sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +==============================================================================+ | bwa 0.7.17-7 (amd64) Mon, 03 Jun 2024 00:12:49 +0000 | +==============================================================================+ Package: bwa Version: 0.7.17-7 Source Version: 0.7.17-7 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-dfad3e6f-edc4-4c01-abe1-04ae13709b9c' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bwa_0.7.17-7 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup bwa_0.7.17-7 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/bwa-k3cV4r/resolver-OKfyYv' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Hit:2 http://localhost:3142/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Hit:3 http://localhost:3142/debian sid InRelease Get:4 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/bwa_0.7.17-7.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/bwa-k3cV4r/bwa-0.7.17' with '<>' I: NOTICE: Log filtering will replace 'build/bwa-k3cV4r' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [643 B] Get:5 copy:/<>/apt_archive ./ Packages [675 B] Fetched 1927 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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1t64 libpipeline1 libsimde-dev libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff 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 bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1t64 libpipeline1 libsimde-dev libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 20.5 MB of archives. After this operation, 83.8 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [896 B] Get:2 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:5 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:6 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get:9 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-7 [95.9 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:11 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get:12 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:13 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:14 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:15 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:16 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:19 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:22 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:23 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:24 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get:27 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get:28 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:29 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:30 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB] Get:32 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libsimde-dev all 0.8.2-1 [465 kB] Get:34 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.5 MB in 0s (134 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 21779 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... 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Setting up libfakeroot:amd64 (1.34-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up fakeroot (1.34-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-2) ... 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 (1.14.0-1) ... Setting up gettext (0.21-14+b1) ... 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 (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64) Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40.1-7 bsdutils_1:2.40.1-7 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libasan8_14.1.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libblkid1_2.40.1-7 libbz2-1.0_1.0.8-5.1 libc-bin_2.38-12 libc-dev-bin_2.38-12 libc-l10n_2.38-12 libc6_2.38-12 libc6-dev_2.38-12 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14.1.0-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-4 libctf0_2.42-4 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.15.3 libdpkg-perl_1.22.6 libeatmydata1_131-2 libelf1t64_0.191-1+b1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.2.0-25 libgcc-s1_14.1.0-1 libgcrypt20_1.10.3-3 libgdbm-compat4t64_1.23-5.1+b1 libgdbm6t64_1.23-5.1+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-4 libgomp1_14.1.0-1 libgpg-error0_1.49-2 