proteinortho →
5.16.b+dfsg-1 →
armhf → 2019-01-10 05:22:58
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| proteinortho 5.16.b+dfsg-1 (armhf) Thu, 10 Jan 2019 05:18:31 +0000 |
+==============================================================================+
Package: proteinortho
Version: 5.16.b+dfsg-1
Source Version: 5.16.b+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-1e7dda25-ac6f-4767-80c1-ea549c86f08a' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'proteinortho' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/proteinortho.git
Please use:
git clone https://salsa.debian.org/med-team/proteinortho.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 109 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main proteinortho 5.16.b+dfsg-1 (dsc) [2074 B]
Get:2 http://172.17.0.1/private buster-staging/main proteinortho 5.16.b+dfsg-1 (tar) [103 kB]
Get:3 http://172.17.0.1/private buster-staging/main proteinortho 5.16.b+dfsg-1 (diff) [4192 B]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/proteinortho-lZ5Wsl/proteinortho-5.16.b+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/proteinortho-lZ5Wsl' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-Lb8GL6/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-Lb8GL6/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Lb8GL6/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Lb8GL6/apt_archive ./ InRelease
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Get:3 copy:/<<BUILDDIR>>/resolver-Lb8GL6/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Lb8GL6/apt_archive ./ Sources [349 B]
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Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
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After this operation, 0 B of additional disk space will be used.
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debconf: delaying package configuration, since apt-utils is not installed
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), ncbi-blast+
Filtered Build-Depends: debhelper (>= 11~), ncbi-blast+
dpkg-deb: building package 'sbuild-build-depends-proteinortho-dummy' in '/<<BUILDDIR>>/resolver-Lb8GL6/apt_archive/sbuild-build-depends-proteinortho-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-proteinortho-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Lb8GL6/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Lb8GL6/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Lb8GL6/apt_archive ./ Release.gpg [370 B]
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Reading package lists...
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Reading package lists...
Install proteinortho build dependencies (apt-based resolver)
------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales
libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libmagic-mgc
libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libpipeline1
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
libsigsegv2 libtool libuchardet0 libxml2 m4 man-db mime-support ncbi-blast+
ncbi-data po-debconf python python-minimal python2 python2-minimal python2.7
python2.7-minimal
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation 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 python-doc python-tk python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libmagic-mgc
libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libpipeline1
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
libsigsegv2 libtool libuchardet0 libxml2 m4 man-db mime-support ncbi-blast+
ncbi-data po-debconf python python-minimal python2 python2-minimal python2.7
python2.7-minimal sbuild-build-depends-proteinortho-dummy
0 upgraded, 48 newly installed, 0 to remove and 5 not upgraded.
Need to get 34.0 MB of archives.
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Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
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Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-1 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-3 [1160 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-5 [394 kB]
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Get:10 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
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Get:19 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
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Get:21 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
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Get:37 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
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Get:40 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
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Get:44 http://172.17.0.1/private buster-staging/main armhf libmbedcrypto3 armhf 2.14.1-2 [185 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libmbedx509-0 armhf 2.14.1-2 [85.8 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libmbedtls12 armhf 2.14.1-2 [121 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf ncbi-data all 6.1.20170106-6 [3692 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf ncbi-blast+ armhf 2.7.1-2 [8218 kB]
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Unpacking libmbedtls12:armhf (2.14.1-2) ...
Selecting previously unselected package ncbi-data.
Preparing to unpack .../29-ncbi-data_6.1.20170106-6_all.deb ...
Unpacking ncbi-data (6.1.20170106-6) ...
Selecting previously unselected package ncbi-blast+.
Preparing to unpack .../30-ncbi-blast+_2.7.1-2_armhf.deb ...
Unpacking ncbi-blast+ (2.7.1-2) ...
Selecting previously unselected package sbuild-build-depends-proteinortho-dummy.
Preparing to unpack .../31-sbuild-build-depends-proteinortho-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-proteinortho-dummy (0.invalid.0) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up mime-support (3.61) ...
Installing new version of config file /etc/mime.types ...
Setting up libicu63:armhf (63.1-5) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libelf1:armhf (0.175-2) ...
