sbuild (Debian sbuild) 0.85.10 (30 May 2024) on carme.larted.org.uk +==============================================================================+ | libbio-db-hts-perl 3.01-4+b4 (amd64) Fri, 02 Aug 2024 08:00:17 +0000 | +==============================================================================+ Package: libbio-db-hts-perl Version: 3.01-4+b4 Source Version: 3.01-4 Distribution: perl-5.40 Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-3fcc02b7-d317-4043-aea3-5a02d2214d9d' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup libbio-db-hts-perl_3.01-4 perl-5.40 amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup libbio-db-hts-perl_3.01-4 perl-5.40 amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/libbio-db-hts-perl-0S2q2o/resolver-GvyvUF' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3036 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3036 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://localhost:3142/debian sid InRelease Get:4 file:/srv/reprepro perl-5.40/main amd64 Packages [58.3 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/libbio-db-hts-perl_3.01-4.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/libbio-db-hts-perl-0S2q2o/libbio-db-hts-perl-3.01' with '<>' I: NOTICE: Log filtering will replace 'build/libbio-db-hts-perl-0S2q2o' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libbio-perl-perl, libextutils-cbuilder-perl, libextutils-pkgconfig-perl, libhts-dev, libmodule-build-perl, perl, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libbio-perl-perl, libextutils-cbuilder-perl, libextutils-pkgconfig-perl, libhts-dev, libmodule-build-perl, perl, 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 [730 B] Get:5 copy:/<>/apt_archive ./ Packages [762 B] Fetched 2101 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 libbio-perl-perl libbrotli-dev libbrotli1 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdata-stag-perl libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libextutils-pkgconfig-perl libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libio-string-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1t64 libmodule-build-perl libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkg-config pkgconf pkgconf-bin po-debconf sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff bioperl libxml-sax-expatxs-perl libcurl4-doc libidn-dev libkrb5-dev libldap2-dev gmp-doc libgmp10-doc libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-doc krb5-user liblzma-doc libnghttp2-doc p11-kit-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-libxml-perl libwww-perl ca-certificates perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libarchive-cpio-perl krb5-locales libmodule-signature-perl libpod-readme-perl libsoftware-license-perl publicsuffix libtasn1-doc 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 libbio-perl-perl libbrotli-dev libbrotli1 libcom-err2 libcurl3t64-gnutls libcurl4-gnutls-dev libdata-stag-perl libdebhelper-perl libdeflate-dev libdeflate0 libelf1t64 libevent-2.1-7t64 libextutils-pkgconfig-perl libfakeroot libfile-stripnondeterminism-perl libgmp-dev libgmpxx4ldbl libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssapi-krb5-2 libhts-dev libhts3t64 libhtscodecs2 libicu72 libidn2-dev libio-string-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1t64 libmodule-build-perl libnghttp2-14 libnghttp2-dev libnghttp3-9 libnghttp3-dev libngtcp2-16 libngtcp2-crypto-gnutls-dev libngtcp2-crypto-gnutls8 libngtcp2-dev libp11-kit-dev libpipeline1 libpkgconf3 libpsl-dev libpsl5t64 librtmp-dev librtmp1 libssh2-1-dev libssh2-1t64 libssl-dev libtasn1-6-dev libtool libuchardet0 libunbound8 libxml2 libzstd-dev m4 man-db nettle-dev pkg-config pkgconf pkgconf-bin po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 39.2 MB of archives. After this operation, 140 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [932 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] 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http://deb.debian.org/debian unstable/main amd64 libmodule-build-perl all 0.423400-2 [252 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.2 MB in 0s (130 MB/s) Selecting previously unselected package sensible-utils. 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Preparing to unpack .../76-libdeflate-dev_1.20-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.20-1) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../77-pkg-config_1.8.1-3_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-3) ... Selecting previously unselected package libextutils-pkgconfig-perl. Preparing to unpack .../78-libextutils-pkgconfig-perl_1.16-3_all.deb ... Unpacking libextutils-pkgconfig-perl (1.16-3) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../79-libhtscodecs2_1.6.0-1+b1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.0-1+b1) ... Selecting previously unselected package libhts3t64:amd64. Preparing to unpack .../80-libhts3t64_1.20+ds-1_amd64.deb ... Unpacking libhts3t64:amd64 (1.20+ds-1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../81-liblzma-dev_5.6.2-2_amd64.deb ... Unpacking liblzma-dev:amd64 (5.6.2-2) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../82-libhts-dev_1.20+ds-1_amd64.deb ... Unpacking libhts-dev:amd64 (1.20+ds-1) ... Selecting previously unselected package libmodule-build-perl. Preparing to unpack .../83-libmodule-build-perl_0.423400-2_all.deb ... Adding 'diversion of /usr/bin/config_data to /usr/bin/config_data.diverted by libmodule-build-perl' Adding 'diversion of /usr/share/man/man1/config_data.1.gz to /usr/share/man/man1/config_data.diverted.1.gz by libmodule-build-perl' Unpacking libmodule-build-perl (0.423400-2) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../84-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libgnutls-openssl27t64:amd64 (3.8.6-2) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-5) ... Setting up libzstd-dev:amd64 (1.5.6+dfsg-1) ... 