libgprofng0_2.42-4 libhogweed6t64_3.9.1-2.2 libhwasan0_14.1.0-1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.1.0-1 libjansson4_2.14-2+b2 libksba8_1.6.6-1 libldap-2.5-0_2.5.17+dfsg-1+b1 liblsan0_14.1.0-1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.1-7 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.9.1-2.2 libnpth0t64_1.6-3.1 libp11-kit0_0.25.3-5 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0~rc1-1 libpipeline1_1.5.7-2 libquadmath0_14.1.0-1 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1 libselinux1_3.5-2+b2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b3 libsepol2_3.5-2+b1 libsframe1_2.42-4 libsimde-dev_0.8.2-1 libsmartcols1_2.40.1-7 libsqlite3-0_3.46.0-1 libssl3t64_3.2.1-3 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 libsystemd0_256~rc3-7 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.1.0-1 libubsan1_14.1.0-1 libuchardet0_0.0.8-1+b1 libudev1_256~rc3-7 libunistring5_1.2-1 libuuid1_2.40.1-7 libxml2_2.12.7+dfsg-2 libxxhash0_0.8.2-2+b1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.12-1 locales-all_2.38-12 login_1:4.13+dfsg1-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.13+dfsg1-4 patch_2.7.6-7 perl_5.40.0~rc1-1 perl-base_5.40.0~rc1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0~rc1-1 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.09-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.1-7 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bwa Binary: bwa, libbwa-dev Architecture: any Version: 0.7.17-7 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille , Carlos Borroto , Ognyan Kulev , Michael R. Crusoe Homepage: http://bio-bwa.sourceforge.net/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/bwa Vcs-Git: https://salsa.debian.org/med-team/bwa.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), zlib1g-dev, libsimde-dev Package-List: bwa deb science optional arch=any libbwa-dev deb libdevel optional arch=any Checksums-Sha1: 77f9aac723110227ea51cb42011336d291d03723 232593 bwa_0.7.17.orig.tar.gz 6fec29cceeea8141a11afd85a0af448fed80ea6e 10668 bwa_0.7.17-7.debian.tar.xz Checksums-Sha256: 980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd 232593 bwa_0.7.17.orig.tar.gz 5a314c240f2dddb9f0ab848fe2b1bacf37f794d1addbf023187ba5ce5aa8f1e7 10668 bwa_0.7.17-7.debian.tar.xz Files: 63c54309e7dda2311d4658e18c7adffb 232593 bwa_0.7.17.orig.tar.gz 3640eaef26aa14b5c4428dc2012586a7 10668 bwa_0.7.17-7.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmIlHc0ACgkQYAMWptwn dHaeug//XGse19+JuWA2BgZedo3/3pt6Or//HXDplLWvXtvQDTCgwgocdNmp2rkN 53ku/f5v9GqWXcUrwhNeDcuH+uGDpm+2f7VQojFXrQ7m578UGwwtbSc8AAV1yzR4 Ye3C7DnnZ2Bl0IIDBkqupJy60ls74opiQF0L1xPx9+U3ydx4Hys1m82dragQsuEi VVeUo/NmWnLQh2cQcLTlE/Gq2ox0VHuxCGCI6t0kAYynfw1nccCIAlYI9U8W8MME 8RX3T55ZdvlGnajciXQ5pIAe1TCt1WlL5npnS2igzphVnODAO7ECb2j3pyBZuCYV R+bYviGBNH39lZ2oXtHV2mK/QQZYcCmHEO+YEY5l+kw3JeIK7+0L+J3fpHvz1mXH 2Q/UC3uyDTaoyhvBFGi88U6LHPk+GeGqkB/8oGHI+rJnVUsJZ03060fKqyycoF8E nkId/1KzNEWoUe+UAjBNNNfm7z6cwCjneG6Ed2Hzj7cM4AFBqHpdBXIbYKdU64Ys B3wSsiZGyPIFOU+H5QEbb6w/nfby33n73Rwi+S1M3QtE+IUlLEaxJBua2zE3MiMA crpBnMrcQTnpLnSErSpRwvYt8ZSut9/Ef1vYrrB2XPENkN4ut7sox4jXgIga3AIc nLBG1co2UJHrUqwkhOdOaWB0KxeSKToPAbcUTCGtxigpXLUEOWI= =Hmxf -----END PGP SIGNATURE----- gpgv: Signature made Sun Mar 6 20:47:09 2022 UTC gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bwa_0.7.17-7.dsc: no acceptable signature found dpkg-source: info: extracting bwa in /<> dpkg-source: info: unpacking bwa_0.7.17.orig.tar.gz dpkg-source: info: unpacking bwa_0.7.17-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_heap_block_overrun dpkg-source: info: applying fix_build_on_freebsd.patch dpkg-source: info: applying CVE-2019-10269.patch dpkg-source: info: applying simde dpkg-source: info: applying spelling dpkg-source: info: applying gcc10.patch dpkg-source: info: applying hurd Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bwa_0.7.17-7 perl-5.40-throwaway amd64 ------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network bwa_0.7.17-7 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-dfad3e6f-edc4-4c01-abe1-04ae13709b9c SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package bwa dpkg-buildpackage: info: source version 0.7.17-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j2 clean make[1]: Entering directory '/<>' rm -f gmon.out *.o a.out bwa *~ *.a make[1]: Leaving directory '/<>' dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building bwa using existing ./bwa_0.7.17.