuid-runtime amd64 2.39.2-6ubuntu1 [32.9 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3 [7936 B] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3 [69.8 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-runtime all 1.5.2-9.1ubuntu1 [41.5 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage-common all 3.5-1build1 [9982 B] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage2 amd64 3.5-1build1 [92.9 kB] Get:92 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libncursesw6 amd64 6.4+20231118-1 [147 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtinfo6 amd64 6.4+20231118-1 [106 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libproc2-0 amd64 2:4.0.4-2ubuntu1 [59.0 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20231102-1 [126 kB] Get:96 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 procps amd64 2:4.0.4-2ubuntu1 [708 kB] Get:97 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 krb5-locales all 1.20.1-5 [13.6 kB] Get:98 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsqlite3-0 amd64 3.44.0-1 [689 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 openssl amd64 3.0.10-1ubuntu3 [1188 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bsdextrautils amd64 2.39.2-6ubuntu1 [73.5 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16 amd64 1.6.40-2 [186 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 xz-utils amd64 5.4.4-0.1 [268 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg-dev all 1.22.1ubuntu2 [1148 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 libdpkg-perl all 1.22.1ubuntu2 [285 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 44 [12.4 kB] Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.32.2-1 [32.1 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.32.2-1 [67.1 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 optipng amd64 0.7.7-3 [83.3 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 pinentry-curses amd64 1.2.1-3ubuntu1 [34.9 kB] Preconfiguring packages ... Fetched 95.2 MB in 4s (23.1 MB/s) (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../00-libnsl-dev_1.3.0-3_amd64.deb ... Unpacking libnsl-dev:amd64 (1.3.0-3) over (1.3.0-2build2) ... Preparing to unpack .../01-libc6-dev_2.38-3ubuntu1_amd64.deb ... Unpacking libc6-dev:amd64 (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Preparing to unpack .../02-libc-dev-bin_2.38-3ubuntu1_amd64.deb ... Unpacking libc-dev-bin (2.38-3ubuntu1) over (2.38-1ubuntu6) ... Preparing to unpack .../03-libtirpc-common_1.3.4+ds-1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1) over (1.3.3+ds-1) ... Preparing to unpack .../04-libtirpc-dev_1.3.4+ds-1_amd64.deb ... Unpacking libtirpc-dev:amd64 (1.3.4+ds-1) over (1.3.3+ds-1) ... Preparing to unpack .../05-libgssapi-krb5-2_1.20.1-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-5) over (1.20.1-3ubuntu1) ... Preparing to unpack .../06-libkrb5-3_1.20.1-5_amd64.deb ... 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Setting up gcc-13-base:amd64 (13.2.0-6ubuntu1) ... (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../libgcc-s1_13.2.0-6ubuntu1_amd64.deb ... Unpacking libgcc-s1:amd64 (13.2.0-6ubuntu1) over (13.2.0-4ubuntu3) ... Setting up libgcc-s1:amd64 (13.2.0-6ubuntu1) ... (Reading database ... 13648 files and directories currently installed.) Preparing to unpack .../00-libgomp1_13.2.0-6ubuntu1_amd64.deb ... Unpacking libgomp1:amd64 (13.2.0-6ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../01-libitm1_13.2.0-6ubuntu1_amd64.deb ... Unpacking libitm1:amd64 (13.2.0-6ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../02-libatomic1_13.2.0-6ubuntu1_amd64.deb ... Unpacking libatomic1:amd64 (13.2.0-6ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../03-libasan8_13.2.0-6ubuntu1_amd64.deb ... Unpacking libasan8:amd64 (13.2.0-6ubuntu1) over (13.2.0-4ubuntu3) ... Preparing to unpack .../04-liblsan0_13.2.0-6ubuntu1_amd64.deb ... 