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 libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.62.1-2) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libevent-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.35.1-1) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libpsl-dev:amd64 (0.21.2-1.1) ... Setting up libmodule-build-perl (0.423400-2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... 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 libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up libunbound8:amd64 (1.20.0-1+b1) ... Setting up libpkgconf3:amd64 (1.8.1-3) ... Setting up libgmpxx4ldbl:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up libgnutls-dane0t64:amd64 (3.8.6-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libssl-dev:amd64 (3.2.2-1) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-3) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libidn2-dev:amd64 (2.3.7-2) ... Setting up autoconf (2.71-3) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up libnghttp3-dev:amd64 (1.4.0-1) ... Setting up liblzma-dev:amd64 (5.6.2-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libssh2-1t64:amd64 (1.11.0-6) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b2) ... Setting up libdeflate-dev:amd64 (1.20-1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b4) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libp11-kit-dev:amd64 (0.25.5-2) ... 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 (0.22.5-2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-2+b1) ... Setting up nettle-dev:amd64 (3.10-1) ... Setting up libtool (2.4.7-7) ... Setting up libngtcp2-crypto-gnutls-dev:amd64 (1.6.0-1) ... Setting up libngtcp2-dev:amd64 (1.6.0-1) ... Setting up pkgconf:amd64 (1.8.1-3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up pkg-config:amd64 (1.8.1-3) ... Setting up libssh2-1-dev:amd64 (1.11.0-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libgnutls28-dev:amd64 (3.8.6-2) ... Setting up libnghttp2-dev:amd64 (1.62.1-2) ... Setting up libextutils-pkgconfig-perl (1.16-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3t64-gnutls:amd64 (8.9.1-1) ... Setting up man-db (2.12.1-2) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up debhelper (13.16) ... Setting up libcurl4-gnutls-dev:amd64 (8.9.1-1) ... Setting up libhts-dev:amd64 (1.20+ds-1) ... 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_14.1.0-5 gcc-13_13.3.0-4 gcc-14_14.1.0-5 libc6-dev_2.39-6 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.1.0-5 libstdc++6_14.1.0-5 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_14.1.0-5 cpp-14-x86-64-linux-gnu_14.1.0-5 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_14.1.0-5 g++-14-x86-64-linux-gnu_14.1.0-5 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_14.1.0-5 gcc-14-base_14.1.0-5 gcc-14-x86-64-linux-gnu_14.1.0-5 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_14.1.0-5 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-5 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 libbio-perl-perl_1.7.8-1 libblkid1_2.40.2-1 libbrotli-dev_1.1.0-2+b4 libbrotli1_1.1.0-2+b4 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_14.1.0-5 libcom-err2_1.47.1-1 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 libcurl3t64-gnutls_8.9.1-1 libcurl4-gnutls-dev_8.9.1-1 libdata-stag-perl_0.14-3 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.16 libdeflate-dev_1.20-1 libdeflate0_1.20-1 libdpkg-perl_1.22.11 libeatmydata1_131-2 libelf1t64_0.191-2 libevent-2.1-7t64_2.1.12-stable-10 libextutils-pkgconfig-perl_1.16-3 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_14.1.0-5 libgcc-s1_14.1.0-5 libgcrypt20_1.11.0-5 libgdbm-compat4t64_1.23-6 libgdbm6t64_1.23-6 libgmp-dev_2:6.3.0+dfsg-2+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgmpxx4ldbl_2:6.3.0+dfsg-2+b1 libgnutls-dane0t64_3.8.6-2 libgnutls-openssl27t64_3.8.6-2 libgnutls28-dev_3.8.6-2 libgnutls30t64_3.8.6-2 libgomp1_14.1.0-5 libgpg-error0_1.49-2 libgprofng0_2.42.90.20240720-2 libgssapi-krb5-2_1.21.3-3 libhogweed6t64_3.10-1 libhts-dev_1.20+ds-1 libhts3t64_1.20+ds-1 libhtscodecs2_1.6.0-1+b1 libhwasan0_14.1.0-5 libicu72_72.1-5 libidn2-0_2.3.7-2 libidn2-dev_2.3.7-2 libio-string-perl_1.08-4 libisl23_0.26-3+b2 libitm1_14.1.0-5 libjansson4_2.14-2+b2 libk5crypto3_1.21.3-3 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librtmp1_2.4+20151223.gitfa8646d.1-2+b4 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 libssh2-1-dev_1.11.0-6 libssh2-1t64_1.11.0-6 libssl-dev_3.2.2-1 libssl3t64_3.2.2-1 libstdc++-13-dev_13.3.0-4 libstdc++-14-dev_14.1.0-5 libstdc++6_14.1.0-5 libsystemd0_256.4-2 libtasn1-6_4.19.0-3+b2 libtasn1-6-dev_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.1.0-5 libubsan1_14.1.0-5 libuchardet0_0.0.8-1+b1 libudev1_256.4-2 libunbound8_1.20.0-1+b1 libunistring5_1.2-1 libuuid1_2.40.2-1 libxml2_2.12.7+dfsg-3+b1 libxxhash0_0.8.2-2+b1 libzstd-dev_1.5.6+dfsg-1 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 nettle-dev_3.10-1 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 pkg-config_1.8.1-3 pkgconf_1.8.1-3 pkgconf-bin_1.8.1-3 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 zlib1g-dev_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-db-hts-perl Binary: libbio-db-hts-perl Architecture: any Version: 3.01-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://metacpan.org/release/Bio-DB-HTS Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/libbio-db-hts-perl Vcs-Git: https://salsa.debian.org/med-team/libbio-db-hts-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper-compat (= 