maffilter →
1.3.1+dfsg-5 →
armhf → 2023-09-23 11:36:15
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| maffilter 1.3.1+dfsg-5 (armhf) Sat, 23 Sep 2023 11:25:54 +0000 |
+==============================================================================+
Package: maffilter
Version: 1.3.1+dfsg-5
Source Version: 1.3.1+dfsg-5
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-121adae7-a026-4f4f-bc10-78fa8f85b9b3' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.1 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.6 MB]
Fetched 28.7 MB in 12s (2330 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'maffilter' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/maffilter.git
Please use:
git clone https://salsa.debian.org/med-team/maffilter.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 78.7 MB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main maffilter 1.3.1+dfsg-5 (dsc) [2238 B]
Get:2 http://172.17.4.1/private trixie-staging/main maffilter 1.3.1+dfsg-5 (tar) [78.7 MB]
Get:3 http://172.17.4.1/private trixie-staging/main maffilter 1.3.1+dfsg-5 (diff) [4728 B]
Fetched 78.7 MB in 10s (7573 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/maffilter-v1PZs5/maffilter-1.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/maffilter-v1PZs5' 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-tZmJph/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-tZmJph/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-tZmJph/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-tZmJph/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tZmJph/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tZmJph/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-tZmJph/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tZmJph/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (7771 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 packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils sgml-base util-linux-extra
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 12 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-tZmJph/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 (63.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11775 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) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), cmake, texinfo, libbpp-phyl-omics-dev, libboost-iostreams-dev, zlib1g-dev, libbz2-dev
Filtered Build-Depends: debhelper-compat (= 13), cmake, texinfo, libbpp-phyl-omics-dev, libboost-iostreams-dev, zlib1g-dev, libbz2-dev
dpkg-deb: building package 'sbuild-build-depends-maffilter-dummy' in '/<<BUILDDIR>>/resolver-tZmJph/apt_archive/sbuild-build-depends-maffilter-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-maffilter-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-tZmJph/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tZmJph/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tZmJph/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-tZmJph/apt_archive ./ Sources [543 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tZmJph/apt_archive ./ Packages [618 B]
Fetched 2494 B in 0s (9314 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install maffilter 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:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl
libarchive13 libboost-iostreams-dev libboost-iostreams1.74-dev
libboost-iostreams1.74.0 libboost-regex1.74-dev libboost-regex1.74.0
libboost1.74-dev libbpp-core-dev libbpp-core4 libbpp-phyl-dev
libbpp-phyl-omics-dev libbpp-phyl-omics3 libbpp-phyl12 libbpp-seq-dev
libbpp-seq-omics-dev libbpp-seq-omics3 libbpp-seq12 libbrotli1 libbz2-dev
libcurl4 libdebhelper-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libicu-dev libicu72 libjsoncpp25
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libproc2-0 libpsl5
librhash0 librtmp1 libssh2-1 libsub-override-perl libtext-unidecode-perl
libtool libuchardet0 libuv1 libxml-libxml-perl libxml-namespacesupport-perl
libxml-sax-base-perl libxml-sax-perl libxml2 m4 man-db po-debconf procps
tex-common texinfo texinfo-lib ucf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
elpa-cmake-mode ninja-build dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff lrzip libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev
libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev
libboost-numpy1.74-dev libboost-program-options1.74-dev
libboost-python1.74-dev libboost-random1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
icu-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor
less www-browser libmail-box-perl texlive-base texlive-latex-base
texlive-plain-generic texlive-fonts-recommended
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
publicsuffix libltdl-dev libwww-perl libxml-sax-expat-perl
libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base icu-devtools intltool-debian libarchive-zip-perl
libarchive13 libboost-iostreams-dev libboost-iostreams1.74-dev
libboost-iostreams1.74.0 libboost-regex1.74-dev libboost-regex1.74.0
libboost1.74-dev libbpp-core-dev libbpp-core4 libbpp-phyl-dev
libbpp-phyl-omics-dev libbpp-phyl-omics3 libbpp-phyl12 libbpp-seq-dev
libbpp-seq-omics-dev libbpp-seq-omics3 libbpp-seq12 libbrotli1 libbz2-dev
libcurl4 libdebhelper-perl libelf1 libexpat1
libfile-stripnondeterminism-perl libicu-dev libicu72 libjsoncpp25
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libproc2-0 libpsl5
librhash0 librtmp1 libssh2-1 libsub-override-perl libtext-unidecode-perl
libtool libuchardet0 libuv1 libxml-libxml-perl libxml-namespacesupport-perl
libxml-sax-base-perl libxml-sax-perl libxml2 m4 man-db po-debconf procps
sbuild-build-depends-maffilter-dummy tex-common texinfo texinfo-lib ucf
zlib1g-dev
0 upgraded, 74 newly installed, 0 to remove and 12 not upgraded.