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27012353 amd64 noble-proposed -c chroot:build-PACKAGEBUILD-27012353 --arch=amd64 --dist=noble-proposed --nolog -A samtools-legacy_0.1.19+dfsg-6ubuntu1.dsc Initiating build PACKAGEBUILD-27012353 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-164-generic #181-Ubuntu SMP Fri Sep 1 13:41:22 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-amd64-012.buildd +==============================================================================+ | samtools-legacy 0.1.19+dfsg-6ubuntu1 (amd64) Tue, 21 Nov 2023 23:09:01 +0000 | +==============================================================================+ Package: samtools-legacy Version: 0.1.19+dfsg-6ubuntu1 Source Version: 0.1.19+dfsg-6ubuntu1 Distribution: noble-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27012353/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-legacy-F3ilRZ/resolver-KvrFx3' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- samtools-legacy_0.1.19+dfsg-6ubuntu1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/samtools-legacy-F3ilRZ/samtools-legacy-0.1.19+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/samtools-legacy-F3ilRZ' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libncurses5-dev, zlib1g-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libncurses5-dev, 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 [387 B] Get:5 copy:/<>/apt_archive ./ Packages [469 B] Fetched 1813 B in 0s (0 B/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 ca-certificates debconf-i18n krb5-locales libgpg-error-l10n libgpm2 liblocale-gettext-perl libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 openssl psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1 libncurses-dev libncurses6 libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libdw1 libelf1 libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1 libncurses-dev libncurses6 libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 20.3 MB of archives. After this operation, 72.5 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [682 B] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libelf1 amd64 0.190-1 [57.0 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libicu72 amd64 72.1-3ubuntu3 [10.8 MB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libxml2 amd64 2.9.14+dfsg-1.3build1 [769 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic-mgc amd64 1:5.45-2 [307 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic1 amd64 1:5.45-2 [86.1 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 file amd64 1:5.45-2 [21.9 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 gettext-base amd64 0.21-13build1 [38.3 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libuchardet0 amd64 0.0.7-1build2 [76.9 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 groff-base amd64 1.23.0-3 [1023 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libncurses6 amd64 6.4+20231118-1 [111 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 man-db amd64 2.12.0-1 [1229 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 m4 amd64 1.4.19-4 [243 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 autoconf all 2.71-3 [339 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 autopoint all 0.21-13build1 [422 kB] Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdebhelper-perl all 13.11.8ubuntu1 [85.9 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libtool all 2.4.7-7 [166 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 dh-autoreconf all 20 [16.1 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-override-perl all 0.09-4 [8706 B] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libdw1 amd64 0.190-1 [260 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 dwz amd64 0.15-1 [112 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 gettext amd64 0.21-13build1 [865 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debhelper all 13.11.8ubuntu1 [940 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libncurses-dev amd64 6.4+20231118-1 [383 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1ubuntu5 [895 kB] Preconfiguring packages ... Fetched 20.3 MB in 1s (14.8 MB/s) Selecting previously unselected package libelf1:amd64. (Reading database ... 13673 files and directories currently installed.) Preparing to unpack .../00-libelf1_0.190-1_amd64.deb ... Unpacking libelf1:amd64 (0.190-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../01-libicu72_72.1-3ubuntu3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3ubuntu3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../02-libxml2_2.9.14+dfsg-1.3build1_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3build1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-2_amd64.deb ... Unpacking libmagic-mgc (1:5.45-2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../04-libmagic1_1%3a5.45-2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.45-2) ... Selecting previously unselected package file. 