Setting up libglib2.0-0:armhf (2.58.2-3) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-9) ...
Setting up libpipeline1:armhf (1.5.0-2) ...
Setting up m4 (1.4.18-2) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up libmagic1:armhf (1:5.34-2) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up ncbi-data (6.1.20170106-6) ...
Processing triggers for libc-bin (2.28-2) ...
Setting up dwz (0.12-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up libmbedcrypto3:armhf (2.14.1-2) ...
Setting up libmbedx509-0:armhf (2.14.1-2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpython2.7-stdlib:armhf (2.7.15-5) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up libfile-stripnondeterminism-perl (1.0.0-1) ...
Setting up gettext (0.19.8.1-9) ...
Setting up groff-base (1.22.4-1) ...
Setting up python2.7 (2.7.15-5) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libmbedtls12:armhf (2.14.1-2) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.4-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython2-stdlib:armhf (2.7.15-3) ...
Setting up libtool (2.4.6-6) ...
Setting up po-debconf (1.0.21) ...
Setting up python2 (2.7.15-3) ...
Setting up libpython-stdlib:armhf (2.7.15-3) ...
Setting up python (2.7.15-3) ...
Setting up ncbi-blast+ (2.7.1-2) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.0.0-1) ...
Setting up debhelper (12) ...
Setting up sbuild-build-depends-proteinortho-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-2) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-13+rpi1 gcc-8_8.2.0-13+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-13+rpi1 dash_0.5.10.2-4 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.69 debhelper_12 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.145-4.1+b5 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-13+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-13+rpi1 gcc-8-base_8.2.0-13+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.1-3 groff-base_1.22.4-1 gzip_1.9-2.1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.2-1 libacl1_2.2.52-3 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-13+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-13+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33-0.2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcap-ng0_0.7.9-1+b1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-13+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-13+rpi1 libgcc1_1:8.2.0-13+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2+rpi1 libgomp1_8.2.0-13+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgssapi-krb5-2_1.16.2-1 libhogweed4_3.4.1~rc1-1 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.16.2-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.2-1 libkrb5support0_1.16.2-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-1 libldap-common_2.4.47+dfsg-1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmbedcrypto3_2.14.1-2 libmbedtls12_2.14.1-2 libmbedx509-0_2.14.1-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnpth0_1.6-1 libnss-systemd_240-2+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_240-2+rpi1 libpam0g_1.1.8-3.8 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-5 libpython2.7-stdlib_2.7.15-5 libreadline7_7.0-5 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-1 libsemanage1_2.8-1+b1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 libsystemd0_240-2+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-13+rpi1 libuchardet0_0.0.6-3 libudev1_240-2+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33-0.2 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.5+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-3 mawk_1.3.3-17 mime-support_3.61 mount_2.33-0.2 multiarch-support_2.28-2 nano_3.2-1 ncbi-blast+_2.7.1-2 ncbi-data_6.1.20170106-6 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-3 python-minimal_2.7.15-3 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-minimal_2.7.15-5 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-proteinortho-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-2+rpi1 systemd-sysv_240-2+rpi1 sysvinit-utils_2.93-2 tar_1.30+dfsg-3+rpi1 tzdata_2018i-1 udev_240-2+rpi1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Jan 8 08:36:36 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./proteinortho_5.16.b+dfsg-1.dsc