Need to get 62.3 MB of archives.
After this operation, 393 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-tZmJph/apt_archive ./ sbuild-build-depends-maffilter-dummy 0.invalid.0 [912 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.22.4-10 [774 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-1 [80.5 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-3 [1342 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libproc2-0 armhf 2:4.0.3-1 [54.2 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf procps armhf 2:4.0.3-1 [731 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-12 [156 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf ucf all 3.0043+nmu1 [55.2 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-3 [9009 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libarchive13 armhf 3.6.2-1 [293 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.56.0-1 [60.5 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 7.88.1-10+rpi1 [343 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libjsoncpp25 armhf 1.9.5-6 [64.7 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libuv1 armhf 1.44.2-1+rpi1 [125 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf cmake-data all 3.27.5-1 [2103 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf cmake armhf 3.27.5-1 [7747 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.6 [81.9 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-12 [1201 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.6 [952 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf icu-devtools armhf 72.1-3 [175 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libboost1.74-dev armhf 1.74.0+ds1-21 [9508 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.74.0 armhf 1.74.0+ds1-21 [420 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libicu-dev armhf 72.1-3 [9959 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libboost-regex1.74-dev armhf 1.74.0+ds1-21 [525 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.74.0 armhf 1.74.0+ds1-21 [235 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams1.74-dev armhf 1.74.0+ds1-21 [245 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libboost-iostreams-dev armhf 1.74.0.3+b4 [4592 B]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libbpp-core4 armhf 2.4.1-11 [486 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libbpp-core-dev armhf 2.4.1-11 [885 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libbpp-seq12 armhf 2.4.1-10 [407 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libbpp-phyl12 armhf 2.4.1-9 [1348 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libbpp-seq-dev armhf 2.4.1-10 [677 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libbpp-phyl-dev armhf 2.4.1-9 [2926 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libbpp-seq-omics3 armhf 2.4.1-10 [183 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libbpp-phyl-omics3 armhf 2.4.1-5 [62.9 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libbpp-seq-omics-dev armhf 2.4.1-10 [361 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libbpp-phyl-omics-dev armhf 2.4.1-5 [140 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf libtext-unidecode-perl all 1.30-3 [101 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf libxml-libxml-perl armhf 2.0207+dfsg+really+2.0134-1+b2 [305 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf tex-common all 6.18 [32.5 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf texinfo-lib armhf 7.0.3-2 [279 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf texinfo all 7.0.3-2 [1776 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
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update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
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Processing triggers for libc-bin (2.36-9+rpi1+deb12u1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.40-2+rpi2 dpkg-dev_1.21.22+rpi1 g++-12_12.2.0-14+rpi1 gcc-12_12.2.0-14+rpi1 libc6-dev_2.36-9+rpi1+deb12u1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 linux-libc-dev_6.1.38-1+rpi1