13), libbio-perl-perl, libextutils-cbuilder-perl, libextutils-pkgconfig-perl, libhts-dev, libmodule-build-perl, perl Package-List: libbio-db-hts-perl deb science optional arch=any Checksums-Sha1: 292b7464e502437666907f849b8cd91465afd042 5250834 libbio-db-hts-perl_3.01.orig.tar.gz 3044ce114f16475a8a845b6a204d9328f73b5294 3836 libbio-db-hts-perl_3.01-4.debian.tar.xz Checksums-Sha256: 12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42 5250834 libbio-db-hts-perl_3.01.orig.tar.gz f61254cb6dacbb3f8849f625e2b8a50169955b3a26ee36ff9edd2ef3ba41e243 3836 libbio-db-hts-perl_3.01-4.debian.tar.xz Files: 7b7f991deddb12084cf85e0fa3d91819 5250834 libbio-db-hts-perl_3.01.orig.tar.gz 581435791a88040638e91ab2da6e36e7 3836 libbio-db-hts-perl_3.01-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmM+n5QRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH++A/+OgAu2K3OMtOyQjh7ZvJKjTqNW0ozfAnr 5LJyzLILdpZcchdixevwClFVsi3fUD7DoYHt4R9MGNL4unfoJBdCXoQuh8EqyusX bwhfhFeizl0C4lQgETo1HuTwWa5nHWdhZYeHKjXVagFGH9GEPjqNEwwl8y/DoNM0 AKPAiZ4M2WJB+pvoSsPNwtJVlQMcHBgC9aTQm+HiiHIWY1mNYiIRCac7orr6MwTJ HqmbYSuxAd2+mb0Jzc2+3hgiouMDP+MkdMx6FC2AQ1nKBKP7e+1GYv3XEfQBHiIs mhidqIS4j0iCcs+uUFTuPpy70ZlukpghXXOPek6/7ynPPKBDT28kNKDfBj/PE1ru aCDHV3u6A4P38l1KNSA9wIm13XE8VZ7wBslIEkmVaALoCRi2gMf2PTLw1jVbBoRl jPCH9uBYOAWMwe7rT4/xAyEKMoj3wYO4Lg9ntgSqaeJlp/uH3MKbYuH5XZb02jj/ //hXFg3oBGqQVXePEAnVrn89AVNcjwBfoAaNUxvgRwkPgDo0GM1fP0SUg3ThIDnY 83GlIt2S08Ch2U/7+weXXeSBjg5iNd90kHF23v9LBD7KbcQaoA2BUf5FUnLFEJVz ZpMhp/HZl+M7tDvbNusp91Tzg1TJECo7zQfYH0XnQqQNXAAO8gZAeoOxE9zoTPXJ u/Pw1Flxj2w= =SUmk -----END PGP SIGNATURE----- gpgv: Signature made Thu Oct 6 09:27:48 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libbio-db-hts-perl_3.01-4.dsc: no acceptable signature found dpkg-source: info: extracting libbio-db-hts-perl in /<> dpkg-source: info: unpacking libbio-db-hts-perl_3.01.orig.tar.gz dpkg-source: info: unpacking libbio-db-hts-perl_3.01-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying find_htslib.patch Check disk space ---------------- Sufficient free space for build Hack binNMU version ------------------- Created changelog entry for binNMU version 3.01-4+b4 +------------------------------------------------------------------------------+ | Starting Timed Build Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network libbio-db-hts-perl_3.01-4 perl-5.40 amd64 ---------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network libbio-db-hts-perl_3.01-4 perl-5.40 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-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-3fcc02b7-d317-4043-aea3-5a02d2214d9d SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -mDebian Perl autobuilder -B -rfakeroot -Zxz dpkg-buildpackage: info: source package libbio-db-hts-perl dpkg-buildpackage: info: source version 3.01-4+b4 dpkg-buildpackage: info: source distribution perl-5.40 dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a /usr/bin/perl Build.PL --installdirs vendor --config "optimize=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" --config "ld=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now" Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Bio-DB-HTS' version '3.01' dh_auto_build -a /usr/bin/perl Build Building Bio-DB-HTS x86_64-linux-gnu-gcc -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE '-DVERSION="3.01"' '-DXS_VERSION="3.01"' -fPIC '-D_IOLIB=2' '-D_FILE_OFFSET_BITS=64' -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE '-D_FILE_OFFSET_BITS=64' -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/<>=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/<>=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -Wdate-time '-D_FORTIFY_SOURCE=2' -o lib/Bio/DB/HTS.o lib/Bio/DB/HTS.c lib/Bio/DB/HTS.xs: In function ‘XS_Bio__DB__HTS__VCF__Header_fmt_text’: lib/Bio/DB/HTS.xs:1769:5: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 1769 | RETVAL = newSVpv(bcf_hdr_fmt_text(header, is_bcf, &len), 0); | ^~~~~~ In file included from lib/Bio/DB/HTS.xs:59: /usr/include/htslib/vcf.h:591:11: note: declared here 591 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) | ^~~~~~~~~~~~~~~~ lib/Bio/DB/HTS.xs: In function ‘XS_Bio__DB__HTS__VCF__Row_print’: lib/Bio/DB/HTS.xs:1785:13: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long int’} [-Wformat=] 1785 | printf("position:%d\t", (row->pos+1)); | ^~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | hts_pos_t {aka long int} ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/HTS.bs') x86_64-linux-gnu-gcc -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/<>=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/HTS.so lib/Bio/DB/HTS.o -lhts -lpthread -lz x86_64-linux-gnu-gcc -I/usr/lib/x86_64-linux-gnu/perl/5.40/CORE '-DVERSION="3.01"' '-DXS_VERSION="3.01"' -fPIC '-D_IOLIB=2' '-D_FILE_OFFSET_BITS=64' -Wno-error -Wno-unused-result -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE '-D_FILE_OFFSET_BITS=64' -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/<>=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/<>=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -Wdate-time '-D_FORTIFY_SOURCE=2' -o lib/Bio/DB/HTS/Faidx.o lib/Bio/DB/HTS/Faidx.c ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.bs') x86_64-linux-gnu-gcc -g -O2 '-Werror=implicit-function-declaration' '-ffile-prefix-map=/<>=.' -fstack-protector-strong -fstack-clash-protection -Wformat '-Werror=format-security' -fcf-protection -Wl,-z,relro -Wl,-z,now -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/HTS/Faidx/Faidx.so lib/Bio/DB/HTS/Faidx.o -lhts -lpthread -lz dh_auto_test -a /usr/bin/perl Build test --verbose 1 t/00load.t ....... ok 1 - use Bio::DB::HTS; ok 2 - use Bio::DB::HTS::Tabix; ok 3 - use Bio::DB::HTS::Tabix::Iterator; ok 4 - use Bio::DB::HTS::Kseq; 1..4 ok t/01bam.t ........ 