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Setting up gettext-base (0.21-13build1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-2) ... Setting up autotools-dev (20220109.1) ... Setting up libncurses6:amd64 (6.4+20231118-1) ... Setting up autopoint (0.21-13build1) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1ubuntu5) ... Setting up libuchardet0:amd64 (0.0.7-1build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libelf1:amd64 (0.190-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3build1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:amd64 (0.190-1) ... Setting up libncurses-dev:amd64 (6.4+20231118-1) ... Setting up gettext (0.21-13build1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up debugedit (1:5.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up debhelper (13.11.8ubuntu1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-164-generic #181-Ubuntu SMP Fri Sep 1 13:41:22 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.41-6ubuntu1 dpkg-dev_1.22.1ubuntu2 g++-13_13.2.0-6ubuntu1 gcc-13_13.2.0-6ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-6ubuntu1 libstdc++6_13.2.0-6ubuntu1 linux-libc-dev_6.5.0-9.9 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.6 apt-utils_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13build1 autotools-dev_20220109.1 base-files_13ubuntu4 base-passwd_3.6.2 bash_5.2.15-2ubuntu2 bash-completion_1:2.11-8 binutils_2.41-6ubuntu1 binutils-common_2.41-6ubuntu1 binutils-x86-64-linux-gnu_2.41-6ubuntu1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 coreutils_9.1-1ubuntu2 cpp_4:13.2.0-1ubuntu1 cpp-13_13.2.0-6ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.82 debconf-i18n_1.5.82 debhelper_13.11.8ubuntu1 debianutils_5.14 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.1ubuntu2 dpkg-dev_1.22.1ubuntu2 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1ubuntu1 g++-13_13.2.0-6ubuntu1 gcc_4:13.2.0-1ubuntu1 gcc-13_13.2.0-6ubuntu1 gcc-13-base_13.2.0-6ubuntu1 gettext_0.21-13build1 gettext-base_0.21-13build1 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 gpgconf_2.2.40-1.1ubuntu1 gpgv_2.2.40-1.1ubuntu1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1ubuntu1 hostname_3.23+nmu1ubuntu1 init_1.65.2ubuntu1 init-system-helpers_1.65.2ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5 libacl1_2.3.1-3 libapparmor1_4.0.0~alpha2-0ubuntu6 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_13.2.0-6ubuntu1 libassuan0_2.5.6-1 libatomic1_13.2.0-6ubuntu1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1build1 libaudit1_1:3.1.1-1build1 libbinutils_2.41-6ubuntu1 libblkid1_2.39.2-6ubuntu1 libbz2-1.0_1.0.8-5build1 libc-bin_2.38-3ubuntu1 libc-dev-bin_2.38-3ubuntu1 libc6_2.38-3ubuntu1 libc6-dev_2.38-3ubuntu1 libcap-ng0_0.8.3-1build3 libcap2_1:2.66-4ubuntu1 libcc1-0_13.2.0-6ubuntu1 libcom-err2_1.47.0-2ubuntu1 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libcryptsetup12_2:2.6.1-5ubuntu1 libctf-nobfd0_2.41-6ubuntu1 libctf0_2.41-6ubuntu1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.270ubuntu1 libdebhelper-perl_13.11.8ubuntu1 libdevmapper1.02.1_2:1.02.185-2ubuntu1 libdpkg-perl_1.22.1ubuntu2 libdw1_0.190-1 libelf1_0.190-1 libext2fs2_1.47.0-2ubuntu1 libfakeroot_1.32.2-1 libfdisk1_2.39.2-6ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-6ubuntu1 libgcc-s1_13.2.0-6ubuntu1 libgcrypt20_1.10.2-3ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.3.0+dfsg-2ubuntu4 libgnutls30_3.8.1-4ubuntu4 libgomp1_13.2.0-6ubuntu1 libgpg-error-l10n_1.47-3 libgpg-error0_1.47-3 libgpm2_1.20.7-10build1 libgprofng0_2.41-6ubuntu1 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhwasan0_13.2.0-6ubuntu1 libicu72_72.1-3ubuntu3 libidn2-0_2.3.4-1build1 libip4tc2_1.8.9-2ubuntu2 libisl23_0.26-3 libitm1_13.2.0-6ubuntu1 libjansson4_2.14-2 libjson-c5_0.17-1 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkmod2_30+20230519-1ubuntu3 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 liblocale-gettext-perl_1.07-6 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblsan0_13.2.0-6ubuntu1 liblz4-1_1.9.4-1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-6ubuntu1 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncurses-dev_6.4+20231118-1 libncurses6_6.4+20231118-1 libncursesw6_6.4+20231118-1 libnettle8_3.9.1-2 libnpth0_1.6-3build2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnss-nis_3.1-0ubuntu6 libnss-nisplus_1.3-0ubuntu6 libp11-kit0_0.25.0-4ubuntu1 libpam-modules_1.5.2-9.1ubuntu1 libpam-modules-bin_1.5.2-9.1ubuntu1 libpam-runtime_1.5.2-9.1ubuntu1 libpam0g_1.5.2-9.1ubuntu1 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-9ubuntu1 libpipeline1_1.5.7-1 libpng16-16_1.6.40-2 libproc2-0_2:4.0.4-2ubuntu1 