cd-hit →
4.6.8-2 →
armhf → 2018-09-28 05:19:52
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| cd-hit 4.6.8-2 (armhf) Fri, 28 Sep 2018 05:10:47 +0000 |
+==============================================================================+
Package: cd-hit
Version: 4.6.8-2
Source Version: 4.6.8-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/buster-staging-armhf-sbuild-a26ddf88-d9a9-40a6-8f3a-bdb3660852f7' 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 [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.8 MB]
Fetched 23.9 MB in 28s (841 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'cd-hit' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/cd-hit.git
Please use:
git clone https://salsa.debian.org/med-team/cd-hit.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 942 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main cd-hit 4.6.8-2 (dsc) [1974 B]
Get:2 http://172.17.0.1/private buster-staging/main cd-hit 4.6.8-2 (tar) [933 kB]
Get:3 http://172.17.0.1/private buster-staging/main cd-hit 4.6.8-2 (diff) [7528 B]
Fetched 942 kB in 0s (6893 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/cd-hit-ioe05x/cd-hit-4.6.8' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/cd-hit-ioe05x' 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-tLthJQ/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-tLthJQ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-tLthJQ/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-tLthJQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2846 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-tLthJQ/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 70 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (78.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15506 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), help2man
Filtered Build-Depends: debhelper (>= 11~), help2man
dpkg-deb: building package 'sbuild-build-depends-cd-hit-dummy' in '/<<BUILDDIR>>/resolver-tLthJQ/apt_archive/sbuild-build-depends-cd-hit-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-cd-hit-dummy sbuild-build-depends-core-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-tLthJQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Sources [494 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Packages [577 B]
Fetched 2404 B in 1s (3356 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-tLthJQ/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install cd-hit 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 e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libelf1 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0
libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 liblocale-gettext-perl
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool
libxml2 m4 man-db po-debconf
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
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 help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libelf1 libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0
libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 liblocale-gettext-perl
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libtimedate-perl libtool
libxml2 m4 man-db po-debconf sbuild-build-depends-cd-hit-dummy
0 upgraded, 38 newly installed, 0 to remove and 70 not upgraded.
Need to get 19.4 MB of archives.
After this operation, 67.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-tLthJQ/apt_archive ./ sbuild-build-depends-cd-hit-dummy 0.invalid.0 [860 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b2 [18.3 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2 [1161 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-4 [547 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8.1-2 [402 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.8-2+rpi1 [860 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.6 [169 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 19.4 MB in 2s (8389 kB/s)
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 15506 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-3+b2_armhf.deb ...
Unpacking liblocale-gettext-perl (1.07-3+b2) ...
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Preparing to unpack .../03-groff-base_1.22.3-10_armhf.deb ...
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Setting up libarchive-zip-perl (1.64-1) ...
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Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.58.1-2) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-7) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.34-2) ...
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Setting up libgraphite2-3:armhf (1.3.12-1) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up liblocale-gettext-perl (1.07-3+b2) ...
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 autopoint (0.19.8.1-7) ...
Setting up libfile-stripnondeterminism-perl (0.042-1) ...
Setting up libharfbuzz0b:armhf (1.8.8-2+rpi1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up automake (1:1.16.1-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.6) ...