Package versions: adduser_3.137 apt_2.7.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.1 bash_5.2.15-2 binutils_2.40-2+rpi2 binutils-arm-linux-gnueabihf_2.40-2+rpi2 binutils-common_2.40-2+rpi2 bsdextrautils_2.39.2-1 bsdutils_1:2.39.2-1 build-essential_12.9 bzip2_1.0.8-5+b2 cmake_3.27.5-1 cmake-data_3.27.5-1 coreutils_9.1-1 cpp_4:12.2.0-3+rpi1 cpp-12_12.2.0-14+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.6 debianutils_5.13 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dirmngr_2.2.40-1.1 dpkg_1.21.22+rpi1 dpkg-dev_1.21.22+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-4 g++_4:12.2.0-3+rpi1 g++-12_12.2.0-14+rpi1 gcc_4:12.2.0-3+rpi1 gcc-12_12.2.0-14+rpi1 gcc-12-base_12.2.0-14+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_0.21-12 gettext-base_0.21-12 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1 hostname_3.23+nmu1 icu-devtools_72.1-3 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-3 libacl1_2.3.1-3 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libarchive13_3.6.2-1 libasan8_12.2.0-14+rpi1 libassuan0_2.5.6-1 libatomic1_12.2.0-14+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.40-2+rpi2 libblkid1_2.39.2-1 libboost-iostreams-dev_1.74.0.3+b4 libboost-iostreams1.74-dev_1.74.0+ds1-21 libboost-iostreams1.74.0_1.74.0+ds1-21 libboost-regex1.74-dev_1.74.0+ds1-21 libboost-regex1.74.0_1.74.0+ds1-21 libboost1.74-dev_1.74.0+ds1-21 libbpp-core-dev_2.4.1-11 libbpp-core4_2.4.1-11 libbpp-phyl-dev_2.4.1-9 libbpp-phyl-omics-dev_2.4.1-5 libbpp-phyl-omics3_2.4.1-5 libbpp-phyl12_2.4.1-9 libbpp-seq-dev_2.4.1-10 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libhogweed6_3.9.1-2 libicu-dev_72.1-3 libicu72_72.1-3 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjsoncpp25_1.9.5-6 libk5crypto3_1.20.1-3 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-3 libkrb5support0_1.20.1-3 libksba8_1.6.3-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.4-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncursesw6_6.4+20230625-2 libnettle8_3.9.1-2 libnghttp2-14_1.56.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.0-4 libpam-cap_1:2.66-4 libpam-modules_1.5.2-7 libpam-modules-bin_1.5.2-7 libpam-runtime_1.5.2-7 libpam0g_1.5.2-7 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libproc2-0_2:4.0.3-1 libpsl5_0.21.2-1+b1 libreadline8_8.2-1.3 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.4-1+b2 libsepol1_3.1-1 libsepol2_3.5-1 libsmartcols1_2.39.2-1 libsqlite3-0_3.43.1-1 libss2_1.47.0-2 libssh2-1_1.11.0-2 libssl1.1_1.1.1o-1 libssl3_3.0.10-1 libstdc++-12-dev_12.2.0-14+rpi1 libstdc++6_12.2.0-14+rpi1 libsub-override-perl_0.09-4 libsystemd0_252.12-1~deb12u1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtext-unidecode-perl_1.30-3 libtinfo6_6.4+20230625-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_12.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_252.12-1~deb12u1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-1 libuv1_1.44.2-1+rpi1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b2 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.1-1 libzstd1_1.5.5+dfsg2-1 linux-libc-dev_6.1.38-1+rpi1 login_1:4.13+dfsg1-1 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.11.2-3 mawk_1.3.4.20230808-1 mount_2.39.2-1 nano_7.2-1 ncurses-base_6.4+20230625-2 ncurses-bin_6.4+20230625-2 netbase_6.4 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 procps_2:4.0.3-1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-maffilter-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.07-1 tar_1.34+dfsg-1.2 tex-common_6.18 texinfo_7.0.3-2 texinfo-lib_7.0.3-2 tzdata_2023c-10 ucf_3.0043+nmu1 usrmerge_37 util-linux_2.39.2-1 util-linux-extra_2.39.2-1 xz-utils_5.4.4-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Sun Aug 13 11:09:25 2023 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./maffilter_1.3.1+dfsg-5.dsc: no acceptable signature found
dpkg-source: info: extracting maffilter in /<<BUILDDIR>>/maffilter-1.3.1+dfsg
dpkg-source: info: unpacking maffilter_1.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking maffilter_1.3.1+dfsg-5.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-121adae7-a026-4f4f-bc10-78fa8f85b9b3
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package maffilter
dpkg-buildpackage: info: source version 1.3.1+dfsg-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg'
dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo
cd obj-arm-linux-gnueabihf && DEB_PYTHON_INSTALL_LAYOUT=deb cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DCMAKE_BUILD_TYPE=RelWithDebInfo ..