libquadmath0_13.2.0-6ubuntu1 libreadline8_8.2-1.3 libseccomp2_2.5.4-2ubuntu1 libselinux1_3.5-1build1 libsemanage-common_3.5-1build1 libsemanage2_3.5-1build1 libsepol2_3.5-1 libsframe1_2.41-6ubuntu1 libsmartcols1_2.39.2-6ubuntu1 libsqlite3-0_3.44.0-1 libss2_1.47.0-2ubuntu1 libssl3_3.0.10-1ubuntu3 libstdc++-13-dev_13.2.0-6ubuntu1 libstdc++6_13.2.0-6ubuntu1 libsub-override-perl_0.09-4 libsystemd-shared_253.5-1ubuntu7 libsystemd0_253.5-1ubuntu7 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-iconv-perl_1.7-8 libtext-wrapi18n-perl_0.06-10 libtinfo6_6.4+20231118-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libtsan2_13.2.0-6ubuntu1 libubsan1_13.2.0-6ubuntu1 libuchardet0_0.0.7-1build2 libudev1_253.5-1ubuntu7 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-6ubuntu1 libxml2_2.9.14+dfsg-1.3build1 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.0-9.9 lockfile-progs_0.1.19build1 login_1:4.13+dfsg1-1ubuntu1 logsave_1.47.0-2ubuntu1 lto-disabled-list_44 m4_1.4.19-4 make_4.3-4.1build1 man-db_2.12.0-1 mawk_1.3.4.20231102-1 mount_2.39.2-6ubuntu1 ncurses-base_6.4+20231118-1 ncurses-bin_6.4+20231118-1 openssl_3.0.10-1ubuntu3 optipng_0.7.7-3 passwd_1:4.13+dfsg1-1ubuntu1 patch_2.7.6-7build2 perl_5.36.0-9ubuntu1 perl-base_5.36.0-9ubuntu1 perl-modules-5.36_5.36.0-9ubuntu1 pinentry-curses_1.2.1-3ubuntu1 pkgbinarymangler_154 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:4.0.4-2ubuntu1 psmisc_23.6-1 readline-common_8.2-1.3 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 systemd_253.5-1ubuntu7 systemd-dev_253.5-1ubuntu7 systemd-sysv_253.5-1ubuntu7 sysvinit-utils_3.08-3ubuntu1 tar_1.34+dfsg-1.2ubuntu1 tzdata_2023c-9ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_35ubuntu1 util-linux_2.39.2-6ubuntu1 uuid-runtime_2.39.2-6ubuntu1 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-1ubuntu5 zlib1g-dev_1:1.2.13.dfsg-1ubuntu5 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: samtools-legacy Binary: libbam-dev Architecture: any Version: 0.1.19+dfsg-6ubuntu1 Maintainer: Ubuntu Developers Uploaders: Charles Plessy Homepage: https://www.htslib.org/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/samtools-legacy Vcs-Git: https://salsa.debian.org/med-team/samtools-legacy.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, samtools Build-Depends: debhelper-compat (= 13), libncurses5-dev, zlib1g-dev Package-List: libbam-dev deb libdevel optional arch=any Checksums-Sha1: 5fd99dde7fbf878d1bb3e7793a378ed6177b5c65 370876 samtools-legacy_0.1.19+dfsg.orig.tar.xz ecc03bbbabd485936dfacde2055b9e54ac4fd786 10784 samtools-legacy_0.1.19+dfsg-6ubuntu1.debian.tar.xz Checksums-Sha256: 485c3dfb668465449b393c5fd3b217f5262bb3f686232f6fddbc22d3c7b2f0bf 370876 samtools-legacy_0.1.19+dfsg.orig.tar.xz 7fca427aa868d7e46bfaf1304f70c75a0b5cd5e609819db3e1b51a3264ffa3f3 10784 samtools-legacy_0.1.19+dfsg-6ubuntu1.debian.tar.xz Files: 89dc3cc456c90901f7314580f1787ebb 370876 samtools-legacy_0.1.19+dfsg.orig.tar.xz 98d8f8e235809e06c28d154a8c2a215e 10784 samtools-legacy_0.1.19+dfsg-6ubuntu1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP 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verify inline signature for ./samtools-legacy_0.1.19+dfsg-6ubuntu1.dsc: no acceptable signature found dpkg-source: info: extracting samtools-legacy in /<> dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg.orig.tar.xz dpkg-source: info: unpacking samtools-legacy_0.1.19+dfsg-6ubuntu1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_example_makefile.patch dpkg-source: info: applying fix_segfault_with_small_ref.patch dpkg-source: info: applying fix_coverage_cap.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying gcc-11.patch dpkg-source: info: applying 515f6df-Remove-compressBound-assertions-PR-1258.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-27012353 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27012353 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27012353 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 samtools-legacy dpkg-buildpackage: info: source version 0.1.19+dfsg-6ubuntu1 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>' make[2]: Entering directory '/<>' rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib make[2]: Leaving directory '/<>' make[2]: Entering directory '/<>/bcftools' rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so* make[2]: Leaving directory '/<>/bcftools' make[2]: Entering directory '/<>/misc' rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a make[2]: Leaving