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Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-4) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
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Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up gettext (0.19.8.1-7) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up debhelper (11.3.5) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-cd-hit-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.1.0-12+rpi1 gcc-8_8.1.0-12+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.1.0-12+rpi1 dash_0.5.8-2.10 debconf_1.5.69 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 g++_4:8.1.0-1+rpi1 g++-8_8.1.0-12+rpi1 gcc_4:8.1.0-1+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_8.1.0-12+rpi1 gcc-8-base_8.1.0-12+rpi1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gnupg_2.2.9-1+rpi1 gnupg-agent_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2 help2man_1.47.6 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.6.3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.1.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.1.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.31.1-2+rpi1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-12+rpi1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.1.0-12+rpi1 libgcc1_1:8.1.0-12+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.1.0-12+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libharfbuzz0b_1.8.8-2+rpi1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnpth0_1.6-1 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-10 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 libsystemd0_239-7 libtasn1-6_4.13-3 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-4 libubsan1_8.1.0-12+rpi1 libudev1_239-7 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-cd-hit-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-7 util-linux_2.32.1-0.1 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 Wed Sep 26 05:59:36 2018 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 ./cd-hit_4.6.8-2.dsc
dpkg-source: info: extracting cd-hit in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking cd-hit_4.6.8.orig.tar.gz
dpkg-source: info: unpacking cd-hit_4.6.8-2.debian.tar.xz
dpkg-source: info: applying enable_help2man.patch
Check disc 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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-a26ddf88-d9a9-40a6-8f3a-bdb3660852f7
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package cd-hit
dpkg-buildpackage: info: source version 4.6.8-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build cd-hit-4.6.8
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f *.o cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- openmp=yes
make -j4 "INSTALL=install --strip-program=true" openmp=yes
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-common.c++ -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-utility.c++ -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit.c++ -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est.c++ -c
cdhit-utility.c++:9:79: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
char cd_hit_ver[] = "\t\t====== CD-HIT version " CDHIT_VERSION " (built on " __DATE__ ") ======";
^~~~~~~~
cdhit-common.c++:322:16: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
strcpy( date, __DATE__ );
^~~~~~~~
cdhit-common.c++:326:66: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
printf( "Program: CD-HIT, V" CDHIT_VERSION WITH_OPENMP ", %s, " __TIME__ "\n", date );
^~~~~~~~
cdhit-common.c++: In member function 'void SequenceDB::DoClustering(const Options&)':
cdhit-common.c++:3363:10: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
printf( "\nApprixmated maximum memory consumption: %liM\n", mem );
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-2d.c++ -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est-2d.c++ -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-div.c++ -c
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-454.c++ -c
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/c++/8/valarray:38,
from cdhit-common.h:38,
from cdhit-common.c++:28:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/c++/8/valarray:38,
from cdhit-common.h:38,
from cdhit-common.c++:28:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/c++/8/valarray:38,
from cdhit-common.h:38,
from cdhit-common.c++:28:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void SequenceDB::WriteClusters(const char*, const char*, const char*, const char*, const Options&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void SequenceDB::WriteClusters(const char*, const char*, const Options&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/c++/8/valarray:38,
from cdhit-common.h:38,
from cdhit-common.c++:28:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/c++/8/valarray:38,
from cdhit-common.h:38,
from cdhit-common.c++:28:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void SequenceDB::WriteExtra2D(SequenceDB&, const Options&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void SequenceDB::WriteExtra1D(const Options&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-est
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-2d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-est-2d.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-est-2d
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-div.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-div
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -O2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security cdhit-454.o cdhit-common.o cdhit-utility.o -Wl,-z,relro -Wl,-z,now -o cd-hit-454
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
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 '/<<PKGBUILDDIR>>'
dh_auto_install -- PREFIX=debian/cd-hit/usr/lib/cd-hit
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/cd-hit AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=debian/cd-hit/usr/lib/cd-hit
make[2]: Entering directory '/<<PKGBUILDDIR>>'
for prog in cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454; do \
install -m 0755 $prog debian/cd-hit/usr/lib/cd-hit; \
done
install -m 0755 *.pl debian/cd-hit/usr/lib/cd-hit;
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1/
help2man --no-info --no-discard-stderr --version-string='4.6.8' \
--name='quickly group sequences' \
/<<PKGBUILDDIR>>/cd-hit > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//cd-hit.1
help2man --no-info --no-discard-stderr --version-string='4.6.8' \
--name='quickly group sequences, optimised for 454 data' \
/<<PKGBUILDDIR>>/cd-hit-454 > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//cd-hit-454.1
help2man --no-info --no-discard-stderr --version-string='4.6.8' \
--name='quickly group sequences in db1 or db2 format' \
/<<PKGBUILDDIR>>/cd-hit-2d > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//cd-hit-2d.1
help2man --no-info --no-discard-stderr --version-string='4.6.8' \
--name='run CD-HIT algorithm on RNA/DNA sequences' \
/<<PKGBUILDDIR>>/cd-hit-est > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//cd-hit-est.1
help2man --no-info --no-discard-stderr --version-string='4.6.8' \
--name='run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format' \
/<<PKGBUILDDIR>>/cd-hit-est-2d > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//cd-hit-est-2d.1
help2man --no-info --no-discard-stderr --version-string='4.6.8' \
--name='divide a big clustering job into pieces to run cd-hit-2d or cd-hit-est-2d jobs' \
/<<PKGBUILDDIR>>/cd-hit-2d-para.pl > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//cd-hit-2d-para.1
help2man --no-info --no-discard-stderr --version-string='4.6.8' \
--name='divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs' \
/<<PKGBUILDDIR>>/cd-hit-para.pl > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//cd-hit-para.1
help2man --no-info --no-discard-stderr --version-string='4.6.8' \
--name='divide a FASTA file into pieces' \
/<<PKGBUILDDIR>>/cd-hit-div.pl > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//cd-hit-div.1
