raxml →
8.2.12+dfsg-7 →
armhf → 2021-10-13 07:45:53
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| raxml 8.2.12+dfsg-7 (armhf) Wed, 13 Oct 2021 07:40:42 +0000 |
+==============================================================================+
Package: raxml
Version: 8.2.12+dfsg-7
Source Version: 8.2.12+dfsg-7
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-c871904d-fd8d-4f92-804c-39812ced83d3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 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: 'raxml' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/raxml.git
Please use:
git clone https://salsa.debian.org/med-team/raxml.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 981 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main raxml 8.2.12+dfsg-7 (dsc) [2011 B]
Get:2 http://172.17.0.1/private bookworm-staging/main raxml 8.2.12+dfsg-7 (tar) [959 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main raxml 8.2.12+dfsg-7 (diff) [19.6 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/raxml-8iemNC/raxml-8.2.12+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/raxml-8iemNC' 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-mjC3lH/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-mjC3lH/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-mjC3lH/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-mjC3lH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mjC3lH/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mjC3lH/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mjC3lH/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mjC3lH/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (9825 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 29 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-mjC3lH/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12484 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
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Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libsimde-dev
Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev
dpkg-deb: building package 'sbuild-build-depends-raxml-dummy' in '/<<BUILDDIR>>/resolver-mjC3lH/apt_archive/sbuild-build-depends-raxml-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-raxml-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-mjC3lH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-mjC3lH/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-mjC3lH/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-mjC3lH/apt_archive ./ Sources [498 B]
Get:5 copy:/<<BUILDDIR>>/resolver-mjC3lH/apt_archive ./ Packages [579 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install raxml build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
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 libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu67 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsimde-dev 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 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 libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu67 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsimde-dev libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-raxml-dummy
sensible-utils
0 upgraded, 33 newly installed, 0 to remove and 29 not upgraded.
Need to get 17.8 MB of archives.
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Get:1 copy:/<<BUILDDIR>>/resolver-mjC3lH/apt_archive ./ sbuild-build-depends-raxml-dummy 0.invalid.0 [868 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-3 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.4-2 [819 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libsimde-dev all 0.7.2-4 [259 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
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Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
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Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up automake (1:1.16.4-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-raxml-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-9+rpi1 gcc-10_10.3.0-9+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.51 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-3 bsdutils_1:2.37.2-1 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-9+rpi1 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-9+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-9+rpi1 gcc-10-base_10.3.0-9+rpi1 gcc-11-base_11.2.0-4+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-4+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-4+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-5+rpi1 libblkid1_2.37.2-1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_11.2.0-4+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-9+rpi1 libgcc-s1_11.2.0-4+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-4+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.23-1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-2 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-5 libpipeline1_1.5.3-1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsimde-dev_0.7.2-4 libsmartcols1_2.37.2-1 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-9+rpi1 libstdc++6_11.2.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.9-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_247.9-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-1 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-5 perl-base_5.32.1-5 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-raxml-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.37.2-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.YHfdzVaT/trustedkeys.kbx': General error
gpgv: Signature made Mon Oct 11 06:47:35 2021 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 ./raxml_8.2.12+dfsg-7.dsc
dpkg-source: info: extracting raxml in /<<BUILDDIR>>/raxml-8.2.12+dfsg
dpkg-source: info: unpacking raxml_8.2.12+dfsg.orig.tar.xz
dpkg-source: info: unpacking raxml_8.2.12+dfsg-7.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying simde
dpkg-source: info: applying hardening
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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-c871904d-fd8d-4f92-804c-39812ced83d3
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package raxml
dpkg-buildpackage: info: source version 8.2.12+dfsg-7
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
for mfile in Makefile.AVX.PTHREADS.gcc; do /usr/bin/make -f ${mfile} clean ; done