directory '/<>/misc' make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- all all-recur razip lib CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make -j4 "INSTALL=install --strip-program=true" all all-recur razip lib "CFLAGS=-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2" make[2]: Entering directory '/<>' gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o make[3]: Entering directory '/<>' gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o bam2bcf_indel.c: In function ‘bcf_call_gap_prep’: bam2bcf_indel.c:305:26: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 305 | inscns = calloc(n_types * max_ins, 1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bam.h:46, from bam2bcf_indel.c:4: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o bam_index.c: In function ‘bam_index_core’: bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ bam_index.c: In function ‘bam_index_load_core’: bam_index.c:335:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o bam_index.c: In function ‘bam_index_core’: bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ bam_index.c: In function ‘bam_index_load_core’: bam_index.c:335:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o razip.c: In function ‘main’: razip.c:131:33: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | write(f_dst, buffer, c); | ^~~~~~~~~~~~~~~~~~~~~~~ razip.c: In function ‘write_open’: razip.c:32:25: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 32 | scanf("%c", &c); | ^~~~~~~~~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o razf.c: In function ‘razf_flush’: razf.c:221:17: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:234:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 234 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function ‘_razf_write’: razf.c:201:17: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function ‘razf_close’: razf.c:804:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 804 | write(rz->x.fpw, &rz->in, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:805:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 805 | write(rz->x.fpw, &rz->out, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:808:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 808 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:810:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 810 | write(rz->x.fpw, &v64, sizeof(int64_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function ‘razf_end_flush’: razf.c:258:25: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 258 | write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c: In function ‘save_zindex’: razf.c:96:19: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | if(is_be) write(fd, &rz->index->size, sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:99:17: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | write(fd, &v32, sizeof(uint32_t)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:106:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ razf.c:107:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 107 | write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o In file included from knetfile.c:46: knetfile.c: In function ‘kftp_send_cmd’: knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:236:9: note: in expansion of macro ‘netwrite’ 236 | netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); | ^~~~~~~~ knetfile.c: In function ‘khttp_connect_file’: knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 9 | #define netwrite(fd, ptr, len) write(fd, ptr, len) | ^~~~~~~~~~~~~~~~~~~ knetfile.c:415:9: note: in expansion of macro ‘netwrite’ 415 | netwrite(fp->fd, buf, l); | ^~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o bam_index.c: In function ‘bam_index_core’: bam_index.c:178:42: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int32_t’ {aka ‘int’} changes value from ‘last_bin = 4294967295’ to ‘-1’ [-Woverflow] 178 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ bam_index.c: In function ‘bam_index_load_core’: bam_index.c:335:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 335 | fread(magic, 1, 4, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:342:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 342 | fread(&idx->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:355:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 355 | fread(&size, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:358:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 358 | fread(&key, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~ bam_index.c:362:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 362 | fread(&p->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~ bam_index.c:366:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 366 | fread(p->list, 16, p->n, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:376:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 376 | fread(&index2->n, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ bam_index.c:380:17: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 380 | fread(index2->offset, index2->n, 8, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/<>' make[3]: Entering directory '/<>/bcftools' gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/<>' make[4]: Entering directory '/<>/bcftools' gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/<>/bcftools' make[3]: Entering directory '/<>/misc' make[3]: Nothing to be done for 'lib'. make[3]: Leaving directory '/<>/misc' gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-Bsymbolic-functions -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o ar: `u' modifier ignored since `D' is the default (see `U') make[4]: Leaving directory '/<>/bcftools' make[4]: Entering directory '/<>/misc' make[4]: Nothing to be done for 'lib'. make[4]: Leaving directory '/<>/misc' gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-Bsymbolic-functions -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread make[3]: Leaving directory '/<>' make[3]: Entering directory '/<>/bcftools' gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread make[3]: Leaving directory '/<>/bcftools' make[3]: Entering directory '/<>/misc' gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c gcc -c -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz make[3]: Leaving directory '/<>/misc' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' /usr/bin/make -C examples all make[2]: Entering directory '/<>/examples' ../samtools faidx ex1.fa ../samtools import ex1.fa.fai ex1.sam.gz ex1.bam [sam_header_read2] 2 sequences loaded. ../samtools index ex1.bam ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam [samopen] SAM header is present: 2 sequences. ../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam [samopen] SAM header is present: 2 sequences. (echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg ../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam ../samtools rmdup ex1f.bam ex1f-rmduppe.bam [bam_rmdup_core] processing reference seq1... [bam_rmdup_core] processing reference seq2... [bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1' [bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b' ../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam [bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1' [bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b' ../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf [mpileup] 1 samples in 1 input files Set max per-file depth to 8000 cc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/samtools-legacy-0.1.19+dfsg-6ubuntu1 -fPIC -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread -Wl,-Bsymbolic-functions -Wl,-z,relro # You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa' make[2]: Leaving directory '/<>/examples' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/libbam-dev/ dh_install dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs NEWS make[1]: Leaving directory '/<>' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libbam-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 pkgstriptranslations: processing libbam-dev (in debian/libbam-dev); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/libbam-dev/DEBIAN/control, package libbam-dev, directory debian/libbam-dev .. removing usr/share/doc/libbam-dev/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package libbam-dev ... pkgstripfiles: No PNG files. dpkg-deb: building package 'libbam-dev' in '../libbam-dev_0.1.19+dfsg-6ubuntu1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../samtools-legacy_0.1.19+dfsg-6ubuntu1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../samtools-legacy_0.1.19+dfsg-6ubuntu1_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 2023-11-21T23:09:14Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ samtools-legacy_0.1.19+dfsg-6ubuntu1_amd64.changes: --------------------------------------------------- Format: 1.8 Date: Tue, 21 Nov 2023 16:22:27 -0600 Source: samtools-legacy Binary: libbam-dev Built-For-Profiles: noudeb