sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | repeatmasker-recon 1.08-8 (amd64) Mon, 05 Aug 2024 00:14:37 +0000 | +==============================================================================+ Package: repeatmasker-recon Version: 1.08-8 Source Version: 1.08-8 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-4dfdbb8e-6311-4bdf-b47c-9479b4b2e0df' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup repeatmasker-recon_1.08-8 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup repeatmasker-recon_1.08-8 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/repeatmasker-recon-zSsfcx/resolver-QKEYiJ' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://localhost:3142/debian sid InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] 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/repeatmasker-recon_1.08-8.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/repeatmasker-recon-zSsfcx/repeatmasker-recon-1.08' with '<>' I: NOTICE: Log filtering will replace 'build/repeatmasker-recon-zSsfcx' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), 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 [617 B] Get:5 copy:/<>/apt_archive ./ Packages [649 B] Fetched 1875 B in 0s (115 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following 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 libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils 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 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 19.7 MB of archives. After this operation, 75.4 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [880 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-1 [96.1 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-2 [1411 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.16 [88.6 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3+b1 [671 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.16 [891 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libfakeroot amd64 1.35.1-1 [28.6 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 fakeroot amd64 1.35.1-1 [74.5 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.7 MB in 0s (161 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 22966 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... 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_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... 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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Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../31-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.16) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.35.1-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up fakeroot (1.35.1-1) ... 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 (0.22.5-2) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... 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 (0.22.5-2) ... 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 (1.23.0-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.16) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.39-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.9.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.9.7-1 (2024-06-27) amd64 (x86_64) Toolchain package versions: binutils_2.42.90.20240720-2 dpkg-dev_1.22.11 g++-13_13.3.0-4 g++-14_14.2.0-1 gcc-13_13.3.0-4 gcc-14_14.2.0-1 libc6-dev_2.39-6 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 linux-libc-dev_6.9.12-1 Package versions: adduser_3.137 apt_2.9.