1..452 # Running under perl version 5.040000 for linux # Current time local: Fri Aug 2 08:00:33 2024 # Current time GMT: Fri Aug 2 08:00:33 2024 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 ok 163 ok 164 ok 165 ok 166 ok 167 ok 168 ok 169 ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 ok 251 ok 252 ok 253 ok 254 ok 255 ok 256 ok 257 ok 258 ok 259 ok 260 ok 261 ok 262 ok 263 ok 264 ok 265 ok 266 ok 267 ok 268 ok 269 ok 270 ok 271 ok 272 ok 273 ok 274 ok 275 ok 276 ok 277 ok 278 ok 279 ok 280 ok 281 ok 282 ok 283 ok 284 ok 285 ok 286 ok 287 ok 288 ok 289 ok 290 ok 291 ok 292 ok 293 ok 294 ok 295 ok 296 ok 297 ok 298 ok 299 ok 300 ok 301 ok 302 ok 303 ok 304 ok 305 ok 306 ok 307 ok 308 ok 309 ok 310 ok 311 ok 312 ok 313 ok 314 ok 315 ok 316 ok 317 ok 318 ok 319 ok 320 ok 321 ok 322 ok 323 ok 324 ok 325 ok 326 ok 327 ok 328 ok 329 ok 330 ok 331 ok 332 ok 333 ok 334 ok 335 ok 336 ok 337 ok 338 ok 339 ok 340 ok 341 ok 342 ok 343 ok 344 ok 345 ok 346 ok 347 ok 348 ok 349 ok 350 ok 351 ok 352 ok 353 ok 354 ok 355 ok 356 ok 357 ok 358 ok 359 ok 360 ok 361 ok 362 ok 363 ok 364 ok 365 ok 366 ok 367 ok 368 ok 369 ok 370 ok 371 ok 372 ok 373 ok 374 ok 375 ok 376 ok 377 ok 378 ok 379 ok 380 ok 381 ok 382 ok 383 ok 384 ok 385 ok 386 ok 387 ok 388 ok 389 ok 390 ok 391 ok 392 ok 393 ok 394 ok 395 ok 396 ok 397 ok 398 ok 399 ok 400 ok 401 ok 402 ok 403 ok 404 ok 405 ok 406 ok 407 ok 408 ok 409 ok 410 ok 411 ok 412 ok 413 ok 414 ok 415 ok 416 ok 417 ok 418 ok 419 ok 420 ok 421 ok 422 ok 423 ok 424 ok 425 ok 426 ok 427 ok 428 ok 429 ok 430 ok 431 ok 432 ok 433 ok 434 ok 435 ok 436 ok 437 ok 438 ok 439 ok 440 ok 441 ok 442 ok 443 ok 444 ok 445 ok 446 ok 447 ok 448 ok 449 ok 450 ok 451 ok 452 ok t/02faidx.t ...... 1..15 ok 1 - use Bio::DB::HTS; ok 2 - use Bio::DB::HTS::Faidx; ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 # 230218 ok 13 - length of I ok 14 - has sequence I ok 15 - Does not have sequence II ok t/03cram.t ....... 1..139 # Running under perl version 5.040000 for linux # Current time local: Fri Aug 2 08:00:34 2024 # Current time GMT: Fri Aug 2 08:00:34 2024 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok t/04tabix.t ...... 1..21 ok 1 - use Bio::DB::HTS::Tabix; ok 2 - \#CHROM FROM TO GERP ok 3 - \#CHROM FROM TO GERP ok 4 - can query a region ok 5 - can get a value from the iterator ok 6 - row value is correct ok 7 - correct number of values come back from the iterator ok 8 - A reference of type 'ARRAY' isa 'ARRAY' ok 9 - seqnames are correct ok 10 - can query a region with ':' in chr ok 11 - can get a value from the iterator ok 12 - row value is correct with ':' in chr ok 13 - can query a region with ':' in chr, no end ok 14 - can get a value from the iterator ok 15 - row value is correct with ':' in chr, no end ok 16 - can query a region with ':' in chr, no coord ok 17 - can get a value from the iterator ok 18 - row value is correct with ':' in chr, no coord ok 19 - querying non existent chrom ok 20 - \#\#fileformat=VCFv4.2 ok 21 - \#\#reference=human_b36_both.fasta ok t/05vcf.t ........ 1..177 ok 1 - use Bio::DB::HTS::VCF; ok 2 - use Bio::DB::HTS::VCF::Row; ok 3 - use Bio::DB::HTS::VCF::RowPtr; ok 4 - use Bio::DB::HTS::VCF::Header; ok 5 - use Bio::DB::HTS::VCF::HeaderPtr; ok 6 - Chromosome value read ok 7 - Chromosome value read ok 8 - Position value read ok 9 - Quality value read ok 10 - Quality value read ok 11 - ID value read ok 12 - Number of alleles value read ok 13 - A reference of type 'ARRAY' isa 'ARRAY' ok 14 - alleles are correct ok 15 - VCF file open ok 16 - correct number of variants identified in file ok 17 - Header formatted string ok 18 - VCF Header version matches ok 19 - Number of samples ok 20 - sample names correct ok 21 - Number of seqnames ok 22 ok 23 - sequence names correct ok 24 - Next row ok 25 - Chromosome value read ok 26 - Position value read ok 27 - ID value read ok 28 - Num Filters OK ok 29 - Actual Filter present ok 30 - PASS filter absent ok 31 - Variant type matches ok 32 - info read correctly ok 33 - A reference of type 'ARRAY' isa 'ARRAY' ok 34 - info flag read correctly ok 35 - info flag type correct ok 36 - A reference of type 'ARRAY' isa 'ARRAY' ok 37 - info float read correctly ok 38 - info float type correct ok 39 - A reference of type 'ARRAY' isa 'ARRAY' ok 40 - info string read correctly ok 41 - info String type correct ok 42 - A reference of type 'ARRAY' isa 'ARRAY' ok 43 - info ints read correctly ok 44 - info int type correct ok 45 - format int read ok 46 - format int read ok 47 - format id not present ok 48 - format read ok 49 - Next row ok 50 - Chromosome value read ok 51 - Position value read ok 52 - Quality value read ok 53 - Reference value read ok 54 - Num Alleles ok 55 - Is SNP ok 56 - A reference of type 'ARRAY' isa 'ARRAY' ok 57 - alleles are correct ok 58 - Num Filters OK ok 59 - PASS Filter present ok 60 - Actual Filter absent ok 61 - Made up filter not existing ok 62 - info read correctly ok 63 - format int read ok 64 - format int read ok 65 - format id not present ok 66 - format read ok 67 - Next row ok 68 - Chromosome value read ok 69 - int format type correct ok 70 - format int read ok 71 - format int read ok 72 - format int read # !!! Not sure this is correct !!! ok 73 - format int read ok 74 - format read ok 75 - A reference of type 'ARRAY' isa 'ARRAY' ok 76 - genotypes read correctly ok 77 - format id not found ok 78 - info id not found ok 79 - info read correctly ok 80 - can query a region ok 81 - can get a value from the iterator ok 82 - chr ok 83 - position ok 84 - id ok 85 - reference ok 86 - info ok 87 - info ok 88 - info ok 89 - info ok 90 - can get a value from the iterator ok 91 - chr ok 92 - position ok 93 - id ok 94 - reference ok 95 - info ok 96 - no more results ok 97 - BCF file open