make[2]: Entering directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
rm -f *.o raxmlHPC-PTHREADS-AVX
make[2]: Leaving directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
rm -rf /<<BUILDDIR>>/raxml-8.2.12+dfsg/debian/tmpbuild
make[1]: Leaving directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
mkdir -p /<<BUILDDIR>>/raxml-8.2.12+dfsg/debian/tmpbuild
set -e ; for mfile in Makefile.AVX.PTHREADS.gcc; do \
dh_auto_build --buildsystem=makefile -- -f ${mfile} CFLAGS="-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3"; \
curexe=`ls raxmlHPC* | head -n 1` ; \
if [ -e /<<BUILDDIR>>/raxml-8.2.12+dfsg/debian/tmpbuild/${curexe} ] ; then \
echo "**** ERROR: ${curexe} was created before!!" && false ; \
else \
mv ${curexe} /<<BUILDDIR>>/raxml-8.2.12+dfsg/debian/tmpbuild/${curexe} ; \
fi ; \
/usr/bin/make -f ${mfile} clean ; \
done
make -j4 "INSTALL=install --strip-program=true" -f Makefile.AVX.PTHREADS.gcc "CFLAGS=-g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3"
make[2]: Entering directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
rm -f *.o raxmlHPC-PTHREADS-AVX
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o axml.o axml.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o optimizeModel.o optimizeModel.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o multiple.o multiple.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o searchAlgo.o searchAlgo.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o topologies.o topologies.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o parsePartitions.o parsePartitions.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o treeIO.o treeIO.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o models.o models.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bipartitionList.o bipartitionList.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o rapidBootstrap.o rapidBootstrap.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o evaluatePartialGenericSpecial.o evaluatePartialGenericSpecial.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o evaluateGenericSpecial.o evaluateGenericSpecial.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o newviewGenericSpecial.o newviewGenericSpecial.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o makenewzGenericSpecial.o makenewzGenericSpecial.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o classify.o classify.c
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -o fastDNAparsimony.o fastDNAparsimony.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o fastSearch.o fastSearch.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o leaveDropping.o leaveDropping.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o rmqs.o rmqs.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o rogueEPA.o rogueEPA.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o ancestralStates.o ancestralStates.c
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -o avxLikelihood.o avxLikelihood.c
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mem_alloc.o mem_alloc.c
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/raxml-8.2.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -c -o eigen.o eigen.c
gcc -o raxmlHPC-PTHREADS-AVX axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o avxLikelihood.o mem_alloc.o eigen.o -lm -pthread -Wl,-z,relro -Wl,-z,now
make[2]: Leaving directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
make[2]: Entering directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
rm -f *.o raxmlHPC-PTHREADS-AVX
make[2]: Leaving directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_installdirs -a
dh_auto_install --destdir=debian/raxml/ -a
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
dh_install
dh_link usr/bin/raxmlHPC-PTHREADS-AVX usr/bin/raxmlHPC
make[1]: Leaving directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
dh_installexamples
# fix perl path in example scripts
for pscript in `ls usefulScripts/*.pl` ; do \
sed 's?/usr/local/bin/perl?/usr/bin/perl?' ${pscript} > /<<BUILDDIR>>/raxml-8.2.12+dfsg/debian/raxml/usr/share/doc/raxml/examples/`basename ${pscript}` ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
debian/rules override_dh_installman
make[1]: Entering directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
dh_installman
for cexe in `ls /<<BUILDDIR>>/raxml-8.2.12+dfsg/debian/tmpbuild/raxmlHPC*` ; do \
curexe=`basename ${cexe}` ; \
if [ ${curexe} != raxmlHPC ] ; then \
ln -s raxmlHPC.1.gz /<<BUILDDIR>>/raxml-8.2.12+dfsg/debian/raxml/usr/share/man/man1/${curexe}.1.gz ; \
fi ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/raxml/usr/bin/raxmlHPC-PTHREADS-AVX was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
debian/rules override_dh_gencontrol
make[1]: Entering directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.2-4), "
make[1]: Leaving directory '/<<BUILDDIR>>/raxml-8.2.12+dfsg'
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'raxml' in '../raxml_8.2.12+dfsg-7_armhf.deb'.
dpkg-deb: building package 'raxml-dbgsym' in '../raxml-dbgsym_8.2.12+dfsg-7_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../raxml_8.2.12+dfsg-7_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 2021-10-13T07:45:39Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
raxml_8.2.12+dfsg-7_armhf.changes:
----------------------------------
Format: 1.8
Date: Mon, 11 Oct 2021 08:13:38 +0200
Source: raxml
Binary: raxml raxml-dbgsym
Architecture: armhf
Version: 8.2.12+dfsg-7
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
raxml - Randomized Axelerated Maximum Likelihood of phylogenetic trees
Changes:
raxml (8.2.12+dfsg-7) unstable; urgency=medium
.
[ Michael R. Crusoe ]
* Team upload.
* Update homepage
.
[ Andreas Tille ]
* Fix watchfile to detect new versions on github
* Standards-Version: 4.6.0 (routine-update)
* debhelper-compat 13 (routine-update)
* watch file standard 4 (routine-update)
Checksums-Sha1:
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Checksums-Sha256:
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Files:
21aa59841881289623b6416c875f0009 921540 debug optional raxml-dbgsym_8.2.12+dfsg-7_armhf.deb
3dd2058db5096e3cdb9e956948f240e3 4898 science optional raxml_8.2.12+dfsg-7_armhf.buildinfo
4e6bdd3822f6509b77b181ab747a8615 926664 science optional raxml_8.2.12+dfsg-7_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
raxml-dbgsym_8.2.12+dfsg-7_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 921540 bytes: control archive=536 bytes.
