clearcut →
1.0.9-6 →
armhf → 2020-12-07 10:32:59
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| clearcut 1.0.9-6 (armhf) Mon, 07 Dec 2020 10:28:53 +0000 |
+==============================================================================+
Package: clearcut
Version: 1.0.9-6
Source Version: 1.0.9-6
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-8eeada35-4b3d-4552-b2b2-46d167d9e9d9' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/clearcut-r6szw4/resolver-GYKLoT' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.9 MB in 13s (1845 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'clearcut' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/clearcut.git
Please use:
git clone https://salsa.debian.org/med-team/clearcut.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 358 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main clearcut 1.0.9-6 (dsc) [1991 B]
Get:2 http://172.17.0.1/private bullseye-staging/main clearcut 1.0.9-6 (tar) [350 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main clearcut 1.0.9-6 (diff) [5984 B]
Fetched 358 kB in 0s (800 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/clearcut-r6szw4/clearcut-1.0.9' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/clearcut-r6szw4' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 12), build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [369 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [453 B]
Fetched 1779 B in 0s (48.2 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl
libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl 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 bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl
libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils
0 upgraded, 34 newly installed, 0 to remove and 51 not upgraded.
Need to get 18.6 MB of archives.
After this operation, 68.4 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [868 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf bsdextrautils armhf 2.36.1-2 [133 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.3-2 [1178 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 18.6 MB in 4s (4332 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12445 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.36.1-2_armhf.deb ...
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Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up bsdextrautils (2.36.1-2) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-4) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.3-2) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.2.1) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.182-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (13.2.1) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-16+rpi1 gcc-10_10.2.0-16+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.11 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc2-1 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36.1-2 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-16+rpi1 dash_0.5.11+git20200708+dd9ef66-2 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 file_1:5.38-5 findutils_4.7.0+git20201010-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-16+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-16+rpi1 gcc-10-base_10.2.0-16+rpi1 gcc-7-base_7.5.0-6+rpi1+b1 gcc-8-base_8.4.0-4+rpi1+b1 gcc-9-base_9.3.0-18+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg6.0_2.1.11 libarchive-zip-perl_1.68-1 libasan6_10.2.0-16+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-16+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbinutils_2.35.1-2+rpi1 libblkid1_2.36-3 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcap-ng0_0.7.9-2.2 libcc1-0_10.2.0-16+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.255 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-16+rpi1 libgcc-s1_10.2.0-16+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.3-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-16+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-3 libisl22_0.22.1-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 libldap-2.4-2_2.4.56+dfsg-1+rpi1+b1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libreadline8_8.1~rc2-2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.0-3+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1h-1 libstdc++-10-dev_10.2.0-16+rpi1 libstdc++6_10.2.0-16+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.6-2+rpi1 libtasn1-6_4.16.0-2 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-16+rpi1 libuchardet0_0.0.7-1 libudev1_246.6-2+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxml2_2.9.10+dfsg-6.3 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.1~rc2-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: clearcut