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.4 base-passwd_3.6.4 bash_5.2.21-2.1 binutils_2.42.90.20240720-2 binutils-common_2.42.90.20240720-2 binutils-x86-64-linux-gnu_2.42.90.20240720-2 bsdextrautils_2.40.2-1 bsdutils_1:2.40.2-1 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-13_13.3.0-4 cpp-13-x86-64-linux-gnu_13.3.0-4 cpp-14_14.2.0-1 cpp-14-x86-64-linux-gnu_14.2.0-1 cpp-x86-64-linux-gnu_4:14.1.0-2 dash_0.5.12-9 debconf_1.5.87 debhelper_13.16 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-8 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.35.1-1 file_1:5.45-3 findutils_4.10.0-2 g++_4:14.1.0-2 g++-13_13.3.0-4 g++-13-x86-64-linux-gnu_13.3.0-4 g++-14_14.2.0-1 g++-14-x86-64-linux-gnu_14.2.0-1 g++-x86-64-linux-gnu_4:14.1.0-2 gcc_4:14.1.0-2 gcc-13_13.3.0-4 gcc-13-base_13.3.0-4 gcc-13-x86-64-linux-gnu_13.3.0-4 gcc-14_14.2.0-1 gcc-14-base_14.2.0-1 gcc-14-x86-64-linux-gnu_14.2.0-1 gcc-x86-64-linux-gnu_4:14.1.0-2 gettext_0.22.5-2 gettext-base_0.22.5-2 gnupg_2.2.43-8 gnupg-l10n_2.2.43-8 gnupg-utils_2.2.43-8 gpg_2.2.43-8 gpg-agent_2.2.43-8 gpg-wks-client_2.2.43-8 gpgconf_2.2.43-8 gpgsm_2.2.43-8 gpgv_2.2.43-8 grep_3.11-4 groff-base_1.23.0-5 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_2.9.7 libarchive-zip-perl_1.68-1 libasan8_14.2.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.2.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-4 libaudit1_1:3.1.2-4+b1 libbinutils_2.42.90.20240720-2 libblkid1_2.40.2-1 libbsd0_0.12.2-1 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-6 libc-dev-bin_2.39-6 libc-l10n_2.39-6 libc6_2.39-6 libc6-dev_2.39-6 libcap-ng0_0.8.5-1+b1 libcap2_1:2.66-5 libcc1-0_14.2.0-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42.90.20240720-2 libctf0_2.42.90.20240720-2 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.16 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libfakeroot_1.35.1-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.3.0-4 libgcc-14-dev_14.2.0-1 libgcc-s1_14.2.0-1 libgcrypt20_1.11.0-5 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.6-2 libgomp1_14.2.0-1 libgpg-error0_1.50-2 libgprofng0_2.42.90.20240720-2 libhogweed6t64_3.10-1 libhwasan0_14.2.0-1 libicu72_72.1-5 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.2.0-1 libjansson4_2.14-2+b2 libksba8_1.6.7-2 libldap-2.5-0_2.5.18+dfsg-2+b1 liblsan0_14.2.0-1 liblz4-1_1.9.4-3 liblzma5_5.6.2-2 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.2-1 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.10-1 libnpth0t64_1.6-3.1 libp11-kit0_0.25.5-2 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_5.40.0-1 libpipeline1_1.5.7-2 libquadmath0_14.2.0-1 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1+b1 libselinux1_3.5-2+b3 libsemanage-common_3.5-1 libsemanage2_3.5-1+b4 libsepol2_3.5-2+b1 libsframe1_2.42.90.20240720-2 libsmartcols1_2.40.2-1 libsqlite3-0_3.46.0-1 libssl3t64_3.3.1-2 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.2.0-1 libstdc++6_14.2.0-1 libsystemd0_256.4-2 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.2.0-1 libubsan1_14.2.0-1 libuchardet0_0.0.8-1+b1 libudev1_256.4-2 libunistring5_1.2-1 libuuid1_2.40.2-1 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd1_1.5.6+dfsg-1 linux-libc-dev_6.9.12-1 locales-all_2.39-6 login_1:4.15.3-3 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-2 mawk_1.3.4.20240622-2 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.15.3-3 patch_2.7.6-7 perl_5.40.0-1 perl-base_5.40.0-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0-1 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_0.0.24 sysvinit-utils_3.09-2 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.2-1 xz-utils_5.6.2-2 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: repeatmasker-recon Binary: repeatmasker-recon Architecture: any Version: 1.08-8 Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Andreas Tille , Homepage: https://www.repeatmasker.org/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/repeatmasker-recon Vcs-Git: https://salsa.debian.org/med-team/repeatmasker-recon.