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building bwa in bwa_0.7.17-7.debian.tar.xz dpkg-source: info: building bwa in bwa_0.7.17-7.dsc 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 -- CFLAGS="-Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS="-DHAVE_PTHREAD" make -j2 "INSTALL=install --strip-program=true" "CFLAGS=-Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now" DFLAGS=-DHAVE_PTHREAD make[2]: Entering directory '/<>' gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD utils.c -o utils.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kthread.c -o kthread.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kstring.c -o kstring.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD ksw.c -o ksw.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt.c -o bwt.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bntseq.c -o bntseq.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwa.c -o bwa.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem.c -o bwamem.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem_pair.c -o bwamem_pair.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwamem_extra.c -o bwamem_extra.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD malloc_wrap.c -o malloc_wrap.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD QSufSort.c -o QSufSort.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o bwt_gen.c: In function ‘BWTIncBuildRelativeRank’: bwt_gen.c:879:17: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable] 879 | bgint_t oldInverseSa0RelativeRank = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~ bwt_gen.c: In function ‘BWTIncMergeBwt’: bwt_gen.c:953:22: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable] 953 | unsigned int bitsInWordMinusBitPerChar; | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD rope.c -o rope.o rope.c: In function ‘rope_restore_node’: rope.c:282:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 282 | fread(&is_bottom, 1, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:283:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 283 | fread(&n, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~~ rope.c:291:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 291 | fread(p[i].c, 8, 6, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c:292:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 292 | fread(q, 2, 1, fp); | ^~~~~~~~~~~~~~~~~~ rope.c:293:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 293 | fread(q + 1, 1, *q, fp); | ^~~~~~~~~~~~~~~~~~~~~~~ rope.c: In function ‘rope_restore’: rope.c:312:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 312 | fread(&r->max_nodes, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rope.c:313:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 313 | fread(&r->block_len, 4, 1, fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD rle.c -o rle.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD is.c -o is.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtindex.c -o bwtindex.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwashm.c -o bwashm.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwase.c -o bwase.o bwashm.c: In function ‘bwa_shm_stage’: bwashm.c:33:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 33 | ftruncate(shmid, BWA_CTL_SIZE); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bwashm.c:70:9: warning: ignoring return value of ‘ftruncate’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 70 | ftruncate(shmid, idx->l_mem); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtgap.c -o bwtgap.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtaln.c -o bwtaln.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bamlite.c -o bamlite.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwape.c -o bwape.