# psi-cd-hit.pl is throwing some errors which are fixed using sed
# ... at least in versions <= 4.6.4 - now help2man does not work at all
#help2man --no-info --no-discard-stderr --version-string='4.6.8' \
# --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities' \
# /<<PKGBUILDDIR>>/psi-cd-hit.pl | \
# sed -e '/^Name "main::.*" used only once:/d' \
# > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//psi-cd-hit.1
# help2man does not work at all since version 4.6.4
#help2man --no-info --no-discard-stderr --version-string='4.6.8' \
# --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \
# /<<PKGBUILDDIR>>/psi-cd-hit-2d.pl > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d.1
# FIXME: what is the difference between psi-cd-hit-2d.pl and psi-cd-hit-2d-g1.pl ?
# help2man does not work at all since version 4.6.4
#help2man --no-info --no-discard-stderr --version-string='4.6.8' \
# --name='runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format' \
# /<<PKGBUILDDIR>>/psi-cd-hit-2d-g1.pl > /<<PKGBUILDDIR>>/debian/cd-hit/usr/share/man/man1//psi-cd-hit-2d-g1.1
# No help output from
# clstr2tree.pl
# clstr_merge.pl
# clstr_merge_noorder.pl
# clstr_reduce.pl
# clstr_renumber.pl
# clstr_rev.pl
# clstr_sort_by.pl
# clstr_sort_prot_by
# make_multi_seq
# psi-cd-hit-local.pl -> even throws several "used only once: possible typo" errors
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-est contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-454 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-2d contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-div contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/cd-hit/usr/lib/cd-hit/cd-hit-est-2d contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/cd-hit/usr/lib/cd-hit/cd-hit-est debian/cd-hit/usr/lib/cd-hit/cd-hit-454 debian/cd-hit/usr/lib/cd-hit/cd-hit-2d debian/cd-hit/usr/lib/cd-hit/cd-hit-div debian/cd-hit/usr/lib/cd-hit/cd-hit debian/cd-hit/usr/lib/cd-hit/cd-hit-est-2d were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/cd-hit/usr/lib/cd-hit/cd-hit-est debian/cd-hit/usr/lib/cd-hit/cd-hit-454 debian/cd-hit/usr/lib/cd-hit/cd-hit-2d debian/cd-hit/usr/lib/cd-hit/cd-hit-div debian/cd-hit/usr/lib/cd-hit/cd-hit debian/cd-hit/usr/lib/cd-hit/cd-hit-est-2d were not linked against libpthread.so.0 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'cd-hit' in '../cd-hit_4.6.8-2_armhf.deb'.
dpkg-deb: building package 'cd-hit-dbgsym' in '../cd-hit-dbgsym_4.6.8-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../cd-hit_4.6.8-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build cd-hit-4.6.8
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-09-28T05:19:43Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
cd-hit_4.6.8-2_armhf.changes:
-----------------------------
Format: 1.8
Date: Wed, 19 Sep 2018 14:47:50 +0200
Source: cd-hit
Binary: cd-hit
Architecture: armhf
Version: 4.6.8-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
cd-hit - suite of programs designed to quickly group sequences
Changes:
cd-hit (4.6.8-2) unstable; urgency=medium
.
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
Checksums-Sha1:
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78a9b5318dfec84de29627c6a2fac8fdc5a23948 4650 cd-hit_4.6.8-2_armhf.buildinfo
739ca9ac377c5636201cd78fd5a83b87cb0ee2a6 491908 cd-hit_4.6.8-2_armhf.deb
Checksums-Sha256:
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a560d3e60ef0e3ffe884f1a3f856aa4c3ee77e5e946222cf728c19745ffb21bd 4650 cd-hit_4.6.8-2_armhf.buildinfo
1ef3e8a6d28dddd95d4c7532b7119a9f0d7086dcb602c88b7f878dd340478f17 491908 cd-hit_4.6.8-2_armhf.deb
Files:
2f5a9e53674338ae87ba77e7417bb96c 2512124 debug optional cd-hit-dbgsym_4.6.8-2_armhf.deb
ca430bbb3ae455b5c77c5ef9a8230298 4650 science optional cd-hit_4.6.8-2_armhf.buildinfo
1bfba6060f03b16993ca8201fa83a528 491908 science optional cd-hit_4.6.8-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
cd-hit-dbgsym_4.6.8-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 2512124 bytes: control archive=800 bytes.