Architecture: amd64 Version: 0.1.19+dfsg-6ubuntu1 Distribution: noble-proposed Urgency: low Maintainer: Launchpad Build Daemon Changed-By: Aaron Rainbolt Description: libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format Launchpad-Bugs-Fixed: 2044194 Changes: samtools-legacy (0.1.19+dfsg-6ubuntu1) noble; urgency=low . * Merge from Debian unstable. (LP: #2044194) Remaining changes: - Add backport of upstream commit 515f6df as d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch in support of fixing 'zlib: compressBound() returns an incorrect result on z15'. * Fixed a couple of spelling errors in the description of d/p/515f6df-Remove-compressBound-assertions-PR-1258.patch. Checksums-Sha1: e685578c0b599bcd013a524d3cd90218680187fa 117484 libbam-dev_0.1.19+dfsg-6ubuntu1_amd64.deb 1ab97f4cc4ea64ce3c629fb4e656fa98a041fad2 5564 samtools-legacy_0.1.19+dfsg-6ubuntu1_amd64.buildinfo Checksums-Sha256: 8e63e141c2e10d427b789990a80c651f693ccb66863587e1efccd54b0b1d6675 117484 libbam-dev_0.1.19+dfsg-6ubuntu1_amd64.deb ae144993011dde4253f7c039a7d8943d5c8f4833421c2bf68b76c294cdd410d1 5564 samtools-legacy_0.1.19+dfsg-6ubuntu1_amd64.buildinfo Files: b834259f4a1f86e682e362a2531d1e11 117484 libdevel optional libbam-dev_0.1.19+dfsg-6ubuntu1_amd64.deb 148582ee506077941cde82fdc959ab88 5564 science optional samtools-legacy_0.1.19+dfsg-6ubuntu1_amd64.buildinfo Original-Maintainer: Debian Med Packaging Team /<>/samtools-legacy_0.1.19+dfsg-6ubuntu1_amd64.changes.new could not be renamed to /<>/samtools-legacy_0.1.19+dfsg-6ubuntu1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: samtools-legacy Binary: libbam-dev Architecture: amd64 Version: 0.1.19+dfsg-6ubuntu1 Checksums-Md5: b834259f4a1f86e682e362a2531d1e11 117484 libbam-dev_0.1.19+dfsg-6ubuntu1_amd64.deb Checksums-Sha1: e685578c0b599bcd013a524d3cd90218680187fa 117484 libbam-dev_0.1.19+dfsg-6ubuntu1_amd64.deb Checksums-Sha256: 8e63e141c2e10d427b789990a80c651f693ccb66863587e1efccd54b0b1d6675 117484 libbam-dev_0.1.19+dfsg-6ubuntu1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Tue, 21 Nov 2023 23:09:14 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-13build1), autotools-dev (= 20220109.1), base-files (= 13ubuntu4), base-passwd (= 3.6.2), bash (= 5.2.15-2ubuntu2), binutils (= 2.41-6ubuntu1), binutils-common (= 2.41-6ubuntu1), binutils-x86-64-linux-gnu (= 2.41-6ubuntu1), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), coreutils (= 9.1-1ubuntu2), cpp (= 4:13.2.0-1ubuntu1), cpp-13 (= 13.2.0-6ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.8ubuntu1), debianutils (= 5.14), debugedit (= 1:5.0-5), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.1ubuntu2), dpkg-dev (= 1.22.1ubuntu2), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-1ubuntu1), g++-13 (= 13.2.0-6ubuntu1), gcc (= 4:13.2.0-1ubuntu1), gcc-13 (= 13.2.0-6ubuntu1), gcc-13-base (= 13.2.0-6ubuntu1), gettext (= 0.21-13build1), gettext-base (= 0.21-13build1), grep (= 3.11-3), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), init-system-helpers (= 1.65.2ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.2.0-6ubuntu1), libatomic1 (= 13.2.0-6ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.1-1build1), libaudit1 (= 1:3.1.1-1build1), libbinutils (= 2.41-6ubuntu1), libblkid1 (= 2.39.2-6ubuntu1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.38-3ubuntu1), libc-dev-bin (= 2.38-3ubuntu1), libc6 (= 2.38-3ubuntu1), libc6-dev (= 2.38-3ubuntu1), libcap-ng0 (= 0.8.3-1build3), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.2.0-6ubuntu1), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41-6ubuntu1), libctf0 (= 2.41-6ubuntu1), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.270ubuntu1), libdebhelper-perl (= 13.11.8ubuntu1), libdpkg-perl (= 1.22.1ubuntu2), libdw1 (= 0.190-1), libelf1 (= 0.190-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-6ubuntu1), libgcc-s1 (= 13.2.0-6ubuntu1), libgcrypt20 (= 1.10.2-3ubuntu1), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgomp1 (= 13.2.0-6ubuntu1), libgpg-error0 (= 1.47-3), libgprofng0 (= 2.41-6ubuntu1), libgssapi-krb5-2 (= 1.20.1-5), libhwasan0 (= 13.2.0-6ubuntu1), libicu72 (= 72.1-3ubuntu3), libisl23 (= 0.26-3), libitm1 (= 13.2.0-6ubuntu1), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-5), libkeyutils1 (= 1.6.3-2), libkrb5-3 (= 1.20.1-5), libkrb5support0 (= 1.20.1-5), liblsan0 (= 13.2.0-6ubuntu1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.4-0.1), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-1), libmount1 (= 