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: repeatmasker-recon deb science optional arch=any Checksums-Sha1: a91b9f54dc277248c6848c2584531f7538bec3b4 108477 repeatmasker-recon_1.08.orig.tar.gz 7742af75fe931bb48fed7f73097141e28ec8d5c4 5980 repeatmasker-recon_1.08-8.debian.tar.xz Checksums-Sha256: 699765fa49d18dbfac9f7a82ecd054464b468cb7521abe9c2bd8caccf08ee7d8 108477 repeatmasker-recon_1.08.orig.tar.gz 4d1ac5ddbc014ba414efad01003c4df7fcb6046debba1f75376aca2123be36b6 5980 repeatmasker-recon_1.08-8.debian.tar.xz Files: 48c5c650a312bc1cc3fdddcfd943deb0 108477 repeatmasker-recon_1.08.orig.tar.gz 1835d963ebdb4632412a087475e79aa5 5980 repeatmasker-recon_1.08-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmXxv+oACgkQPCZ2P2xn 5uK6Uw//YuwYNshpmxC7WNweGtXXYB2aC+D9cdEn0mxwg8iXhpNHdnA0e+NzpDSe +HHjf73zzbwYjibS/tMcU5+PKCRrwuReRw9A0b9+iSxtCzL/hFoTgivzLnPK6Lkg 9tUOUHWH+m3uw1/2qnpaMA8sfaEBynKFNZPv6vDXlXTs5a66zSj9biUM+8CGqae9 sUH+VHwln3vmiBRS6/UtIsXIl82KkXms3ql/jOgH+J06+wqIfBjQ/tkwqgup+V9v 9e3VdLqzLISXdqJflX8OsdnsU4SPLHyd1ju5GC/y8WLK3KIU1OsQX6O6+G9LYfAU RXjaSADmFd4WJk5V7OnfOhcbUA+skq0EbmFI2FaFe2WDxwUPlMH3qJ2SnwNqJL6f CmIrLPp+vs8vxLmf8zbeQ98I2/K1Ln3gKzEs2Vb6LRGeo5/bjllUUdXxlU8THxEi jtoNyEeCiOU8Ko3RRvRjxiD1M9kiT99eIoQbFwmukcxvUoor4XrQ0KVxUYvga3et xF6EydndzXKZGSTspk/iFezuBAsH6ukoBqyd1PcLBc7lz1byAa5bAAs8Ijb/k5/b w5+13tiLK1mXcTPinSRnTLEzR5zpfbuETeNbDhiYZW5pwA6aj2N+1/uuk4lr3i5u kyBCl4CkeRiLrIG9ZnHdaCQcdMLjsDGITyq4ZOF+SEnlO27Pp7I= =u+mC -----END PGP SIGNATURE----- gpgv: Signature made Wed Mar 13 15:02:02 2024 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./repeatmasker-recon_1.08-8.dsc: no acceptable signature found dpkg-source: info: extracting repeatmasker-recon in /<> dpkg-source: info: unpacking repeatmasker-recon_1.08.orig.tar.gz dpkg-source: info: unpacking repeatmasker-recon_1.08-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-udpate-paths.patch dpkg-source: info: applying 0002-fix_binary_name.patch dpkg-source: info: applying 0003-hardening.patch dpkg-source: info: applying 0004-missing-include.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network repeatmasker-recon_1.08-8 perl-5.40-throwaway amd64 -------------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network repeatmasker-recon_1.08-8 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-4dfdbb8e-6311-4bdf-b47c-9479b4b2e0df 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 repeatmasker-recon dpkg-buildpackage: info: source version 1.08-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j2 clean make[1]: Entering directory '/<>/src' rm -f imagespread eledef eleredef edgeredef famdef *.o *~ *.Addrs *.Counts *.pixie Makefile.bak core imagespread eledef eleredef edgeredef famdef TAGS make[1]: Leaving directory '/<>/src' dh_autoreconf_clean -O--sourcedirectory=src debian/rules override_dh_clean make[1]: Entering directory '/<>' rm -rf bin dh_clean make[1]: Leaving directory '/<>' dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building repeatmasker-recon using existing ./repeatmasker-recon_1.08.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: warning: ignoring deletion of directory bin dpkg-source: info: building repeatmasker-recon in repeatmasker-recon_1.08-8.debian.tar.xz dpkg-source: info: building repeatmasker-recon in repeatmasker-recon_1.08-8.dsc debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src cd src && make -j2 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro imagespread.c -o imagespread gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eledef.c -o eledef In file included from eledef.c:1: msps.h: In function ‘scan_msp’: msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function ‘GetSeqNames’: seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from imagespread.c:2: msps.h: In function ‘scan_msp’: msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d eledef.c: In function ‘main’: eledef.c:95:13: warning: ignoring return value of ‘freopen’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:246:7: note: in expansion of macro ‘DUMBBELL’ 246 | DUMBBELL; | ^~~~~~~~ eledef.c:95:13: warning: ignoring return value of ‘freopen’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 95 | freopen(ele_name, "w", all_ele);\ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eledef.c:253:5: note: in expansion of macro ‘DUMBBELL’ 253 | DUMBBELL; | ^~~~~~~~ In file included from msps.h:4: seqlist.h: In function ‘GetSeqNames’: seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro eleredef.c -o eleredef In file included from ele.h:1, from eleredef.c:5: msps.h: In function ‘scan_msp’: msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d eleredef.c: In function ‘main’: eleredef.c:239:70: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long unsigned int’ [-Wformat=] 239 | printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) ); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int long unsigned int | %ld In file included from msps.h:4: seqlist.h: In function ‘GetSeqNames’: seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro edgeredef.c -o edgeredef In file included from ele.h:1, from edgeredef.c:1: msps.h: In function ‘scan_msp’: msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function ‘GetSeqNames’: seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ edgeredef.c: In function ‘general_edge_redef’: edgeredef.c:200:5: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 200 | system(command); | ^~~~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro famdef.c -o famdef In file included from ele.h:1, from famdef.c:1: msps.h: In function ‘scan_msp’: msps.h:116:25: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 3 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:32: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 5 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:36: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 6 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:43: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 8 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d msps.h:116:47: warning: format ‘%ld’ expects argument of type ‘long int *’, but argument 9 has type ‘int32_t *’ {aka ‘int *’} [-Wformat=] 116 | if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) { | ~~^ ~~~~~~~~~~~~~~~~~~~ | | | | long int * int32_t * {aka int *} | %d In file included from msps.h:4: seqlist.h: In function ‘GetSeqNames’: seqlist.h:19:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 19 | fgets(line, 255, seq_list); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ make[1]: Leaving directory '/<>/src' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' echo "Do not run tests since there exists no testsuite.sh needed to run those in the package" Do not run tests since there exists no testsuite.sh needed to run those in the package make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules execute_before_dh_auto_install make[1]: Entering directory '/<>' mkdir -p bin make[1]: Leaving directory '/<>' dh_auto_install --destdir=debian/repeatmasker-recon/ -O--sourcedirectory=src cd src && make -j2 install DESTDIR=/<>/debian/repeatmasker-recon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>/src' cp imagespread eledef eleredef edgeredef famdef ../bin/ make[1]: Leaving directory '/<>/src' dh_install -O--sourcedirectory=src debian/rules execute_after_dh_install make[1]: Entering directory '/<>' cp scripts/recon.pl debian/repeatmasker-recon/usr/bin/repeatmasker-recon cp scripts/MSPCollect.pl debian/repeatmasker-recon/usr/bin/MSPCollect make[1]: Leaving directory '/<>' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'repeatmasker-recon' in '../repeatmasker-recon_1.08-8_amd64.deb'. dpkg-deb: building package 'repeatmasker-recon-dbgsym' in '../repeatmasker-recon-dbgsym_1.08-8_amd64.deb'. dpkg-genbuildinfo -O../repeatmasker-recon_1.08-8_amd64.buildinfo dpkg-genchanges -O../repeatmasker-recon_1.08-8_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 2024-08-05T00:15:05Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ repeatmasker-recon_1.08-8_amd64.changes: ---------------------------------------- Format: 1.8 Date: Wed, 13 Mar 2024 16:00:34 +0100 Source: repeatmasker-recon Binary: repeatmasker-recon repeatmasker-recon-dbgsym Architecture: source amd64 Version: 1.08-8 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: repeatmasker-recon - finds repeat families from biological sequences Changes: repeatmasker-recon (1.08-8) unstable; urgency=medium . * Team upload. * Add patch to add in missing include. Close: #1066541 * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 