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD kopen.c -o kopen.o In file included from /usr/include/string.h:548, from kopen.c:6: In function ‘strncpy’, inlined from ‘cmd2argv’ at kopen.c:248:2, inlined from ‘kopen’ at kopen.c:306:13: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ specified bound between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘cmd2argv’, inlined from ‘kopen’ at kopen.c:306:13: kopen.c:247:32: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 247 | argv[0] = str = (char*)calloc(end - beg + 1, 1); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from kopen.c:7: /usr/include/stdlib.h: In function ‘kopen’: /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 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD pemerge.c -o pemerge.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD maxk.c -o maxk.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD fastmap.c -o fastmap.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwtsw2_pair.c -o bwtsw2_pair.o gcc -c -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD main.c -o main.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o ar: `u' modifier ignored since `D' is the default (see `U') gcc -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -DHAVE_PTHREAD bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' dh_auto_test create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/<>' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs NEWS.md make[1]: Leaving directory '/<>' dh_installexamples dh_installman 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 debian/rules override_dh_gencontrol make[1]: Entering directory '/<>' dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.8.2-1), " dpkg-gencontrol: warning: package bwa: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package bwa: substitution variable ${perl:Depends} unused, but is defined make[1]: Leaving directory '/<>' dh_md5sums dh_builddeb dpkg-deb: building package 'libbwa-dev' in '../libbwa-dev_0.7.17-7_amd64.deb'. dpkg-deb: building package 'bwa' in '../bwa_0.7.17-7_amd64.deb'. dpkg-deb: building package 'bwa-dbgsym' in '../bwa-dbgsym_0.7.17-7_amd64.deb'. dpkg-genbuildinfo -O../bwa_0.7.17-7_amd64.buildinfo dpkg-genchanges -O../bwa_0.7.17-7_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2024-06-03T00:13:06Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ bwa_0.7.17-7_amd64.changes: --------------------------- Format: 1.8 Date: Sun, 06 Mar 2022 21:43:27 +0100 Source: bwa Binary: bwa bwa-dbgsym libbwa-dev Architecture: source amd64 Version: 0.7.17-7 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: bwa - Burrows-Wheeler Aligner libbwa-dev - Burrows-Wheeler Aligner source files Changes: bwa (0.7.17-7) unstable; urgency=medium . * Team upload * Installing all header files in /usr/include/bwa * Standards-Version: 4.6.0 (routine-update) . [ Steffen Möller ] * Update metadata - ref to guix Checksums-Sha1: 1eb624b80502d0a85d6a4509e521623737762520 1233 bwa_0.7.17-7.dsc 05af5d34eccd20425c18d025bd3b45e0fdc00da3 10676 bwa_0.7.17-7.debian.tar.xz ec56cc3e5d47de67562ab163f9d68aebd97c836b 452636 bwa-dbgsym_0.7.17-7_amd64.deb b188f9099502a9ca820deb267c740b0ee8570254 5438 bwa_0.7.17-7_amd64.buildinfo 18e3eb244cec3ed0557aef44d20cecc513bd0d50 212020 bwa_0.7.17-7_amd64.deb 285b55530ab5599c44c8b61e1064503a8165579f 155768 libbwa-dev_0.7.17-7_amd64.deb Checksums-Sha256: 238a1eae74740b26fcae938da766975dc0f5c0ce35d12be3fcf7cac35fc924b5 1233 bwa_0.7.17-7.dsc 9bbfdab0d3f8de5050c10bd6629d45a05f57a7cb479cfd4740ebc2046c3a9922 10676 bwa_0.7.17-7.debian.tar.xz ccd4c08bcbdaadd6346f67f9eeea08a1367b9c1fce693eff9b3f2ca49282ffe2 452636 bwa-dbgsym_0.7.17-7_amd64.deb 3396271d80a09dcb4bb716ca3fe3e82e662c31aae1598cc35952a26480f432e5 5438 bwa_0.7.17-7_amd64.buildinfo 8346cb519488c8e00b8fb0ad4f80797aacf0af7ac9a93761f82e7b18d17b43de 212020 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+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 (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13.2), base-passwd (= 3.6.3), bash (= 5.2.21-2+b1), binutils (= 2.42-4), binutils-common (= 2.42-4), binutils-x86-64-linux-gnu (= 2.42-4), bsdextrautils (= 2.40.1-7), bsdutils (= 1:2.40.1-7), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-25), cpp-13-x86-64-linux-gnu (= 13.2.0-25), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-8), debconf (= 1.5.86), debhelper (= 13.15.3), debianutils (= 5.17), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.9.0-6), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-25), g++-13-x86-64-linux-gnu (= 13.2.0-25), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-25), gcc-13-base (= 13.2.0-25), gcc-13-x86-64-linux-gnu (= 13.2.0-25), gcc-14-base (= 14.1.0-1), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+b1), grep (= 3.11-4), groff-base (= 1.23.0-4), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.1.0-1), libatomic1 (= 14.1.