CMake Deprecation Warning at CMakeLists.txt:6 (CMAKE_MINIMUM_REQUIRED):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- The CXX compiler identification is GNU 12.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found /usr/bin/gzip compression program, using file extension .gz
-- bpp-core 4.1.0 found:
-- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.a
-- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0
-- includes: /usr/include
-- bpp-seq 12.0.0 found:
-- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq.a
-- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0
-- includes: /usr/include
-- bpp-seq-omics 3.0.0 found:
-- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq-omics.a
-- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-seq-omics.so.3.0.0
-- includes: /usr/include
-- bpp-phyl 12.0.0 found:
-- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl.a
-- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0
-- includes: /usr/include
-- bpp-phyl-omics 3.0.0 found:
-- static lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.a
-- shared lib: /usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0
-- includes: /usr/include
-- Found Boost: /usr/lib/arm-linux-gnueabihf/cmake/Boost-1.74.0/BoostConfig.cmake (found suitable version "1.74.0", minimum required is "1.34.0") found components: iostreams
-- Boost libraries found here:
includes: /usr/include
dynamic libraries: Boost::iostreams
-- Library z found here:
includes: /usr/include
dynamic libraries: /usr/lib/arm-linux-gnueabihf/libz.so
-- Library bz2 found here:
includes: /usr/include
dynamic libraries: /usr/lib/arm-linux-gnueabihf/libbz2.so
-- Found /usr/bin/makeinfo: 'info' and 'html' target enabled (builds info/html doc)
-- Found texi2dvi: 'pdf' target enabled (builds pdf doc)
-- Configuring done (1.8s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg'
dh_auto_build -a
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<BUILDDIR>>/maffilter-1.3.1+dfsg -B/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
make -f MafFilter/CMakeFiles/maffilter.dir/build.make MafFilter/CMakeFiles/maffilter.dir/depend
make -f doc/CMakeFiles/info.dir/build.make doc/CMakeFiles/info.dir/depend
make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/depend
make[3]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/maffilter-1.3.1+dfsg /<<BUILDDIR>>/maffilter-1.3.1+dfsg/doc /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc/CMakeFiles/info.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/maffilter-1.3.1+dfsg /<<BUILDDIR>>/maffilter-1.3.1+dfsg/MafFilter /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter/CMakeFiles/maffilter.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/maffilter-1.3.1+dfsg /<<BUILDDIR>>/maffilter-1.3.1+dfsg/man /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/man /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/man/CMakeFiles/man.dir/DependInfo.cmake "--color="
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make[3]: Leaving directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
make -f man/CMakeFiles/man.dir/build.make man/CMakeFiles/man.dir/build
make[3]: Leaving directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
make -f MafFilter/CMakeFiles/maffilter.dir/build.make MafFilter/CMakeFiles/maffilter.dir/build
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make[3]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
[ 25%] Compressing manpage maffilter.1
[ 25%] Generating info page
[ 37%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/MafFilter.cpp.o
[ 50%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc && /usr/bin/makeinfo --no-split -o /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc/maffilter.info /<<BUILDDIR>>/maffilter-1.3.1+dfsg/doc/maffilter.texi
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/man && /usr/bin/gzip -c -n -9 /<<BUILDDIR>>/maffilter-1.3.1+dfsg/man/maffilter.1 > /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/man/maffilter.1.gz