ok 98 - correct number of variants identified in file ok 99 - Header formatted string ok 100 - VCF Header version matches ok 101 - Number of samples ok 102 - sample names correct ok 103 - Number of seqnames ok 104 - sequence names correct ok 105 - Next row ok 106 - Chromosome value read ok 107 - Position value read ok 108 - ID value read ok 109 - Num Filters OK ok 110 - Actual Filter present ok 111 - PASS filter absent ok 112 - Variant type matches ok 113 - info read correctly ok 114 - A reference of type 'ARRAY' isa 'ARRAY' ok 115 - info flag read correctly ok 116 - info flag type correct ok 117 - A reference of type 'ARRAY' isa 'ARRAY' ok 118 - info float read correctly ok 119 - info float type correct ok 120 - A reference of type 'ARRAY' isa 'ARRAY' ok 121 - info string read correctly ok 122 - info String type correct ok 123 - A reference of type 'ARRAY' isa 'ARRAY' ok 124 - info ints read correctly ok 125 - info int type correct ok 126 - format int read ok 127 - format int read ok 128 - format ID not present ok 129 - format read ok 130 - Next row ok 131 - Chromosome value read ok 132 - Position value read ok 133 - Quality value read ok 134 - Reference value read ok 135 - Num Alleles ok 136 - Is SNP ok 137 - A reference of type 'ARRAY' isa 'ARRAY' ok 138 - alleles are correct ok 139 - Num Filters OK ok 140 - PASS Filter present ok 141 - Actual Filter absent ok 142 - Made up filter not existing ok 143 - info read correctly ok 144 - format int read ok 145 - format int read ok 146 - format ID not present ok 147 - format read ok 148 - Next row ok 149 - Chromosome value read ok 150 - int format type correct ok 151 - format int read ok 152 - format int read ok 153 - format int read # !!! Not sure this is correct !!! ok 154 - format int read ok 155 - format read ok 156 - A reference of type 'ARRAY' isa 'ARRAY' ok 157 - genotypes read correctly ok 158 - format id not found ok 159 - info id not found ok 160 - info read correctly ok 161 - can query a region ok 162 - can get a value from the iterator ok 163 - chr ok 164 - position ok 165 - id ok 166 - reference ok 167 - info ok 168 - info ok 169 - info ok 170 - info ok 171 - can get a value from the iterator ok 172 - chr ok 173 - position ok 174 - id ok 175 - reference ok 176 - info ok 177 - no more results ok t/06kseq.t ....... ok 1 - correct num. seqs in bug2335 ok 2 - sample sequence obtained ok 3 - seq matches bug2335 ok 4 - desc matches bug2335 ok 5 - name matches bug2335 ok 6 - qual matches bug2335 ok 7 - Checking qual and seq lengths are the same in bug2335 ok 8 - Checking qual and seq lengths are the same using object methods in bug2335 ok 9 - correct num. seqs in evil_wrapping ok 10 - sample sequence obtained ok 11 - seq matches evil_wrapping ok 12 - desc matches evil_wrapping ok 13 - name matches evil_wrapping ok 14 - qual matches evil_wrapping ok 15 - Checking qual and seq lengths are the same in evil_wrapping ok 16 - Checking qual and seq lengths are the same using object methods in evil_wrapping ok 17 - correct num. seqs in example ok 18 - sample sequence obtained ok 19 - seq matches example ok 20 - desc matches example ok 21 - name matches example ok 22 - qual matches example ok 23 - Checking qual and seq lengths are the same in example ok 24 - Checking qual and seq lengths are the same using object methods in example ok 25 - correct num. seqs in illumina_faked ok 26 - sample sequence obtained ok 27 - seq matches illumina_faked ok 28 - desc matches illumina_faked ok 29 - name matches illumina_faked ok 30 - qual matches illumina_faked ok 31 - Checking qual and seq lengths are the same in illumina_faked ok 32 - Checking qual and seq lengths are the same using object methods in illumina_faked ok 33 - correct num. seqs in sanger_93 ok 34 - sample sequence obtained ok 35 - seq matches sanger_93 ok 36 - desc matches sanger_93 ok 37 - name matches sanger_93 ok 38 - qual matches sanger_93 ok 39 - Checking qual and seq lengths are the same in sanger_93 ok 40 - Checking qual and seq lengths are the same using object methods in sanger_93 ok 41 - correct num. seqs in sanger_faked ok 42 - sample sequence obtained ok 43 - seq matches sanger_faked ok 44 - desc matches sanger_faked ok 45 - name matches sanger_faked ok 46 - qual matches sanger_faked ok 47 - Checking qual and seq lengths are the same in sanger_faked ok 48 - Checking qual and seq lengths are the same using object methods in sanger_faked ok 49 - correct num. seqs in solexa_example ok 50 - sample sequence obtained ok 51 - seq matches solexa_example ok 52 - desc matches solexa_example ok 53 - name matches solexa_example ok 54 - qual matches solexa_example ok 55 - Checking qual and seq lengths are the same in solexa_example ok 56 - Checking qual and seq lengths are the same using object methods in solexa_example ok 57 - correct num. seqs in solexa_faked ok 58 - sample sequence obtained ok 59 - seq matches solexa_faked ok 60 - desc matches solexa_faked ok 61 - name matches solexa_faked ok 62 - qual matches solexa_faked ok 63 - Checking qual and seq lengths are the same in solexa_faked ok 64 - Checking qual and seq lengths are the same using object methods in solexa_faked ok 65 - correct num. seqs in test1_sanger ok 66 - sample sequence obtained ok 67 - seq matches test1_sanger ok 68 - desc matches test1_sanger ok 69 - name matches test1_sanger ok 70 - qual matches test1_sanger ok 71 - Checking qual and seq lengths are the same in test1_sanger ok 72 - Checking qual and seq lengths are the same using object methods in test1_sanger ok 73 - correct num. seqs in test2_solexa ok 74 - sample sequence obtained ok 75 - seq matches test2_solexa ok 76 - desc matches test2_solexa ok 77 - name matches test2_solexa ok 78 - qual matches test2_solexa ok 79 - Checking qual and seq lengths