374 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: raxml-dbgsym
Source: raxml
Version: 8.2.12+dfsg-7
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 950
Depends: raxml (= 8.2.12+dfsg-7)
Section: debug
Priority: optional
Description: debug symbols for raxml
Build-Ids: 8b4a885722c7bdad5a27dd054a0046b5f3341c13
drwxr-xr-x root/root 0 2021-10-11 06:13 ./
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/lib/
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/lib/debug/.build-id/8b/
-rw-r--r-- root/root 962432 2021-10-11 06:13 ./usr/lib/debug/.build-id/8b/4a885722c7bdad5a27dd054a0046b5f3341c13.debug
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-10-11 06:13 ./usr/share/doc/raxml-dbgsym -> raxml
raxml_8.2.12+dfsg-7_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 926664 bytes: control archive=1236 bytes.
564 bytes, 14 lines control
1419 bytes, 19 lines md5sums
Package: raxml
Version: 8.2.12+dfsg-7
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1467
Depends: libc6 (>= 2.29)
Built-Using: simde (= 0.7.2-4)
Section: science
Priority: optional
Homepage: https://cme.h-its.org/exelixis/web/software/raxml/index.html
Description: Randomized Axelerated Maximum Likelihood of phylogenetic trees
RAxML is a program for sequential and parallel Maximum Likelihood-based
inference of large phylogenetic trees. It has originally been derived
from fastDNAml.
drwxr-xr-x root/root 0 2021-10-11 06:13 ./
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/bin/
lrwxrwxrwx root/root 0 2021-10-11 06:13 ./usr/bin/raxmlHPC -> raxmlHPC-PTHREADS-AVX
-rwxr-xr-x root/root 879048 2021-10-11 06:13 ./usr/bin/raxmlHPC-PTHREADS-AVX
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/doc-base/
-rw-r--r-- root/root 605 2021-10-11 06:13 ./usr/share/doc-base/raxml.raxml
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/doc/raxml/
-rw-r--r-- root/root 573025 2018-05-29 04:28 ./usr/share/doc/raxml/NewManual.pdf.gz
-rw-r--r-- root/root 2332 2018-05-29 04:28 ./usr/share/doc/raxml/README
-rw-r--r-- root/root 446 2021-10-11 06:13 ./usr/share/doc/raxml/README.test
-rw-r--r-- root/root 2081 2021-10-11 06:13 ./usr/share/doc/raxml/changelog.Debian.gz
-rw-r--r-- root/root 1348 2021-10-11 06:13 ./usr/share/doc/raxml/copyright
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/doc/raxml/examples/
-rw-r--r-- root/root 3264 2021-10-11 06:13 ./usr/share/doc/raxml/examples/ProteinModelSelection.pl
-rw-r--r-- root/root 635 2021-10-11 06:13 ./usr/share/doc/raxml/examples/applyRAxML2AllFilesInDirectory.pl
-rw-r--r-- root/root 677 2021-10-11 06:13 ./usr/share/doc/raxml/examples/bsBranchLengths.pl
-rw-r--r-- root/root 337 2018-05-29 04:28 ./usr/share/doc/raxml/examples/convertFasta2Phylip.sh
-rw-r--r-- root/root 355 2021-10-11 06:13 ./usr/share/doc/raxml/run-unit-test
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/doc/raxml/test_data/
-rw-r--r-- root/root 36 2021-10-11 06:13 ./usr/share/doc/raxml/test_data/testData.txt
-rw-r--r-- root/root 36 2021-10-11 06:13 ./usr/share/doc/raxml/test_data/testData1.txt
-rw-r--r-- root/root 519 2021-10-11 06:13 ./usr/share/doc/raxml/test_data/testData2.txt
-rw-r--r-- root/root 19 2021-10-11 06:13 ./usr/share/doc/raxml/test_data/testTree.txt
-rw-r--r-- root/root 19 2021-10-11 06:13 ./usr/share/doc/raxml/test_data/testTree1.txt
-rw-r--r-- root/root 65 2021-10-11 06:13 ./usr/share/doc/raxml/test_data/testTree2.txt
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/man/
drwxr-xr-x root/root 0 2021-10-11 06:13 ./usr/share/man/man1/
lrwxrwxrwx root/root 0 2021-10-11 06:13 ./usr/share/man/man1/raxmlHPC-PTHREADS-AVX.1.gz -> raxmlHPC.1.gz
-rw-r--r-- root/root 9429 2021-10-11 06:13 ./usr/share/man/man1/raxmlHPC.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 12548
Build-Time: 87
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 191
Job: raxml_8.2.12+dfsg-7
Machine Architecture: armhf
Package: raxml
Package-Time: 297
Source-Version: 8.2.12+dfsg-7
Space: 12548
Status: successful
Version: 8.2.12+dfsg-7
--------------------------------------------------------------------------------
Finished at 2021-10-13T07:45:39Z
Build needed 00:04:57, 12548k disk space