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -std=c++11 -Wall -Weffc++ -Wshadow -O2 -g -DNDEBUG -MD -MT MafFilter/CMakeFiles/maffilter.dir/MafFilter.cpp.o -MF CMakeFiles/maffilter.dir/MafFilter.cpp.o.d -o CMakeFiles/maffilter.dir/MafFilter.cpp.o -c /<<BUILDDIR>>/maffilter-1.3.1+dfsg/MafFilter/MafFilter.cpp
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -std=c++11 -Wall -Weffc++ -Wshadow -O2 -g -DNDEBUG -MD -MT MafFilter/CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o -MF CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o.d -o CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o -c /<<BUILDDIR>>/maffilter-1.3.1+dfsg/MafFilter/OutputAsFeaturesMafIterator.cpp
make[3]: Leaving directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
[ 50%] Built target man
[ 62%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -std=c++11 -Wall -Weffc++ -Wshadow -O2 -g -DNDEBUG -MD -MT MafFilter/CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o -MF CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o.d -o CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o -c /<<BUILDDIR>>/maffilter-1.3.1+dfsg/MafFilter/SystemCallMafIterator.cpp
[ 75%] Compressing info page
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc && /usr/bin/gzip -c -n -9 /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc/maffilter.info > /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/doc/maffilter.info.gz
make[3]: Leaving directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
[ 75%] Built target info
[ 87%] Building CXX object MafFilter/CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_IOSTREAMS_DYN_LINK -std=c++11 -Wall -Weffc++ -Wshadow -O2 -g -DNDEBUG -MD -MT MafFilter/CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o -MF CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o.d -o CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o -c /<<BUILDDIR>>/maffilter-1.3.1+dfsg/MafFilter/TreeBuildingSystemCallMafIterator.cpp
In file included from /usr/include/c++/12/vector:70,
from /usr/include/Bpp/Text/TextTools.h:49,
from /usr/include/Bpp/Numeric/Range.h:43,
from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51,
from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43,
from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43,
from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43,
from /<<BUILDDIR>>/maffilter-1.3.1+dfsg/MafFilter/TreeBuildingSystemCallMafIterator.h:43,
from /<<BUILDDIR>>/maffilter-1.3.1+dfsg/MafFilter/TreeBuildingSystemCallMafIterator.cpp:40:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'std::vector<double, std::allocator<double> > bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:47,
from /usr/include/Bpp/Seq/Io/Maf/MafSequence.h:43,
from /usr/include/Bpp/Seq/Io/Maf/MafBlock.h:43,
from /usr/include/Bpp/Seq/Io/Maf/MafIterator.h:43,
from /<<BUILDDIR>>/maffilter-1.3.1+dfsg/MafFilter/OutputAsFeaturesMafIterator.h:43,
from /<<BUILDDIR>>/maffilter-1.3.1+dfsg/MafFilter/MafFilter.cpp:47:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'bpp::SiteFrequencySpectrumMafStatistics::Categorizer::Categorizer(const std::vector<double, std::allocator<double> >&)' at /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:490:20,
inlined from 'bpp::SiteFrequencySpectrumMafStatistics::SiteFrequencySpectrumMafStatistics(const bpp::Alphabet*, const std::vector<double, std::allocator<double> >&, const std::vector<std::__cxx11::basic_string<char> >&, std::string)' at /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:519:7:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double, allocator<double> > >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from 'bpp::SiteFrequencySpectrumMafStatistics::Categorizer::Categorizer(const std::vector<double, std::allocator<double> >&)' at /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:490:20,