Binary: clearcut
Architecture: any
Version: 1.0.9-6
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Tim Booth <tbooth@ceh.ac.uk>, Andreas Tille <tille@debian.org>
Homepage: https://github.com/sheneman/clearcut
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/clearcut
Vcs-Git: https://salsa.debian.org/med-team/clearcut.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 12)
Package-List:
clearcut deb science optional arch=any
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.egvFOhAh/trustedkeys.kbx': General error
gpgv: Signature made Fri Dec 4 14:24:14 2020 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 ./clearcut_1.0.9-6.dsc
dpkg-source: info: extracting clearcut in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking clearcut_1.0.9.orig.tar.gz
dpkg-source: info: unpacking clearcut_1.0.9-6.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying mothur_trivial_patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying clear-errno-before-checking.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=1ec3ff19654148fab3a02153247d5928
JOURNAL_STREAM=8:145870
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-8eeada35-4b3d-4552-b2b2-46d167d9e9d9
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c39475
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package clearcut
dpkg-buildpackage: info: source version 1.0.9-6
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
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Makefile:124: warning: ignoring prerequisites on suffix rule definition
rm -f *.o a.out *.a clearcut
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
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Makefile:124: warning: ignoring prerequisites on suffix rule definition
gcc -c -I /usr/local/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -funroll-loops -fomit-frame-pointer clearcut.c
gcc -c -I /usr/local/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -funroll-loops -fomit-frame-pointer dist.c
gcc -c -I /usr/local/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -funroll-loops -fomit-frame-pointer dmat.c
gcc -c -I /usr/local/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -funroll-loops -fomit-frame-pointer fasta.c
dist.c: In function ‘NJ_DNA_jc_correction’:
dist.c:268:12: warning: variable ‘k’ set but not used [-Wunused-but-set-variable]
268 | long int k;
| ^
fasta.c: In function ‘NJ_read_fasta’:
fasta.c:307:19: warning: variable ‘x’ set but not used [-Wunused-but-set-variable]
307 | long int index, x, seq;
| ^
clearcut.c: In function ‘NJ_neighbor_joining’:
clearcut.c:1106:9: warning: variable ‘min’ set but not used [-Wunused-but-set-variable]
1106 | float min;
| ^~~
clearcut.c: In function ‘NJ_relaxed_nj’:
clearcut.c:1224:12: warning: variable ‘q’ set but not used [-Wunused-but-set-variable]
1224 | float p, q, x;
| ^
gcc -c -I /usr/local/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -funroll-loops -fomit-frame-pointer cmdargs.c
dist.c: In function ‘NJ_compute_dmat’:
dist.c:154:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
154 | strncpy(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i]));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -c -I /usr/local/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -funroll-loops -fomit-frame-pointer prng.c
gcc -c -I /usr/local/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -funroll-loops -fomit-frame-pointer getopt_long.c
gcc -o clearcut clearcut.o dist.o dmat.o fasta.o cmdargs.o prng.o getopt_long.o -lm -Wl,-z,relro
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_auto_install -a
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
debian/rules override_dh_compress
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_compress -X.dist
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/clearcut/usr/bin/clearcut was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'clearcut' in '../clearcut_1.0.9-6_armhf.deb'.
dpkg-deb: building package 'clearcut-dbgsym' in '../clearcut-dbgsym_1.0.9-6_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../clearcut_1.0.9-6_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 2020-12-07T10:32:53Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
clearcut_1.0.9-6_armhf.changes:
-------------------------------
Format: 1.8
Date: Fri, 04 Dec 2020 15:22:30 +0100
Source: clearcut
Binary: clearcut clearcut-dbgsym
Architecture: armhf
Version: 1.0.9-6
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
clearcut - extremely efficient phylogenetic tree reconstruction