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-4), libblkid1 (= 2.40.1-7), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.38-12), libc-dev-bin (= 2.38-12), libc6 (= 2.38-12), libc6-dev (= 2.38-12), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.1.0-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4), libctf0 (= 2.42-4), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.15.3), libdpkg-perl (= 1.22.6), libelf1t64 (= 0.191-1+b1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.2.0-25), libgcc-s1 (= 14.1.0-1), libgdbm-compat4t64 (= 1.23-5.1+b1), libgdbm6t64 (= 1.23-5.1+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.1.0-1), libgprofng0 (= 2.42-4), libhwasan0 (= 14.1.0-1), libicu72 (= 72.1-4+b1), libisl23 (= 0.26-3+b2), libitm1 (= 14.1.0-1), libjansson4 (= 2.14-2+b2), liblsan0 (= 14.1.0-1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.1-7), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0~rc1-1), libpipeline1 (= 1.5.7-2), libquadmath0 (= 14.1.0-1), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-2+b2), libsframe1 (= 2.42-4), libsimde-dev (= 0.8.2-1), libsmartcols1 (= 2.40.1-7), libssl3t64 (= 3.2.1-3), libstdc++-13-dev (= 13.2.0-25), libstdc++6 (= 14.1.0-1), libsystemd0 (= 256~rc3-7), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.1.0-1), libubsan1 (= 14.1.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256~rc3-7), libunistring5 (= 1.2-1), libuuid1 (= 2.40.1-7), libxml2 (= 2.12.7+dfsg-2), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.12-1), login (= 1:4.13+dfsg1-4), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), patch (= 2.7.6-7), perl (= 5.40.0~rc1-1), perl-base (= 5.40.0~rc1-1), perl-modules-5.40 (= 5.40.0~rc1-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.09-1), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.1-7), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1646599407" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ bwa-dbgsym_0.7.17-7_amd64.deb ----------------------------- new Debian package, version 2.0. size 452636 bytes: control archive=532 bytes. 356 bytes, 12 lines control 106 bytes, 1 lines md5sums Package: bwa-dbgsym Source: bwa Version: 0.7.17-7 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 471 Depends: bwa (= 0.7.17-7) Section: debug Priority: optional Description: debug symbols for bwa Build-Ids: ff2a05630b20aeb761288f220e04a20dc14b3e83 drwxr-xr-x root/root 0 2022-03-06 20:43 ./ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/lib/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/lib/debug/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/lib/debug/.build-id/ff/ -rw-r--r-- root/root 471480 2022-03-06 20:43 ./usr/lib/debug/.build-id/ff/2a05630b20aeb761288f220e04a20dc14b3e83.debug drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/doc/ lrwxrwxrwx root/root 0 2022-03-06 20:43 ./usr/share/doc/bwa-dbgsym -> bwa bwa_0.7.17-7_amd64.deb ---------------------- new Debian package, version 2.0. size 212020 bytes: control archive=1308 bytes. 1015 bytes, 23 lines control 916 bytes, 14 lines md5sums Package: bwa Version: 0.7.17-7 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 455 Depends: libc6 (>= 2.34), zlib1g (>= 1:1.1.4) Recommends: perl Suggests: samtools Built-Using: simde (= 0.8.2-1) Section: science Priority: optional Homepage: http://bio-bwa.sourceforge.net/ Description: Burrows-Wheeler Aligner BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. drwxr-xr-x root/root 0 2022-03-06 20:43 ./ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/bin/ -rwxr-xr-x root/root 404144 2022-03-06 20:43 ./usr/bin/bwa drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/bash-completion/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/bash-completion/completions/ -rw-r--r-- root/root 384 2022-03-06 14:42 ./usr/share/bash-completion/completions/bwa drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/bwa/ -rwxr-xr-x root/root 613 2022-03-06 20:43 ./usr/share/bwa/qualfa2fq.pl -rwxr-xr-x root/root 727 2022-03-06 20:43 ./usr/share/bwa/xa2multi.pl drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/doc/bwa/ -rw-r--r-- root/root 4216 2017-10-23 17:10 ./usr/share/doc/bwa/README-alt.md.gz -rw-r--r-- root/root 3511 2017-10-23 17:10 ./usr/share/doc/bwa/README.md.gz -rw-r--r-- root/root 823 2022-03-06 20:43 ./usr/share/doc/bwa/changelog.Debian.gz -rw-r--r-- root/root 14186 2022-03-06 20:43 ./usr/share/doc/bwa/changelog.gz -rw-r--r-- root/root 4397 2022-03-06 20:40 ./usr/share/doc/bwa/copyright drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/doc/bwa/examples/ -rw-r--r-- root/root 96 2022-03-06 14:42 ./usr/share/doc/bwa/examples/read1.fq -rw-r--r-- root/root 96 2022-03-06 14:42 ./usr/share/doc/bwa/examples/read2.fq -rw-r--r-- root/root 384 2022-03-06 14:42 ./usr/share/doc/bwa/examples/reads.fq -rw-r--r-- root/root 192 2022-03-06 14:42 ./usr/share/doc/bwa/examples/ref.fa drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/man/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/man/man1/ -rw-r--r-- root/root 10609 2022-03-06 20:43 ./usr/share/man/man1/bwa.1.gz libbwa-dev_0.7.17-7_amd64.deb ----------------------------- new Debian package, version 2.0. size 155768 bytes: control archive=1600 bytes. 1055 bytes, 24 lines control 1558 bytes, 26 lines md5sums Package: libbwa-dev Source: bwa Version: 0.7.17-7 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 472 Suggests: samtools Built-Using: simde (= 0.8.2-1) Section: libdevel Priority: optional Homepage: http://bio-bwa.sourceforge.net/ Description: Burrows-Wheeler Aligner source files BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads. . This package contains the source files for use in other programs. drwxr-xr-x root/root 0 2022-03-06 20:43 ./ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/include/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/include/bwa/ -rw-r--r-- root/root 1646 2017-10-23 17:10 ./usr/include/bwa/QSufSort.h -rw-r--r-- root/root 3124 2017-10-23 17:10 ./usr/include/bwa/bamlite.h -rw-r--r-- root/root 2775 2017-10-23 17:10 ./usr/include/bwa/bntseq.h -rw-r--r-- root/root 2044 2017-10-23 17:10 ./usr/include/bwa/bwa.h -rw-r--r-- root/root 7996 2022-03-06 20:43 ./usr/include/bwa/bwamem.h -rw-r--r-- root/root 1033 2017-10-23 17:10 ./usr/include/bwa/bwase.h -rw-r--r-- root/root 4966 2017-10-23 17:10 ./usr/include/bwa/bwt.h -rw-r--r-- root/root 653 2017-10-23 17:10 ./usr/include/bwa/bwt_lite.h -rw-r--r-- root/root 3833 2017-10-23 17:10 ./usr/include/bwa/bwtaln.h -rw-r--r-- root/root 996 2017-10-23 17:10 ./usr/include/bwa/bwtgap.h -rw-r--r-- root/root 1524 2017-10-23 17:10 ./usr/include/bwa/bwtsw2.h -rw-r--r-- root/root 15889 2017-10-23 17:10 ./usr/include/bwa/kbtree.h -rw-r--r-- root/root 20888 2017-10-23 17:10 ./usr/include/bwa/khash.h -rw-r--r-- root/root 8857 2017-10-23 17:10 ./usr/include/bwa/kseq.h -rw-r--r-- root/root 9718 2017-10-23 17:10 ./usr/include/bwa/ksort.h -rw-r--r-- root/root 2332 2017-10-23 17:10 ./usr/include/bwa/kstring.h -rw-r--r-- root/root 5091 2017-10-23 17:10 ./usr/include/bwa/ksw.h -rw-r--r-- root/root 2940 2017-10-23 17:10 ./usr/include/bwa/kvec.h -rw-r--r-- root/root 1183 2017-10-23 17:10 ./usr/include/bwa/malloc_wrap.h -rw-r--r-- root/root 1910 2022-03-06 20:43 ./usr/include/bwa/rle.h -rw-r--r-- root/root 1548 2017-10-23 17:10 ./usr/include/bwa/rope.h -rw-r--r-- root/root 3821 2017-10-23 17:10 ./usr/include/bwa/utils.h drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/lib/ -rw-r--r-- root/root 338992 2022-03-06 20:43 ./usr/lib/libbwa.a drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-03-06 20:43 ./usr/share/doc/libbwa-dev/ -rw-r--r-- root/root 825 2022-03-06 20:43 ./usr/share/doc/libbwa-dev/changelog.Debian.gz -rw-r--r-- root/root 14186 2022-03-06 20:43 ./usr/share/doc/libbwa-dev/changelog.gz -rw-r--r-- root/root 4397 2022-03-06 20:40 ./usr/share/doc/libbwa-dev/copyright +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 9164 Build-Time: 10 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 5 Job: /srv/debomatic/incoming/bwa_0.7.17-7.dsc Machine Architecture: amd64 Package: bwa Package-Time: 17 Source-Version: 0.7.17-7 Space: 9164 Status: successful Version: 0.7.17-7 -------------------------------------------------------------------------------- Finished at 2024-06-03T00:13:06Z Build needed 00:00:17, 9164k disk space