inlined from 'bpp::SiteFrequencySpectrumMafStatistics::SiteFrequencySpectrumMafStatistics(const bpp::Alphabet*, const std::vector<double, std::allocator<double> >&, const std::vector<std::__cxx11::basic_string<char> >&, std::string)' at /usr/include/Bpp/Seq/Io/Maf/MafStatistics.h:519:7:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/Bpp/Text/TextTools.h:49,
from /usr/include/Bpp/Numeric/Range.h:43,
from /usr/include/Bpp/Seq/Feature/SequenceFeature.h:51:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'std::vector<double, std::allocator<double> > bpp::TreeTemplate<N>::getBranchLengths() [with N = bpp::Node]' at /usr/include/Bpp/Phyl/TreeTemplate.h:351:69:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[100%] Linking CXX executable maffilter
cd /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/MafFilter && /usr/bin/cmake -E cmake_link_script CMakeFiles/maffilter.dir/link.txt --verbose=1
/usr/bin/c++ -std=c++11 -Wall -Weffc++ -Wshadow -O2 -g -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/maffilter.dir/MafFilter.cpp.o CMakeFiles/maffilter.dir/OutputAsFeaturesMafIterator.cpp.o CMakeFiles/maffilter.dir/SystemCallMafIterator.cpp.o CMakeFiles/maffilter.dir/TreeBuildingSystemCallMafIterator.cpp.o -o maffilter /usr/lib/arm-linux-gnueabihf/libbpp-phyl-omics.so.3.0.0 /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so.1.74.0 -lz -lbz2 /usr/lib/arm-linux-gnueabihf/libbpp-seq-omics.so.3.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-phyl.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-seq.so.12.0.0 /usr/lib/arm-linux-gnueabihf/libbpp-core.so.4.1.0
make[3]: Leaving directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
[100%] Built target maffilter
make[2]: Leaving directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
dh_auto_test -a
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dh_prep -a
dh_auto_install -a
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<BUILDDIR>>/maffilter-1.3.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<BUILDDIR>>/maffilter-1.3.1+dfsg -B/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
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make[2]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg/obj-arm-linux-gnueabihf'
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Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "RelWithDebInfo"
-- Installing: /<<BUILDDIR>>/maffilter-1.3.1+dfsg/debian/tmp/usr/bin/maffilter
-- Installing: /<<BUILDDIR>>/maffilter-1.3.1+dfsg/debian/tmp/usr/share/info/maffilter.info.gz
-- Installing: /<<BUILDDIR>>/maffilter-1.3.1+dfsg/debian/tmp/usr/share/man/man1/maffilter.1.gz
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make[1]: Entering directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg'
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find debian/*/usr/share -name "*.bpp" -executable -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/maffilter-1.3.1+dfsg'
dh_missing -a
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dh_shlibdeps -a
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dh_installdeb -a
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dpkg-deb: building package 'maffilter' in '../maffilter_1.3.1+dfsg-5_armhf.deb'.
dpkg-genbuildinfo --build=any -O../maffilter_1.3.1+dfsg-5_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../maffilter_1.3.1+dfsg-5_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 2023-09-23T11:36:11Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
maffilter_1.3.1+dfsg-5_armhf.changes:
-------------------------------------
Format: 1.8
Date: Sun, 13 Aug 2023 12:55:55 +0200
Source: maffilter
Binary: maffilter maffilter-dbgsym
Architecture: armhf
Version: 1.3.1+dfsg-5
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Michael R. Crusoe <crusoe@debian.org>
Description:
maffilter - process genome alignment in the Multiple Alignment Format
Changes:
maffilter (1.3.1+dfsg-5) unstable; urgency=medium
.
* Team upload.
* Standards-Version: 4.6.2 (routine-update)
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
maffilter-dbgsym_1.3.1+dfsg-5_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 3376260 bytes: control archive=540 bytes.