Closes: 975947
Changes:
clearcut (1.0.9-6) unstable; urgency=medium
.
* Fix homepage
Closes: #975947
* Point watch file to Github (even if no tags are set yet)
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+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: clearcut
Binary: clearcut clearcut-dbgsym
Architecture: armhf
Version: 1.0.9-6
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Mon, 07 Dec 2020 10:32:52 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.69-11.1),
automake (= 1:1.16.2-4),
autopoint (= 0.19.8.1-10),
autotools-dev (= 20180224.1),
base-files (= 11+rpi1),
base-passwd (= 3.5.48),
bash (= 5.1~rc2-1),
binutils (= 2.35.1-2+rpi1),
binutils-arm-linux-gnueabihf (= 2.35.1-2+rpi1),
binutils-common (= 2.35.1-2+rpi1),
bsdextrautils (= 2.36.1-2),
bsdutils (= 1:2.36-3),
build-essential (= 12.8),
bzip2 (= 1.0.8-4),
coreutils (= 8.32-4),
cpp (= 4:10.2.0-1+rpi1),
cpp-10 (= 10.2.0-16+rpi1),
dash (= 0.5.11+git20200708+dd9ef66-2),
debconf (= 1.5.74),
debhelper (= 13.2.1),
debianutils (= 4.11.2),
dh-autoreconf (= 19),
dh-strip-nondeterminism (= 1.9.0-1),
diffutils (= 1:3.7-3),
dpkg (= 1.20.5+rpi1),
dpkg-dev (= 1.20.5+rpi1),
dwz (= 0.13-5),
file (= 1:5.38-5),
findutils (= 4.7.0+git20201010-2),
g++ (= 4:10.2.0-1+rpi1),
g++-10 (= 10.2.0-16+rpi1),
gcc (= 4:10.2.0-1+rpi1),
gcc-10 (= 10.2.0-16+rpi1),
gcc-10-base (= 10.2.0-16+rpi1),
gettext (= 0.19.8.1-10),
gettext-base (= 0.19.8.1-10),
grep (= 3.6-1),
groff-base (= 1.22.4-5),
gzip (= 1.10-2),
hostname (= 3.23),
init-system-helpers (= 1.58),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.2.53-8),
libarchive-zip-perl (= 1.68-1),
libasan6 (= 10.2.0-16+rpi1),
libatomic1 (= 10.2.0-16+rpi1),
libattr1 (= 1:2.4.48-5),
libaudit-common (= 1:2.8.5-3.1),
libaudit1 (= 1:2.8.5-3.1),
libbinutils (= 2.35.1-2+rpi1),
libblkid1 (= 2.36-3),
libbz2-1.0 (= 1.0.8-4),
libc-bin (= 2.31-4+rpi1),
libc-dev-bin (= 2.31-4+rpi1),
libc6 (= 2.31-4+rpi1),
libc6-dev (= 2.31-4+rpi1),
libcap-ng0 (= 0.7.9-2.2),
libcc1-0 (= 10.2.0-16+rpi1),
libcom-err2 (= 1.45.6-1),
libcroco3 (= 0.6.13-1),
libcrypt-dev (= 1:4.4.17-1),
libcrypt1 (= 1:4.4.17-1),
libctf-nobfd0 (= 2.35.1-2+rpi1),
libctf0 (= 2.35.1-2+rpi1),
libdb5.3 (= 5.3.28+dfsg1-0.6),
libdebconfclient0 (= 0.255),
libdebhelper-perl (= 13.2.1),
libdpkg-perl (= 1.20.5+rpi1),
libelf1 (= 0.182-1),
libffi7 (= 3.3-5),
libfile-stripnondeterminism-perl (= 1.9.0-1),
libgcc-10-dev (= 10.2.0-16+rpi1),
libgcc-s1 (= 10.2.0-16+rpi1),
libgcrypt20 (= 1.8.7-2),
libgdbm-compat4 (= 1.18.1-5.1),
libgdbm6 (= 1.18.1-5.1),
libglib2.0-0 (= 2.66.3-2),
libgmp10 (= 2:6.2.0+dfsg-6),
libgomp1 (= 10.2.0-16+rpi1),
libgpg-error0 (= 1.38-2),
libgssapi-krb5-2 (= 1.17-10+b3),
libicu67 (= 67.1-4),
libisl22 (= 0.22.1-1),
libk5crypto3 (= 1.17-10+b3),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.17-10+b3),
libkrb5support0 (= 1.17-10+b3),
liblz4-1 (= 1.9.2-2),
liblzma5 (= 5.2.4-1),
libmagic-mgc (= 1:5.38-5),
libmagic1 (= 1:5.38-5),
libmount1 (= 2.36-3),
libmpc3 (= 1.2.0-1),
libmpfr6 (= 4.1.0-3),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libnss-nis (= 3.1-4),
libnss-nisplus (= 1.3-4),
libpam-modules (= 1.3.1-5),
libpam-modules-bin (= 1.3.1-5),
libpam-runtime (= 1.3.1-5),
libpam0g (= 1.3.1-5),
libpcre2-8-0 (= 10.34-7),
libpcre3 (= 2:8.39-13),
libperl5.32 (= 5.32.0-5),
libpipeline1 (= 1.5.3-1),
libseccomp2 (= 2.5.0-3+rpi1),
libselinux1 (= 3.1-2),
libsigsegv2 (= 2.12-2),
libsmartcols1 (= 2.36-3),
libssl1.1 (= 1.1.1h-1),
libstdc++-10-dev (= 10.2.0-16+rpi1),
libstdc++6 (= 10.2.0-16+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 246.6-2+rpi1),
libtinfo6 (= 6.2+20200918-1),
libtirpc-common (= 1.2.6-3),
libtirpc-dev (= 1.2.6-3),
libtirpc3 (= 1.2.6-3),
libtool (= 2.4.6-14),
libubsan1 (= 10.2.0-16+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 246.6-2+rpi1),
libunistring2 (= 0.9.10-4),
libuuid1 (= 2.36-3),
libxml2 (= 2.9.10+dfsg-6.3),
libzstd1 (= 1.4.5+dfsg-4+rpi1),
linux-libc-dev (= 5.7.10-1+rpi1),
login (= 1:4.8.1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-4),
make (= 4.3-4),
man-db (= 2.9.3-2),
mawk (= 1.3.4.20200120-2),
ncurses-base (= 6.2+20200918-1),
ncurses-bin (= 6.2+20200918-1),
patch (= 2.7.6-6),
perl (= 5.32.0-5),
perl-base (= 5.32.0-5),
perl-modules-5.32 (= 5.32.0-5),
po-debconf (= 1.0.21),
sed (= 4.7-1),
sensible-utils (= 0.0.12+nmu1),
sysvinit-utils (= 2.96-5),
tar (= 1.30+dfsg-7),
util-linux (= 2.36-3),
xz-utils (= 5.2.4-1),
zlib1g (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1607091750"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
clearcut-dbgsym_1.0.9-6_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 62084 bytes: control archive=536 bytes.