are the same in test2_solexa ok 80 - Checking qual and seq lengths are the same using object methods in test2_solexa ok 81 - correct num. seqs in test3_illumina ok 82 - sample sequence obtained ok 83 - seq matches test3_illumina ok 84 - desc matches test3_illumina ok 85 - name matches test3_illumina ok 86 - qual matches test3_illumina ok 87 - Checking qual and seq lengths are the same in test3_illumina ok 88 - Checking qual and seq lengths are the same using object methods in test3_illumina ok 89 - correct num. seqs in tricky ok 90 - sample sequence obtained ok 91 - seq matches tricky ok 92 - desc matches tricky ok 93 - name matches tricky ok 94 - qual matches tricky ok 95 - Checking qual and seq lengths are the same in tricky ok 96 - Checking qual and seq lengths are the same using object methods in tricky ok 97 - correct num. seqs in zero_qual ok 98 - sample sequence obtained ok 99 - seq matches zero_qual ok 100 - desc matches zero_qual ok 101 - name matches zero_qual ok 102 - qual matches zero_qual ok 103 - Checking qual and seq lengths are the same in zero_qual ok 104 - Checking qual and seq lengths are the same using object methods in zero_qual 1..104 ok [E::easy_errno] Libcurl reported error 77 (Problem with the SSL CA cert (path? access rights?)) [W::find_file_url] Failed to open reference "https://www.ebi.ac.uk/ena/cram/md5/426e31835a6dfdcbf6c534671edf02f7": Input/output error t/07cramwrite.t .. 1..22 # Running under perl version 5.040000 for linux # Current time local: Fri Aug 2 08:00:37 2024 # Current time GMT: Fri Aug 2 08:00:37 2024 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok t/08bamwrite.t ... 1..22 # Running under perl version 5.040000 for linux # Current time local: Fri Aug 2 08:00:37 2024 # Current time GMT: Fri Aug 2 08:00:37 2024 # Using Test.pm version 1.31 ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok t/09sam.t ........ ok 1 ok 2 # skip Cannot test header reading for htslib < 1.5 ok 3 # skip Cannot test header reading for htslib < 1.5 ok 4 # skip Cannot test header reading for htslib < 1.5 ok 5 # skip Cannot test header reading for htslib < 1.5 ok 6 # skip Cannot test header reading for htslib < 1.5 ok 7 # skip Cannot test header reading for htslib < 1.5 ok 8 # skip Cannot test header reading for htslib < 1.5 ok 9 # skip Cannot test header reading for htslib < 1.5 ok 10 # skip Cannot test header reading for htslib < 1.5 ok 11 # skip Cannot test header reading for htslib < 1.5 ok 12 ok 13 ok 14 # skip Cannot test iterating over alignments for htslib < 1.5 ok 15 # skip Cannot test iterating over alignments for htslib < 1.5 ok 16 # skip Cannot test iterating over alignments for htslib < 1.5 ok 17 # skip Cannot test iterating over alignments for htslib < 1.5 ok 18 ok 19 ok 20 ok 21 ok 22 - An object of class 'Bio::PrimarySeq' isa 'Bio::PrimarySeq' ok 23 1..23 ok t/10leak.t ....... skipped: require Test::LeakTrace All tests successful. Files=11, Tests=979, 5 wallclock secs ( 0.08 usr 0.03 sys + 4.18 cusr 0.40 csys = 4.69 CPU) Result: PASS create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/libbio-db-hts-perl/ -a /usr/bin/perl Build install --destdir /<>/debian/libbio-db-hts-perl --create_packlist 0 Building Bio-DB-HTS Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/DB/HTS/HTS.bs Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/DB/HTS/HTS.so Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/DB/HTS/Faidx/Faidx.bs Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/auto/Bio/DB/HTS/Faidx/Faidx.so Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Pileup.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Constants.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/FetchIterator.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/ReadIterator.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/PileupWrapper.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Faidx.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/AlignWrapper.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Row.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/RowPtr.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Header.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/HeaderPtr.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Iterator.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix/Iterator.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq/Record.pm Installing /<>/debian/libbio-db-hts-perl/usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq/Iterator.pod Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Target.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Tabix.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq::Record.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Tabix::Iterator.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq::Iterator.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Pileup.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::ReadIterator.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::AlignWrapper.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Segment.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Query.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Kseq.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::PileupWrapper.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Constants.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Alignment.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::VCF.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::FetchIterator.