287be3f8edc64a4beb869327f89c4fecff23977c 1187 repeatmasker-recon_1.08-8.dsc 7742af75fe931bb48fed7f73097141e28ec8d5c4 5980 repeatmasker-recon_1.08-8.debian.tar.xz 25a2fed6081a602b3577b93b3d9a2ac976058ed5 112672 repeatmasker-recon-dbgsym_1.08-8_amd64.deb 5f982900b968431ce3a14a6f531bdbf50f2dfccb 5438 repeatmasker-recon_1.08-8_amd64.buildinfo 638cb9b3fc9f6fe49ca0b80b9ca83df6a4530844 85272 repeatmasker-recon_1.08-8_amd64.deb Checksums-Sha256: 86873040915e307faad0dc08912e144adc20ca6afd4158fb5e3be9e11f4a5088 1187 repeatmasker-recon_1.08-8.dsc 4d1ac5ddbc014ba414efad01003c4df7fcb6046debba1f75376aca2123be36b6 5980 repeatmasker-recon_1.08-8.debian.tar.xz 0cdb1323fd4fc5dd6135161f03e133e820bb6dbeb12a499754ed9833c7d217ce 112672 repeatmasker-recon-dbgsym_1.08-8_amd64.deb e63a72d6bc76851caf52ba639984dc6b255efaf16321d96c28c7144d35bf8b6d 5438 repeatmasker-recon_1.08-8_amd64.buildinfo a451f74127b615e16c8ee4654b49aeb69287f93924ee3a71e05b3db27cd5e187 85272 repeatmasker-recon_1.08-8_amd64.deb Files: 320096ecb89a681fc0f5bb47ce69861c 1187 science optional repeatmasker-recon_1.08-8.dsc 1835d963ebdb4632412a087475e79aa5 5980 science optional repeatmasker-recon_1.08-8.debian.tar.xz 5e013ef43b5c6fcba3748c9146689ffd 112672 debug optional repeatmasker-recon-dbgsym_1.08-8_amd64.deb d051550e98d52beb148aee12ade4dc7f 5438 science optional repeatmasker-recon_1.08-8_amd64.buildinfo a8ca853eafae746b63989af73598a9cf 85272 science optional repeatmasker-recon_1.08-8_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: repeatmasker-recon Binary: repeatmasker-recon repeatmasker-recon-dbgsym Architecture: amd64 source Version: 1.08-8 Checksums-Md5: 320096ecb89a681fc0f5bb47ce69861c 1187 repeatmasker-recon_1.08-8.dsc 5e013ef43b5c6fcba3748c9146689ffd 112672 repeatmasker-recon-dbgsym_1.08-8_amd64.deb a8ca853eafae746b63989af73598a9cf 85272 repeatmasker-recon_1.08-8_amd64.deb Checksums-Sha1: 287be3f8edc64a4beb869327f89c4fecff23977c 1187 repeatmasker-recon_1.08-8.dsc 25a2fed6081a602b3577b93b3d9a2ac976058ed5 112672 repeatmasker-recon-dbgsym_1.08-8_amd64.deb 638cb9b3fc9f6fe49ca0b80b9ca83df6a4530844 85272 repeatmasker-recon_1.08-8_amd64.deb Checksums-Sha256: 86873040915e307faad0dc08912e144adc20ca6afd4158fb5e3be9e11f4a5088 1187 repeatmasker-recon_1.08-8.dsc 0cdb1323fd4fc5dd6135161f03e133e820bb6dbeb12a499754ed9833c7d217ce 112672 repeatmasker-recon-dbgsym_1.08-8_amd64.deb a451f74127b615e16c8ee4654b49aeb69287f93924ee3a71e05b3db27cd5e187 85272 repeatmasker-recon_1.08-8_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 05 Aug 2024 00:15:05 +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 (= 0.22.5-2), autotools-dev (= 20220109.1), base-files (= 13.4), base-passwd (= 3.6.4), bash (= 5.2.21-2.1), binutils (= 2.42.90.20240720-2), binutils-common (= 2.42.90.20240720-2), binutils-x86-64-linux-gnu (= 2.42.90.20240720-2), bsdextrautils (= 2.40.2-1), bsdutils (= 1:2.40.2-1), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:14.1.0-2), cpp-13 (= 13.3.0-4), cpp-13-x86-64-linux-gnu (= 13.3.0-4), cpp-14 (= 14.2.0-1), cpp-14-x86-64-linux-gnu (= 14.2.0-1), cpp-x86-64-linux-gnu (= 4:14.1.0-2), dash (= 0.5.12-9), debconf (= 1.5.87), debhelper (= 13.16), debianutils (= 5.20), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.11), dpkg-dev (= 1.22.11), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.10.0-2), g++ (= 4:14.1.0-2), g++-14 (= 14.2.0-1), g++-14-x86-64-linux-gnu (= 14.2.0-1), g++-x86-64-linux-gnu (= 4:14.1.0-2), gcc (= 4:14.1.0-2), gcc-13 (= 13.3.0-4), gcc-13-base (= 13.3.0-4), gcc-13-x86-64-linux-gnu (= 13.3.0-4), gcc-14 (= 14.2.0-1), gcc-14-base (= 14.2.0-1), gcc-14-x86-64-linux-gnu (= 14.2.0-1), gcc-x86-64-linux-gnu (= 4:14.1.0-2), gettext (= 0.22.5-2), gettext-base (= 0.22.5-2), grep (= 3.11-4), groff-base (= 1.23.0-5), 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 (= 14.2.0-1), libatomic1 (= 14.2.