2.39.2-6ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncurses-dev (= 6.4+20231118-1), libncurses6 (= 6.4+20231118-1), libncursesw6 (= 6.4+20231118-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libpam-modules (= 1.5.2-9.1ubuntu1), libpam-modules-bin (= 1.5.2-9.1ubuntu1), libpam-runtime (= 1.5.2-9.1ubuntu1), libpam0g (= 1.5.2-9.1ubuntu1), libpcre2-8-0 (= 10.42-4), libperl5.36 (= 5.36.0-9ubuntu1), libpipeline1 (= 1.5.7-1), libquadmath0 (= 13.2.0-6ubuntu1), libseccomp2 (= 2.5.4-2ubuntu1), libselinux1 (= 3.5-1build1), libsframe1 (= 2.41-6ubuntu1), libsmartcols1 (= 2.39.2-6ubuntu1), libssl3 (= 3.0.10-1ubuntu3), libstdc++-13-dev (= 13.2.0-6ubuntu1), libstdc++6 (= 13.2.0-6ubuntu1), libsub-override-perl (= 0.09-4), libsystemd0 (= 253.5-1ubuntu7), libtinfo6 (= 6.4+20231118-1), libtirpc-common (= 1.3.4+ds-1), libtirpc-dev (= 1.3.4+ds-1), libtirpc3 (= 1.3.4+ds-1), libtool (= 2.4.7-7), libtsan2 (= 13.2.0-6ubuntu1), libubsan1 (= 13.2.0-6ubuntu1), libuchardet0 (= 0.0.7-1build2), libudev1 (= 253.5-1ubuntu7), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libxml2 (= 2.9.14+dfsg-1.3build1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.5.0-9.9), login (= 1:4.13+dfsg1-1ubuntu1), lto-disabled-list (= 44), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-1), mawk (= 1.3.4.20231102-1), ncurses-base (= 6.4+20231118-1), ncurses-bin (= 6.4+20231118-1), patch (= 2.7.6-7build2), perl (= 5.36.0-9ubuntu1), perl-base (= 5.36.0-9ubuntu1), perl-modules-5.36 (= 5.36.0-9ubuntu1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.34+dfsg-1.2ubuntu1), util-linux (= 2.39.2-6ubuntu1), xz-utils (= 5.4.4-0.1), zlib1g (= 1:1.2.13.dfsg-1ubuntu5), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu5) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1700605347" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libbam-dev_0.1.19+dfsg-6ubuntu1_amd64.deb ----------------------------------------- new Debian package, version 2.0. size 117484 bytes: control archive=1007 bytes. 965 bytes, 21 lines control 582 bytes, 9 lines md5sums Package: libbam-dev Source: samtools-legacy Version: 0.1.19+dfsg-6ubuntu1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 390 Depends: zlib1g-dev Section: libdevel Priority: optional Homepage: https://www.htslib.org/ Description: manipulates nucleotide sequence alignments in BAM or SAM format The BAM library provides I/O and various operations on manipulating nucleotide sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence Alignment/Map) format. It now supports importing from or exporting to SAM, sorting, merging, generating pileup, and quickly retrieval of reads overlapped with a specified region. . This library is part of SAMtools version 0.1.19. It is obsolete and provided only to build software that has not yet transitioned to the HTSlib, which replaces this library. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2023-11-21 22:22 ./ drwxr-xr-x root/root 0 2023-11-21 22:22 ./usr/ drwxr-xr-x root/root 0 2023-11-21 22:22 ./usr/include/ drwxr-xr-x root/root 0 2023-11-21 22:22 ./usr/include/samtools/ -rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h -rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h -rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h -rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h -rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h drwxr-xr-x root/root 0 2023-11-21 22:22 ./usr/lib/ -rw-r--r-- root/root 312242 2023-11-21 22:22 ./usr/lib/libbam.a drwxr-xr-x root/root 0 2023-11-21 22:22 ./usr/share/ drwxr-xr-x root/root 0 2023-11-21 22:22 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-11-21 22:22 ./usr/share/doc/libbam-dev/ -rw-r--r-- root/root 381 2022-12-12 16:30 ./usr/share/doc/libbam-dev/README.Debian -rw-r--r-- root/root 1228 2023-11-21 22:22 ./usr/share/doc/libbam-dev/changelog.Debian.gz -rw-r--r-- root/root 3824 2022-12-12 16:30 ./usr/share/doc/libbam-dev/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 12612 Build-Time: 9 Distribution: noble-proposed Host Architecture: amd64 Install-Time: 4 Job: samtools-legacy_0.1.19+dfsg-6ubuntu1.dsc Machine Architecture: amd64 Package: samtools-legacy Package-Time: 13 Source-Version: 0.1.19+dfsg-6ubuntu1 Space: 12612 Status: successful Version: 0.1.19+dfsg-6ubuntu1 -------------------------------------------------------------------------------- Finished at 2023-11-21T23:09:14Z Build needed 00:00:13, 12612k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27012353 Scanning for processes to kill in build PACKAGEBUILD-27012353