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::VCF::Iterator.3pm Installing /<>/debian/libbio-db-hts-perl/usr/share/man/man3/Bio::DB::HTS::Faidx.3pm dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_lintian -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib64/ld-linux-x86-64.so.2 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib64/ld-linux-x86-64.so.2.usr-is-merged dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libbio-db-hts-perl-dbgsym' in '../libbio-db-hts-perl-dbgsym_3.01-4+b4_amd64.deb'. dpkg-deb: building package 'libbio-db-hts-perl' in '../libbio-db-hts-perl_3.01-4+b4_amd64.deb'. dpkg-genbuildinfo --build=any -O../libbio-db-hts-perl_3.01-4+b4_amd64.buildinfo dpkg-genchanges --build=any -mDebian Perl autobuilder -O../libbio-db-hts-perl_3.01-4+b4_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-08-02T08:00:40Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ libbio-db-hts-perl_3.01-4+b4_amd64.changes: ------------------------------------------- Format: 1.8 Date: Fri, 02 Aug 2024 08:00:27 +0000 Source: libbio-db-hts-perl (3.01-4) Binary: libbio-db-hts-perl libbio-db-hts-perl-dbgsym Binary-Only: yes Architecture: amd64 Version: 3.01-4+b4 Distribution: perl-5.40 Urgency: low Maintainer: Debian Perl autobuilder Changed-By: Debian Perl autobuilder Description: libbio-db-hts-perl - Perl interface to the HTS library Changes: libbio-db-hts-perl (3.01-4+b4) perl-5.40; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for Perl 5.40 Checksums-Sha1: 6d2e144494b48567e4058f13710c372c8076457e 187008 libbio-db-hts-perl-dbgsym_3.01-4+b4_amd64.deb 40d57ea3b5e0db73d4f7a8b966c1b7c23cb9955c 7438 libbio-db-hts-perl_3.01-4+b4_amd64.buildinfo 80e84459e457c06cd754a7f028dc4bce5a3ed9fa 139096 libbio-db-hts-perl_3.01-4+b4_amd64.deb Checksums-Sha256: 819daa3ecd92fa9223d6823235dabf221d1d422423c2c0683ccf3d5eb8ac2be4 187008 libbio-db-hts-perl-dbgsym_3.01-4+b4_amd64.deb 151380b340457ed41a309abaec73f10d9dd412c4ad4a31f35b5566f1a24f7e25 7438 libbio-db-hts-perl_3.01-4+b4_amd64.buildinfo b4f3c0b785e46fa50390195ef84b1529ead548fde6ba28e889df29df17874a38 139096 libbio-db-hts-perl_3.01-4+b4_amd64.deb Files: 3bb661760fb14dc08e4cbc8fe4127171 187008 debug optional libbio-db-hts-perl-dbgsym_3.01-4+b4_amd64.deb 12a2fd6bb6d708d810be36aa556e7334 7438 science optional libbio-db-hts-perl_3.01-4+b4_amd64.buildinfo 7b69b179cb9a6d67daf94ba22cc96eb7 139096 science optional libbio-db-hts-perl_3.01-4+b4_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: libbio-db-hts-perl (3.01-4) Binary: libbio-db-hts-perl libbio-db-hts-perl-dbgsym Architecture: amd64 Version: 3.01-4+b4 Binary-Only-Changes: libbio-db-hts-perl (3.01-4+b4) perl-5.40; urgency=low, binary-only=yes . * Binary-only non-maintainer upload for amd64; no source changes. * Rebuild for Perl 5.40 . -- Debian Perl autobuilder Fri, 02 Aug 2024 08:00:27 +0000 Checksums-Md5: 3bb661760fb14dc08e4cbc8fe4127171 187008 libbio-db-hts-perl-dbgsym_3.01-4+b4_amd64.deb 7b69b179cb9a6d67daf94ba22cc96eb7 139096 libbio-db-hts-perl_3.01-4+b4_amd64.deb Checksums-Sha1: 6d2e144494b48567e4058f13710c372c8076457e 187008 libbio-db-hts-perl-dbgsym_3.01-4+b4_amd64.deb 80e84459e457c06cd754a7f028dc4bce5a3ed9fa 139096 libbio-db-hts-perl_3.01-4+b4_amd64.deb Checksums-Sha256: 819daa3ecd92fa9223d6823235dabf221d1d422423c2c0683ccf3d5eb8ac2be4 187008 libbio-db-hts-perl-dbgsym_3.01-4+b4_amd64.deb b4f3c0b785e46fa50390195ef84b1529ead548fde6ba28e889df29df17874a38 139096 libbio-db-hts-perl_3.01-4+b4_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Fri, 02 Aug 2024 08:00:40 +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 (= 14.1.0-5), cpp-14-x86-64-linux-gnu (= 14.1.0-5), 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 (= 14.1.0-5), g++-14-x86-64-linux-gnu (= 14.1.0-5), 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 (= 14.1.0-5), gcc-14-base (= 14.1.0-5), gcc-14-x86-64-linux-gnu (= 14.1.0-5), 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 (= 14.1.0-5), libatomic1 (= 14.1.0-5), 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), libbio-perl-perl (= 1.7.8-1), libblkid1 (= 2.40.2-1), libbrotli-dev (= 1.1.0-2+b4), libbrotli1 (= 1.1.0-2+b4), 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 (= 14.1.0-5), libcom-err2 (= 1.47.1-1), 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), libcurl3t64-gnutls (= 8.9.1-1), libcurl4-gnutls-dev (= 8.9.1-1), libdata-stag-perl (= 0.14-3), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.16), libdeflate-dev (= 1.20-1), libdeflate0 (= 1.20-1), libdpkg-perl (= 1.22.11), libelf1t64 (= 0.191-2), libevent-2.1-7t64 (= 2.1.12-stable-10), 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2.5.18+dfsg-2), liblsan0 (= 14.1.0-5), liblzma-dev (= 5.6.2-2), liblzma5 (= 5.6.2-2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmodule-build-perl (= 0.423400-2), libmount1 (= 2.40.2-1), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libnettle8t64 (= 3.10-1), libnghttp2-14 (= 1.62.1-2), libnghttp2-dev (= 1.62.1-2), libnghttp3-9 (= 1.4.0-1), libnghttp3-dev (= 1.4.0-1), libngtcp2-16 (= 1.6.0-1), libngtcp2-crypto-gnutls-dev (= 1.6.0-1), libngtcp2-crypto-gnutls8 (= 1.6.0-1), libngtcp2-dev (= 1.6.0-1), libp11-kit-dev (= 0.25.5-2), 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), libperl5.40 (= 5.40.0-1), libpipeline1 (= 1.5.7-2), libpkgconf3 (= 1.8.1-3), libpsl-dev (= 0.21.2-1.1), libpsl5t64 (= 0.21.2-1.1), libquadmath0 (= 14.1.0-5), librtmp-dev (= 2.4+20151223.gitfa8646d.1-2+b4), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b4), 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), libsframe1 (= 2.42.90.20240720-2), libsmartcols1 (= 2.40.2-1), libssh2-1-dev (= 1.11.0-6), libssh2-1t64 (= 1.11.0-6), libssl-dev (= 3.2.2-1), libssl3t64 (= 3.2.2-1), libstdc++-14-dev (= 14.1.0-5), libstdc++6 (= 14.1.0-5), libsystemd0 (= 256.4-2), libtasn1-6 (= 4.19.0-3+b2), libtasn1-6-dev (= 4.19.0-3+b2), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.1.0-5), libubsan1 (= 14.1.0-5), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256.4-2), libunbound8 (= 1.20.0-1+b1), libunistring5 (= 1.2-1), libuuid1 (= 2.40.2-1), libxml2 (= 2.12.7+dfsg-3+b1), libzstd-dev (= 1.5.6+dfsg-1), 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), nettle-dev (= 3.10-1), patch (= 2.7.6-7), perl (= 5.40.0-1), perl-base (= 5.40.0-1), perl-modules-5.40 (= 5.40.0-1), pkg-config (= 1.8.1-3), pkgconf (= 1.8.1-3), pkgconf-bin (= 1.8.1-3), 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), zlib1g-dev (= 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="1722585627" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ libbio-db-hts-perl-dbgsym_3.01-4+b4_amd64.deb --------------------------------------------- new Debian package, version 2.0. size 187008 bytes: control archive=652 bytes. 