572 bytes, 12 lines control
636 bytes, 6 lines md5sums
Package: cd-hit-dbgsym
Source: cd-hit
Version: 4.6.8-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2691
Depends: cd-hit (= 4.6.8-2)
Section: debug
Priority: optional
Description: debug symbols for cd-hit
Build-Ids: 1202212102d818d0932f6e0b7f4d7352f9c4e15c 2b0ccf12b78b6cd2f091428f3d64323344ee7bb0 8cb1bac6ea4dc9a2f1f45bbcf1dec3dad6f362c7 b9888dd41f09272add36baeb6e6d3e3cd9406b17 da7c480e3944d1493e8075e50fd01d684b01594b f3398a020b9a9afff30e445fd501eadc0531ec3d
drwxr-xr-x root/root 0 2018-09-19 12:47 ./
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/debug/.build-id/12/
-rw-r--r-- root/root 461076 2018-09-19 12:47 ./usr/lib/debug/.build-id/12/02212102d818d0932f6e0b7f4d7352f9c4e15c.debug
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/debug/.build-id/2b/
-rw-r--r-- root/root 453396 2018-09-19 12:47 ./usr/lib/debug/.build-id/2b/0ccf12b78b6cd2f091428f3d64323344ee7bb0.debug
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/debug/.build-id/8c/
-rw-r--r-- root/root 458900 2018-09-19 12:47 ./usr/lib/debug/.build-id/8c/b1bac6ea4dc9a2f1f45bbcf1dec3dad6f362c7.debug
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/debug/.build-id/b9/
-rw-r--r-- root/root 453692 2018-09-19 12:47 ./usr/lib/debug/.build-id/b9/888dd41f09272add36baeb6e6d3e3cd9406b17.debug
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/debug/.build-id/da/
-rw-r--r-- root/root 453656 2018-09-19 12:47 ./usr/lib/debug/.build-id/da/7c480e3944d1493e8075e50fd01d684b01594b.debug
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/debug/.build-id/f3/
-rw-r--r-- root/root 454816 2018-09-19 12:47 ./usr/lib/debug/.build-id/f3/398a020b9a9afff30e445fd501eadc0531ec3d.debug
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/share/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/share/doc/cd-hit-dbgsym -> cd-hit
cd-hit_4.6.8-2_armhf.deb
------------------------
new Debian package, version 2.0.
size 491908 bytes: control archive=2108 bytes.
898 bytes, 17 lines control
3382 bytes, 51 lines md5sums
Package: cd-hit
Version: 4.6.8-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1207
Depends: libc6 (>= 2.7), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2), perl:any
Section: science
Priority: optional
Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
Description: suite of programs designed to quickly group sequences
cd-hit contains a number of programs designed to quickly group
sequences. cd-hit groups proteins into clusters that meet a user-defined
similarity threshold. cd-hit-est is similar to cd-hit, but designed to
group nucleotide sequences (without introns). cd-hit-est-2d is similar
to cd-hit-2d but designed to compare two nucleotide datasets. A number
of other related programs are also in this package. Please see the
cd-hit user manual, also part of this package, for further information.