dpkg-source: info: extracting proteinortho in /<<BUILDDIR>>/proteinortho-5.16.b+dfsg
dpkg-source: info: unpacking proteinortho_5.16.b+dfsg.orig.tar.xz
dpkg-source: info: unpacking proteinortho_5.16.b+dfsg-1.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-1e7dda25-ac6f-4767-80c1-ea549c86f08a
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package proteinortho
dpkg-buildpackage: info: source version 5.16.b+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -std=gnu++11 -Wno-unused-result -Wl,-z,relro -Wl,-z,now -o proteinortho5_clustering proteinortho5_clustering.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -std=gnu++11 -Wno-unused-result -Wl,-z,relro -Wl,-z,now -o proteinortho5_tree po_tree.c
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg'
./proteinortho5.pl -project=test -synteny -singles test/*.faa
*****************************************************************
Proteinortho with PoFF version 5.16b - An orthology detection tool
*****************************************************************
Detected 8 available CPU threads, Detected NCBI BLAST version 2.7.1+
Checking input files
Checking test/C.faa... test/C.faa 109 genes ok
Checking test/E.faa... test/E.faa 72 genes ok
Checking test/L.faa... test/L.faa 40 genes ok
Checking test/M.faa... test/M.faa 40 genes ok
**Step 1**
Generating indices
Building database for 'test/C.faa' (109 sequences)
Building database for 'test/E.faa' (72 sequences)
Building database for 'test/L.faa' (40 sequences)
Building database for 'test/M.faa' (40 sequences)
**Step 2**
Running blast analysis: 0% (0/6)
Running blast analysis: 100% (6/6)
Running blast analysis: 16.66% (1/6)
Running blast analysis: 33.33% (2/6)
Running blast analysis: 50% (3/6)
Running blast analysis: 83.33% (5/6)
Running blast analysis: 66.66% (4/6)
Running blast analysis: 100% (6/6)
[OUTPUT] -> written to test.blast-graph
**Step 3**
Clustering by similarity (Proteinortho mode)
Reading test.blast-graph
4 species
112 paired proteins
144 bidirectional edges
Clustering: 1.79%
Clustering: 3.57%
Clustering: 5.36%
Clustering: 7.14%
Clustering: 8.93%
Clustering: 10.71%
Clustering: 12.50%
Clustering: 14.29%
Clustering: 16.96%
Clustering: 20.54%
Clustering: 21.43%
Clustering: 23.21%
Clustering: 24.11%
Clustering: 32.14%
Clustering: 36.61%
Clustering: 43.75%
Clustering: 58.93%
Clustering: 62.50%
Clustering: 64.29%
Clustering: 66.07%
Clustering: 67.86%
Clustering: 69.64%
Clustering: 71.43%
Clustering: 73.21%
Clustering: 75.00%
Clustering: 76.79%
Clustering: 78.57%
Clustering: 85.71%
Clustering: 89.29%
Clustering: 93.75%
Clustering: 95.54%
Clustering: 100.00%
Done
Adding singles...
[OUTPUT] -> written to test.proteinortho
Writing graph...
Cleaning edge list...
Removed 26 / 144 edges
Done.
[OUTPUT] -> written to test.proteinortho-graph
Clustering by gene-order (POFF mode)
Reading test.ffadj-graph
4 species
106 paired proteins
104 bidirectional edges
Clustering: 1.89%
Clustering: 4.72%
Clustering: 5.66%
Clustering: 7.55%
Clustering: 9.43%
Clustering: 11.32%
Clustering: 13.21%
Clustering: 15.09%
Clustering: 16.98%
Clustering: 18.87%
Clustering: 20.75%
Clustering: 21.70%
Clustering: 31.13%
Clustering: 33.02%
Clustering: 50.00%
Clustering: 53.77%
Clustering: 56.60%
Clustering: 58.49%
Clustering: 60.38%
Clustering: 62.26%
Clustering: 64.15%
Clustering: 66.04%
Clustering: 67.92%
Clustering: 69.81%
Clustering: 71.70%
Clustering: 73.58%
Clustering: 75.47%
Clustering: 77.36%
Clustering: 78.30%
Clustering: 80.19%
Clustering: 82.08%
Clustering: 83.96%
Clustering: 85.85%
Clustering: 87.74%
Clustering: 89.62%
Clustering: 91.51%
Clustering: 100.00%
Done
Adding singles...
[OUTPUT] -> written to test.poff
Writing graph...
Cleaning edge list...
Removed 0 / 104 edges
Done.