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-4), libaudit1 (= 1:3.1.2-4+b1), libbinutils (= 2.42.90.20240720-2), libblkid1 (= 2.40.2-1), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.39-6), libc-dev-bin (= 2.39-6), libc6 (= 2.39-6), libc6-dev (= 2.39-6), libcap-ng0 (= 0.8.5-1+b1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.2.0-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42.90.20240720-2), libctf0 (= 2.42.90.20240720-2), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.16), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.3.0-4), libgcc-14-dev (= 14.2.0-1), libgcc-s1 (= 14.2.0-1), libgdbm-compat4t64 (= 1.23-6), libgdbm6t64 (= 1.23-6), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.2.0-1), libgprofng0 (= 2.42.90.20240720-2), libhwasan0 (= 14.2.0-1), libicu72 (= 72.1-5), libisl23 (= 0.26-3+b2), libitm1 (= 14.2.0-1), libjansson4 (= 2.14-2+b2), liblsan0 (= 14.2.0-1), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.2-1), 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 (= 5.40.0-1), libpipeline1 (= 1.5.7-2), libquadmath0 (= 14.2.0-1), libseccomp2 (= 2.5.5-1+b1), libselinux1 (= 3.5-2+b3), libsframe1 (= 2.42.90.20240720-2), libsmartcols1 (= 2.40.2-1), libssl3t64 (= 3.3.1-2), libstdc++-14-dev (= 14.2.0-1), libstdc++6 (= 14.2.0-1), libsystemd0 (= 256.4-2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.2.0-1), libubsan1 (= 14.2.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.4-2), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-1), libxml2 (= 2.12.7+dfsg-3+b1), libzstd1 (= 1.5.6+dfsg-1), linux-libc-dev (= 6.9.12-1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-2), mawk (= 1.3.4.20240622-2), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), patch (= 2.7.6-7), perl (= 5.40.0-1), perl-base (= 5.40.0-1), perl-modules-5.40 (= 5.40.0-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.24), sysvinit-utils (= 3.09-2), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.2-1), xz-utils (= 5.6.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1710342034" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ repeatmasker-recon-dbgsym_1.08-8_amd64.deb ------------------------------------------ new Debian package, version 2.0. size 112672 bytes: control archive=808 bytes. 576 bytes, 12 lines control 625 bytes, 6 lines md5sums Package: repeatmasker-recon-dbgsym Source: repeatmasker-recon Version: 1.08-8 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 166 Depends: repeatmasker-recon (= 1.08-8) Section: debug Priority: optional Description: debug symbols for repeatmasker-recon Build-Ids: 0d06ccf6d8e6e64bffc792b342166c186056ae8c 25a15c399ce80b484b1bacfd05019c31515ba09f 3fa9aa8b5b3a91430d21262ee3c510ef2ece007d c94b06034b0154a1ff093defe8c3d969c9515e16 f0795d915aa69f52b1f9eb563c5f5bf02f9988ae drwxr-xr-x root/root 0 2024-03-13 15:00 ./ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/debug/.build-id/0d/ -rw-r--r-- root/root 49496 2024-03-13 15:00 ./usr/lib/debug/.build-id/0d/06ccf6d8e6e64bffc792b342166c186056ae8c.debug drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/debug/.build-id/25/ -rw-r--r-- root/root 33024 2024-03-13 15:00 ./usr/lib/debug/.build-id/25/a15c399ce80b484b1bacfd05019c31515ba09f.debug drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/debug/.build-id/3f/ -rw-r--r-- root/root 30320 2024-03-13 15:00 ./usr/lib/debug/.build-id/3f/a9aa8b5b3a91430d21262ee3c510ef2ece007d.debug drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/debug/.build-id/c9/ -rw-r--r-- root/root 19920 2024-03-13 15:00 ./usr/lib/debug/.build-id/c9/4b06034b0154a1ff093defe8c3d969c9515e16.debug drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/debug/.build-id/f0/ -rw-r--r-- root/root 12368 2024-03-13 15:00 ./usr/lib/debug/.build-id/f0/795d915aa69f52b1f9eb563c5f5bf02f9988ae.debug drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 4600 2024-03-13 15:00 ./usr/lib/debug/.dwz/x86_64-linux-gnu/repeatmasker-recon.debug drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/share/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-03-13 15:00 ./usr/share/doc/repeatmasker-recon-dbgsym -> repeatmasker-recon repeatmasker-recon_1.08-8_amd64.deb ----------------------------------- new Debian package, version 2.0. size 85272 bytes: control archive=1508 bytes. 