468 bytes, 12 lines control 307 bytes, 3 lines md5sums Package: libbio-db-hts-perl-dbgsym Source: libbio-db-hts-perl (3.01-4) Version: 3.01-4+b4 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 217 Depends: libbio-db-hts-perl (= 3.01-4+b4) Section: debug Priority: optional Description: debug symbols for libbio-db-hts-perl Build-Ids: 7a031c3a26a11ee3e909df9d16b41a6cd13c84a4 e923a37bb5f851ae9847625796d7801b73483458 drwxr-xr-x root/root 0 2024-08-02 08:00 ./ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/debug/.build-id/7a/ -rw-r--r-- root/root 167000 2024-08-02 08:00 ./usr/lib/debug/.build-id/7a/031c3a26a11ee3e909df9d16b41a6cd13c84a4.debug drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/debug/.build-id/e9/ -rw-r--r-- root/root 18104 2024-08-02 08:00 ./usr/lib/debug/.build-id/e9/23a37bb5f851ae9847625796d7801b73483458.debug drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/debug/.dwz/x86_64-linux-gnu/ -rw-r--r-- root/root 22320 2024-08-02 08:00 ./usr/lib/debug/.dwz/x86_64-linux-gnu/libbio-db-hts-perl.debug drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/share/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-08-02 08:00 ./usr/share/doc/libbio-db-hts-perl-dbgsym -> libbio-db-hts-perl libbio-db-hts-perl_3.01-4+b4_amd64.deb -------------------------------------- new Debian package, version 2.0. size 139096 bytes: control archive=2252 bytes. 1090 bytes, 22 lines control 4546 bytes, 51 lines md5sums Package: libbio-db-hts-perl Source: libbio-db-hts-perl (3.01-4) Version: 3.01-4+b4 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 422 Depends: perl (>= 5.40.0-1), perlapi-5.40.0, libc6 (>= 2.14), libhts3t64 (>= 1.17), zlib1g (>= 1:1.2.3.3), libbio-perl-perl Section: science Priority: optional Homepage: https://metacpan.org/release/Bio-DB-HTS Description: Perl interface to the HTS library HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM (Sequence Alignment/Map), CRAM and VCF (Variant Call Format), used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang. . HTSlib implements a generalized BAM (binary SAM) index, with file extension 'csi' (coordinate-sorted index). The HTSlib file reader first looks for the new index and then for the old if the new index is absent. . This package provides a Perl interface to the HTS library. drwxr-xr-x root/root 0 2024-08-02 08:00 ./ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/ drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/ -rw-r--r-- root/root 80204 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS.pm drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/ -rw-r--r-- root/root 13925 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/AlignWrapper.pm -rw-r--r-- root/root 17984 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Alignment.pm -rw-r--r-- root/root 2756 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Constants.pm -rw-r--r-- root/root 2298 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Faidx.pm -rw-r--r-- root/root 1068 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/FetchIterator.pm -rw-r--r-- root/root 1799 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq.pm drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq/ -rw-r--r-- root/root 1244 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq/Iterator.pod -rw-r--r-- root/root 1314 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Kseq/Record.pm -rw-r--r-- root/root 2682 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Pileup.pm -rw-r--r-- root/root 2185 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/PileupWrapper.pm -rw-r--r-- root/root 4999 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Query.pm -rw-r--r-- root/root 1296 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/ReadIterator.pm -rw-r--r-- root/root 3074 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Segment.pm -rw-r--r-- root/root 6818 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix.pm drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix/ -rw-r--r-- root/root 2975 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Tabix/Iterator.pm -rw-r--r-- root/root 1754 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/Target.pm -rw-r--r-- root/root 13834 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF.pm drwxr-xr-x root/root 0 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/ -rw-r--r-- root/root 118 2024-08-02 08:00 ./usr/lib/x86_64-linux-gnu/perl5/5.40/Bio/DB/HTS/VCF/Header.pm -rw-r--r-- root/root 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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: any Build-Space: 11200 Build-Time: 13 Distribution: perl-5.40 Host Architecture: amd64 Install-Time: 6 Job: /srv/debomatic/incoming/libbio-db-hts-perl_3.01-4.dsc Machine Architecture: amd64 Package: libbio-db-hts-perl Package-Time: 23 Source-Version: 3.01-4 Space: 11200 Status: successful Version: 3.01-4+b4 -------------------------------------------------------------------------------- Finished at 2024-08-02T08:00:40Z Build needed 00:00:23, 11200k disk space