373 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: clearcut-dbgsym
Source: clearcut
Version: 1.0.9-6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 77
Depends: clearcut (= 1.0.9-6)
Section: debug
Priority: optional
Description: debug symbols for clearcut
Build-Ids: 9c7a87c9def5957473dd87f582350100602c5dd2
drwxr-xr-x root/root 0 2020-12-04 14:22 ./
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/lib/
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 68236 2020-12-04 14:22 ./usr/lib/debug/.build-id/9c/7a87c9def5957473dd87f582350100602c5dd2.debug
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/share/
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-12-04 14:22 ./usr/share/doc/clearcut-dbgsym -> clearcut
clearcut_1.0.9-6_armhf.deb
--------------------------
new Debian package, version 2.0.
size 274112 bytes: control archive=980 bytes.
569 bytes, 14 lines control
737 bytes, 10 lines md5sums
Package: clearcut
Version: 1.0.9-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1191
Depends: libc6 (>= 2.29)
Section: science
Priority: optional
Homepage: https://github.com/sheneman/clearcut
Description: extremely efficient phylogenetic tree reconstruction
Clearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ)
algorithm by J. Evans, L. Sheneman, and J. Foster from the Initiative
for Bioinformatics and Evolutionary Studies (IBEST) at the University of
Idaho.
drwxr-xr-x root/root 0 2020-12-04 14:22 ./
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/bin/
-rwxr-xr-x root/root 67928 2020-12-04 14:22 ./usr/bin/clearcut
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/share/
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/share/doc/clearcut/
-rw-r--r-- root/root 2416 2009-02-09 21:31 ./usr/share/doc/clearcut/README.gz
-rw-r--r-- root/root 821 2020-12-04 14:22 ./usr/share/doc/clearcut/changelog.Debian.gz
-rw-r--r-- root/root 3073 2020-12-04 14:22 ./usr/share/doc/clearcut/copyright
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/share/doc/clearcut/examples/
-rw-r--r-- root/root 322 2009-02-09 21:30 ./usr/share/doc/clearcut/examples/alignment1.dist
-rw-r--r-- root/root 116 2009-02-09 21:30 ./usr/share/doc/clearcut/examples/lower_diag.dist
-rw-r--r-- root/root 211 2009-02-09 21:30 ./usr/share/doc/clearcut/examples/symmetric.dist
-rw-r--r-- root/root 1126705 2009-02-09 21:30 ./usr/share/doc/clearcut/examples/treezilla.dist
-rw-r--r-- root/root 154 2009-02-09 21:30 ./usr/share/doc/clearcut/examples/upper_diag.dist
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/share/man/
drwxr-xr-x root/root 0 2020-12-04 14:22 ./usr/share/man/man1/
-rw-r--r-- root/root 919 2020-12-04 14:22 ./usr/share/man/man1/clearcut.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 3804
Build-Time: 20
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 192
Job: clearcut_1.0.9-6
Machine Architecture: armhf
Package: clearcut
Package-Time: 240
Source-Version: 1.0.9-6
Space: 3804
Status: successful
Version: 1.0.9-6
--------------------------------------------------------------------------------
Finished at 2020-12-07T10:32:53Z
Build needed 00:04:00, 3804k disk space