1126 bytes, 23 lines control 1580 bytes, 22 lines md5sums Package: repeatmasker-recon Version: 1.08-8 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 464 Depends: libc6 (>= 2.34), perl:any Section: science Priority: optional Homepage: https://www.repeatmasker.org/ Description: finds repeat families from biological sequences The RECON package implements a de novo algorithm for the identification of repeat families from biological sequences. . The program implements an approach for the de novo identification and classification of repeat sequence families that is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. The extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. When tested on the human genome, this approach was able to properly identify and group known transposable elements. The program, should be useful for first-pass automatic classification of repeats in newly sequenced genomes. drwxr-xr-x root/root 0 2024-03-13 15:00 ./ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/bin/ -rwxr-xr-x root/root 1370 2024-03-13 15:00 ./usr/bin/MSPCollect -rwxr-xr-x root/root 31216 2024-03-13 15:00 ./usr/bin/edgeredef -rwxr-xr-x root/root 23024 2024-03-13 15:00 ./usr/bin/eledef -rwxr-xr-x root/root 43512 2024-03-13 15:00 ./usr/bin/eleredef -rwxr-xr-x root/root 31208 2024-03-13 15:00 ./usr/bin/famdef -rwxr-xr-x root/root 14768 2024-03-13 15:00 ./usr/bin/imagespread -rwxr-xr-x root/root 1841 2024-03-13 15:00 ./usr/bin/repeatmasker-recon drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/share/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/share/doc/repeatmasker-recon/ -rw-r--r-- root/root 2135 2024-03-13 15:00 ./usr/share/doc/repeatmasker-recon/00README.gz -rw-r--r-- root/root 771 2024-03-13 15:00 ./usr/share/doc/repeatmasker-recon/changelog.Debian.gz -rw-r--r-- root/root 1911 2024-03-13 15:00 ./usr/share/doc/repeatmasker-recon/copyright drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/share/doc/repeatmasker-recon/examples/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/share/doc/repeatmasker-recon/examples/Demos/ -rw-r--r-- root/root 1663 2024-03-13 15:00 ./usr/share/doc/repeatmasker-recon/examples/Demos/README drwxr-xr-x root/root 0 2014-02-05 22:05 ./usr/share/doc/repeatmasker-recon/examples/Demos/input/ -rw-r--r-- root/root 290374 2014-02-05 22:05 ./usr/share/doc/repeatmasker-recon/examples/Demos/input/elegans.msps -rw-r--r-- root/root 36 2014-02-05 22:05 ./usr/share/doc/repeatmasker-recon/examples/Demos/input/seqnames drwxr-xr-x root/root 0 2014-02-05 22:05 ./usr/share/doc/repeatmasker-recon/examples/Demos/output/ drwxr-xr-x root/root 0 2014-02-05 22:05 ./usr/share/doc/repeatmasker-recon/examples/Demos/standard/ -rw-r--r-- root/root 806 2014-02-05 22:05 ./usr/share/doc/repeatmasker-recon/examples/Demos/standard/Tc3.list -rw-r--r-- root/root 1514 2014-02-05 22:05 ./usr/share/doc/repeatmasker-recon/examples/Demos/standard/Tc3.msps drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-13 15:00 ./usr/share/man/man1/ -rw-r--r-- root/root 487 2024-03-13 15:00 ./usr/share/man/man1/MSPCollect.1.gz -rw-r--r-- root/root 385 2024-03-13 15:00 ./usr/share/man/man1/edgeredef.1.gz -rw-r--r-- root/root 373 2024-03-13 15:00 ./usr/share/man/man1/eledef.1.gz -rw-r--r-- root/root 408 2024-03-13 15:00 ./usr/share/man/man1/eleredef.1.gz -rw-r--r-- root/root 339 2024-03-13 15:00 ./usr/share/man/man1/famdef.1.gz -rw-r--r-- root/root 374 2024-03-13 15:00 ./usr/share/man/man1/imagespread.1.gz -rw-r--r-- root/root 711 2024-03-13 15:00 ./usr/share/man/man1/repeatmasker-recon.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 2628 Build-Time: 15 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 7 Job: /srv/debomatic/incoming/repeatmasker-recon_1.08-8.dsc Machine Architecture: amd64 Package: repeatmasker-recon Package-Time: 28 Source-Version: 1.08-8 Space: 2628 Status: successful Version: 1.08-8 -------------------------------------------------------------------------------- Finished at 2024-08-05T00:15:05Z Build needed 00:00:28, 2628k disk space