[OUTPUT] -> written to test.poff-graph
All finished.
rm test.*
Test okay
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg'
dh_auto_install --buildsystem=makefile -- install INSTALLDIR=/<<BUILDDIR>>/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho
make -j4 install DESTDIR=/<<BUILDDIR>>/proteinortho-5.16.b\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install INSTALLDIR=/<<BUILDDIR>>/proteinortho-5.16.b\+dfsg/debian/proteinortho/usr/lib/proteinortho
make[2]: Entering directory '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg'
install -v proteinortho5.pl proteinortho5_clustering proteinortho5_singletons.pl proteinortho5_clean_edges2.pl ffadj_mcs.py po2tree.pl proteinortho5_tree /<<BUILDDIR>>/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho
'proteinortho5.pl' -> '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5.pl'
'proteinortho5_clustering' -> '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_clustering'
'proteinortho5_singletons.pl' -> '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_singletons.pl'
'proteinortho5_clean_edges2.pl' -> '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_clean_edges2.pl'
'ffadj_mcs.py' -> '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/ffadj_mcs.py'
'po2tree.pl' -> '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/po2tree.pl'
'proteinortho5_tree' -> '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_tree'
make[2]: 'install' is up to date.
make[2]: Leaving directory '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/proteinortho-5.16.b+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/proteinortho/usr/lib/proteinortho/proteinortho5_clustering contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package proteinortho: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package proteinortho: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_5.16.b+dfsg-1_armhf.deb'.
dpkg-deb: building package 'proteinortho' in '../proteinortho_5.16.b+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../proteinortho_5.16.b+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-01-10T05:22:56Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
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+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
proteinortho_5.16.b+dfsg-1_armhf.changes:
-----------------------------------------
Format: 1.8
Date: Tue, 08 Jan 2019 09:29:46 +0100
Source: proteinortho
Binary: proteinortho
Architecture: armhf
Version: 5.16.b+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
proteinortho - Detection of (Co-)orthologs in large-scale protein analysis
Changes:
proteinortho (5.16.b+dfsg-1) unstable; urgency=medium
.
* d/watch: Also catch letters in version number
* New upstream version
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Files:
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bb809c984a8a76032101edc62eaf166c 5315 science optional proteinortho_5.16.b+dfsg-1_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
proteinortho-dbgsym_5.16.b+dfsg-1_armhf.deb
-------------------------------------------
new Debian package, version 2.0.
size 6752 bytes: control archive=604 bytes.
442 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: proteinortho-dbgsym
Source: proteinortho
Version: 5.16.b+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 36
Depends: proteinortho (= 5.16.b+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for proteinortho
Build-Ids: 6ac5b87a2d2311598ee6d83d39cac2e5a14900a9 e60df1bb4828f9cea6402b753c641e711ba6074e
drwxr-xr-x root/root 0 2019-01-08 08:29 ./
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/lib/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/lib/debug/.build-id/6a/
-rw-r--r-- root/root 5300 2019-01-08 08:29 ./usr/lib/debug/.build-id/6a/c5b87a2d2311598ee6d83d39cac2e5a14900a9.debug
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/lib/debug/.build-id/e6/
-rw-r--r-- root/root 18560 2019-01-08 08:29 ./usr/lib/debug/.build-id/e6/0df1bb4828f9cea6402b753c641e711ba6074e.debug
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/share/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-01-08 08:29 ./usr/share/doc/proteinortho-dbgsym -> proteinortho
proteinortho_5.16.b+dfsg-1_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 137144 bytes: control archive=1660 bytes.
913 bytes, 17 lines control
2187 bytes, 28 lines md5sums
Package: proteinortho
Version: 5.16.b+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 267
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), ncbi-blast+, python
Section: science
Priority: optional
Homepage: http://www.bioinf.uni-leipzig.de/Software/proteinortho/
Description: Detection of (Co-)orthologs in large-scale protein analysis
Proteinortho is a stand-alone tool that is geared towards large datasets
and makes use of distributed computing techniques when run on multi-core
hardware. It implements an extended version of the reciprocal best
alignment heuristic. Proteinortho was applied to compute orthologous
proteins in the complete set of all 717 eubacterial genomes available at
NCBI at the beginning of 2009. Authors succeeded identifying thirty
proteins present in 99% of all bacterial proteomes.