389 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: maffilter-dbgsym
Source: maffilter
Version: 1.3.1+dfsg-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3560
Depends: maffilter (= 1.3.1+dfsg-5)
Section: debug
Priority: optional
Description: debug symbols for maffilter
Build-Ids: 7b27711001fe46d1ed2c6a985810eacfb862869c
drwxr-xr-x root/root 0 2023-08-13 10:55 ./
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/lib/
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/lib/debug/.build-id/7b/
-rw-r--r-- root/root 3634224 2023-08-13 10:55 ./usr/lib/debug/.build-id/7b/27711001fe46d1ed2c6a985810eacfb862869c.debug
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/share/
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/share/doc/
lrwxrwxrwx root/root 0 2023-08-13 10:55 ./usr/share/doc/maffilter-dbgsym -> maffilter
maffilter_1.3.1+dfsg-5_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 213992 bytes: control archive=2960 bytes.
1346 bytes, 25 lines control
5802 bytes, 72 lines md5sums
Package: maffilter
Version: 1.3.1+dfsg-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1091
Depends: libboost-iostreams1.74.0 (>= 1.74.0+ds1), libbpp-core4 (>= 2.4.1), libbpp-phyl-omics3 (>= 2.4.1), libbpp-phyl12 (>= 2.4.1), libbpp-seq-omics3 (>= 2.4.1), libbpp-seq12 (>= 2.4.1), libc6 (>= 2.34), libgcc-s1 (>= 3.5), libstdc++6 (>= 11)
Suggests: maffilter-examples
Section: science
Priority: optional
Homepage: https://jydu.github.io/maffilter/
Description: process genome alignment in the Multiple Alignment Format
MafFilter applies a series of "filters" to a MAF file, in order to
clean it, extract data and computer statistics while keeping track of
the associated meta-data such as genome coordinates and quality scores.
.
* It can process the alignment to remove low-quality / ambiguous /
masked regions.
* It can export data into a single or multiple alignment file in
format such as Fasta or Clustal.
* It can read annotation data in GFF or GTF format, and extract the
corresponding alignment.
* It can perform sliding windows calculations.
* It can reconstruct phylogeny/genealogy along the genome alignment.
* It can compute population genetics statistics, such as site
frequency spectrum, number of fixed/polymorphic sites, etc.
drwxr-xr-x root/root 0 2023-08-13 10:55 ./
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/bin/
-rwxr-xr-x root/root 636424 2023-08-13 10:55 ./usr/bin/maffilter
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/share/
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/share/doc/
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/share/doc/maffilter/
-rw-r--r-- root/root 161 2018-08-17 13:32 ./usr/share/doc/maffilter/AUTHORS
drwxr-xr-x root/root 0 2023-08-13 10:55 ./usr/share/doc/maffilter/Manual/
-rw-r--r-- root/root 5348 2018-08-17 13:32 ./usr/share/doc/maffilter/Manual/AlnFilter.html
-rw-r--r-- root/root 5566 2018-08-17 13:32 ./usr/share/doc/maffilter/Manual/AlnFilter2.html
-rw-r--r-- root/root 2817 2018-08-17 13:32 ./usr/share/doc/maffilter/Manual/AlnScore.html
-rw-r--r-- root/root 2644 2018-08-17 13:32 ./usr/share/doc/maffilter/Manual/Analyzing.html
-rw-r--r-- root/root 3419 2018-08-17 13:32 ./usr/share/doc/maffilter/Manual/BlockCounts.html
-rw-r--r-- root/root 2823 2018-08-17 13:32 ./usr/share/doc/maffilter/Manual/BlockLength.html
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 143168
Build-Time: 170
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 403
Job: maffilter_1.3.1+dfsg-5
Machine Architecture: armhf
Package: maffilter
Package-Time: 617
Source-Version: 1.3.1+dfsg-5
Space: 143168
Status: successful
Version: 1.3.1+dfsg-5
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Finished at 2023-09-23T11:36:11Z
Build needed 00:10:17, 143168k disk space