drwxr-xr-x root/root 0 2018-09-19 12:47 ./
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/bin/
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cd-hit -> ../lib/cd-hit/cd-hit
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cd-hit-2d -> ../lib/cd-hit/cd-hit-2d
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cd-hit-2d-para -> ../lib/cd-hit/cd-hit-2d-para.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cd-hit-454 -> ../lib/cd-hit/cd-hit-454
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cd-hit-div -> ../lib/cd-hit/cd-hit-div.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cd-hit-est -> ../lib/cd-hit/cd-hit-est
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cd-hit-est-2d -> ../lib/cd-hit/cd-hit-est-2d
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cd-hit-para -> ../lib/cd-hit/cd-hit-para.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cdhit -> cd-hit
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cdhit-2d -> cd-hit-2d
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cdhit-454 -> cd-hit-454
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cdhit-est -> cd-hit-est
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/cdhit-est-2d -> cd-hit-est-2d
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/clstr2tree -> ../lib/cd-hit/clstr2tree.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/clstr_merge -> ../lib/cd-hit/clstr_merge.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/clstr_merge_noorder -> ../lib/cd-hit/clstr_merge_noorder.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/clstr_reduce -> ../lib/cd-hit/clstr_reduce.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/clstr_renumber -> ../lib/cd-hit/clstr_renumber.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/clstr_rev -> ../lib/cd-hit/clstr_rev.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/clstr_sort_by -> ../lib/cd-hit/clstr_sort_by.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/clstr_sort_prot_by -> ../lib/cd-hit/clstr_sort_prot_by.pl
lrwxrwxrwx root/root 0 2018-09-19 12:47 ./usr/bin/make_multi_seq -> ../lib/cd-hit/make_multi_seq.pl
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/lib/cd-hit/
-rwxr-xr-x root/root 3152 2018-09-19 12:47 ./usr/lib/cd-hit/FET.pl
-rwxr-xr-x root/root 108892 2018-09-19 12:47 ./usr/lib/cd-hit/cd-hit
-rwxr-xr-x root/root 108892 2018-09-19 12:47 ./usr/lib/cd-hit/cd-hit-2d
-rwxr-xr-x root/root 12596 2018-09-19 12:47 ./usr/lib/cd-hit/cd-hit-2d-para.pl
-rwxr-xr-x root/root 108976 2018-09-19 12:47 ./usr/lib/cd-hit/cd-hit-454
-rwxr-xr-x root/root 108892 2018-09-19 12:47 ./usr/lib/cd-hit/cd-hit-div
-rwxr-xr-x root/root 992 2018-09-19 12:47 ./usr/lib/cd-hit/cd-hit-div.pl
-rwxr-xr-x root/root 108892 2018-09-19 12:47 ./usr/lib/cd-hit/cd-hit-est
-rwxr-xr-x root/root 112988 2018-09-19 12:47 ./usr/lib/cd-hit/cd-hit-est-2d
-rwxr-xr-x root/root 11859 2018-09-19 12:47 ./usr/lib/cd-hit/cd-hit-para.pl
-rwxr-xr-x root/root 952 2018-09-19 12:47 ./usr/lib/cd-hit/clstr2tree.pl
-rwxr-xr-x root/root 1209 2018-09-19 12:47 ./usr/lib/cd-hit/clstr2txt.pl
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drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/share/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/share/doc-base/
-rw-r--r-- root/root 753 2018-09-19 12:47 ./usr/share/doc-base/cd-hit
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/share/doc/cd-hit/
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drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/share/doc/cd-hit/examples/
-rw-r--r-- root/root 2269 2018-09-19 12:47 ./usr/share/doc/cd-hit/examples/example.fa
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/share/man/
drwxr-xr-x root/root 0 2018-09-19 12:47 ./usr/share/man/man1/
-rw-r--r-- root/root 1146 2018-09-19 12:47 ./usr/share/man/man1/cd-hit-2d-para.1.gz
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-rw-r--r-- root/root 1331 2018-09-19 12:47 ./usr/share/man/man1/cd-hit-454.1.gz
-rw-r--r-- root/root 231 2018-09-19 12:47 ./usr/share/man/man1/cd-hit-div.1.gz
-rw-r--r-- root/root 2146 2018-09-19 12:47 ./usr/share/man/man1/cd-hit-est-2d.1.gz
-rw-r--r-- root/root 2160 2018-09-19 12:47 ./usr/share/man/man1/cd-hit-est.1.gz
-rw-r--r-- root/root 1109 2018-09-19 12:47 ./usr/share/man/man1/cd-hit-para.1.gz
-rw-r--r-- root/root 1737 2018-09-19 12:47 ./usr/share/man/man1/cd-hit.1.gz
+------------------------------------------------------------------------------+
| Post Build |
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+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 20792
Build-Time: 138
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 341
Job: cd-hit_4.6.8-2
Machine Architecture: armhf
Package: cd-hit
Package-Time: 536
Source-Version: 4.6.8-2
Space: 20792
Status: successful
Version: 4.6.8-2
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Finished at 2018-09-28T05:19:43Z
Build needed 00:08:56, 20792k disc space