drwxr-xr-x root/root 0 2019-01-08 08:29 ./
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/bin/
-rwxr-xr-x root/root 52 2019-01-08 08:29 ./usr/bin/proteinortho5
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/lib/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/lib/proteinortho/
-rwxr-xr-x root/root 35339 2019-01-08 08:29 ./usr/lib/proteinortho/ffadj_mcs.py
-rwxr-xr-x root/root 4888 2019-01-08 08:29 ./usr/lib/proteinortho/po2tree.pl
-rwxr-xr-x root/root 40733 2019-01-08 08:29 ./usr/lib/proteinortho/proteinortho5.pl
-rwxr-xr-x root/root 1882 2019-01-08 08:29 ./usr/lib/proteinortho/proteinortho5_clean_edges2.pl
-rwxr-xr-x root/root 50720 2019-01-08 08:29 ./usr/lib/proteinortho/proteinortho5_clustering
-rwxr-xr-x root/root 1616 2019-01-08 08:29 ./usr/lib/proteinortho/proteinortho5_singletons.pl
-rwxr-xr-x root/root 9632 2019-01-08 08:29 ./usr/lib/proteinortho/proteinortho5_tree
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/share/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/share/doc/proteinortho/
-rw-r--r-- root/root 263 2019-01-08 08:29 ./usr/share/doc/proteinortho/README.test
-rw-r--r-- root/root 556 2019-01-08 08:29 ./usr/share/doc/proteinortho/changelog.Debian.gz
-rw-r--r-- root/root 1178 2019-01-08 08:29 ./usr/share/doc/proteinortho/copyright
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/share/doc/proteinortho/examples/
-rw-r--r-- root/root 24290 2017-03-20 21:07 ./usr/share/doc/proteinortho/examples/C.faa.gz
-rw-r--r-- root/root 1867 2017-03-20 20:34 ./usr/share/doc/proteinortho/examples/C.gff.gz
-rw-r--r-- root/root 29389 2017-03-20 21:07 ./usr/share/doc/proteinortho/examples/E.faa.gz
-rw-r--r-- root/root 1880 2017-03-20 20:34 ./usr/share/doc/proteinortho/examples/E.gff.gz
-rw-r--r-- root/root 14172 2017-03-21 13:28 ./usr/share/doc/proteinortho/examples/L.faa.gz
-rw-r--r-- root/root 2376 2017-03-20 20:34 ./usr/share/doc/proteinortho/examples/L.gff
-rw-r--r-- root/root 14230 2017-03-20 20:34 ./usr/share/doc/proteinortho/examples/M.faa.gz
-rw-r--r-- root/root 2317 2017-03-20 20:34 ./usr/share/doc/proteinortho/examples/M.gff
-rwxr-xr-x root/root 238 2017-03-20 20:34 ./usr/share/doc/proteinortho/examples/chk_test.pl
-rw-r--r-- root/root 393 2019-01-08 08:29 ./usr/share/doc/proteinortho/run-unit-test
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/share/doc/proteinortho/tools/
-rw-r--r-- root/root 910 2017-03-21 20:31 ./usr/share/doc/proteinortho/tools/check_graph_duplicate_ids.pl
-rw-r--r-- root/root 1209 2017-03-20 20:34 ./usr/share/doc/proteinortho/tools/comp_bla.pl
-rw-r--r-- root/root 1153 2017-03-23 09:10 ./usr/share/doc/proteinortho/tools/extract_from_graph.pl
-rw-r--r-- root/root 2638 2017-03-20 20:34 ./usr/share/doc/proteinortho/tools/grab_proteins.pl
-rw-r--r-- root/root 197 2017-03-20 20:34 ./usr/share/doc/proteinortho/tools/graph_conv.pl
-rw-r--r-- root/root 627 2017-03-21 20:29 ./usr/share/doc/proteinortho/tools/remove_graph_duplicates.pl
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/share/man/
drwxr-xr-x root/root 0 2019-01-08 08:29 ./usr/share/man/man1/
-rw-r--r-- root/root 1381 2019-01-08 08:29 ./usr/share/man/man1/proteinortho5.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1464
Build-Time: 43
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 206
Job: proteinortho_5.16.b+dfsg-1
Machine Architecture: armhf
Package: proteinortho
Package-Time: 265
Source-Version: 5.16.b+dfsg-1
Space: 1464
Status: successful
Version: 5.16.b+dfsg-1
--------------------------------------------------------------------------------
Finished at 2019-01-10T05:22:56Z
Build needed 00:04:25, 1464k disk space