parsnp →
1.7.2+dfsg-1+b8 →
armhf → 2022-04-22 22:46:54
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| parsnp 1.7.2+dfsg-1+b8 (armhf) Fri, 22 Apr 2022 22:40:28 +0000 |
+==============================================================================+
Package: parsnp
Version: 1.7.2+dfsg-1+b8
Source Version: 1.7.2+dfsg-1
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-f6768967-ce7c-489f-92f8-6f3f10383b11' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.0 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.9 MB]
Fetched 26.8 MB in 12s (2201 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/bookworm-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: 'parsnp' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/parsnp.git
Please use:
git clone https://salsa.debian.org/med-team/parsnp.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 143 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main parsnp 1.7.2+dfsg-1 (dsc) [2078 B]
Get:2 http://172.17.4.1/private bookworm-staging/main parsnp 1.7.2+dfsg-1 (tar) [131 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main parsnp 1.7.2+dfsg-1 (diff) [10.0 kB]
Fetched 143 kB in 0s (2519 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/parsnp-waVDry/parsnp-1.7.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/parsnp-waVDry' 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-4bGV3U/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-4bGV3U/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-4bGV3U/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-4bGV3U/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-4bGV3U/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-4bGV3U/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-4bGV3U/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-4bGV3U/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (3228 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:
netbase sensible-utils
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 53 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-4bGV3U/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 (53.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12608 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)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, cython3, libmuscle-dev
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-all-dev, python3-setuptools, cython3, libmuscle-dev
dpkg-deb: building package 'sbuild-build-depends-parsnp-dummy' in '/<<BUILDDIR>>/resolver-4bGV3U/apt_archive/sbuild-build-depends-parsnp-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-parsnp-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-4bGV3U/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-4bGV3U/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-4bGV3U/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-4bGV3U/apt_archive ./ Sources [532 B]
Get:5 copy:/<<BUILDDIR>>/resolver-4bGV3U/apt_archive ./ Packages [611 B]
Fetched 2476 B in 1s (3752 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install parsnp 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 cython3 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl
libdebhelper-perl libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libicu67 libjs-jquery libjs-sphinxdoc
libjs-underscore libmagic-mgc libmagic1 libmpdec3 libmuscle-dev libmuscle1
libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib
libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib
libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libsmartcols1 libsub-override-perl libtool libuchardet0 libxml2
m4 man-db media-types po-debconf python3 python3-all python3-all-dev
python3-dev python3-distutils python3-lib2to3 python3-minimal
python3-pkg-resources python3-setuptools python3.10 python3.10-dev
python3.10-minimal python3.9 python3.9-dev python3.9-minimal zlib1g
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cython-doc dh-make flit
python3-build python3-tomli python3-installer gettext-doc libasprintf-dev
libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk
python3-venv python-setuptools-doc python3.10-venv python3.10-doc
binfmt-support python3.9-venv python3.9-doc
Recommended packages:
curl | wget | lynx libarchive-cpio-perl javascript-common ca-certificates
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cython3 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl
libdebhelper-perl libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libicu67 libjs-jquery libjs-sphinxdoc
libjs-underscore libmagic-mgc libmagic1 libmpdec3 libmuscle-dev libmuscle1
libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib
libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib
libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
media-types po-debconf python3 python3-all python3-all-dev python3-dev
python3-distutils python3-lib2to3 python3-minimal python3-pkg-resources
python3-setuptools python3.10 python3.10-dev python3.10-minimal python3.9
python3.9-dev python3.9-minimal sbuild-build-depends-parsnp-dummy zlib1g-dev
The following packages will be upgraded:
libsmartcols1 zlib1g
2 upgraded, 69 newly installed, 0 to remove and 51 not upgraded.
Need to get 40.9 MB of archives.
After this operation, 158 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-4bGV3U/apt_archive ./ sbuild-build-depends-parsnp-dummy 0.invalid.0 [896 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.4-1 [811 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf zlib1g armhf 1:1.2.11.dfsg-4 [84.2 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.4-1 [1633 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.4-1 [38.6 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf media-types all 7.1.0 [33.2 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.4-1 [1625 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.4-1 [536 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.4-1 [21.7 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.4-1 [38.1 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.12-1+rpi1 [794 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.12-1+rpi1 [1595 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libsmartcols1 armhf 2.38-4 [149 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38-4 [137 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.5-1 [32.9 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-1 [1362 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-6 [171 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-6 [510 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf cython3 armhf 0.29.28-3+rpi1 [1456 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.7.1 [195 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-3 [526 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.13+dfsg-1 [593 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-6 [1214 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.7.1 [1071 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.12-1 [79.9 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.9.12-1 [146 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220403 [113 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.4.8-1 [137 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.6.0+dfsg+~3.5.13-1 [316 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libjs-underscore all 1.13.2~dfsg-2 [116 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libjs-sphinxdoc all 4.5.0-3 [142 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libmuscle1 armhf 3.7+4565-7 [202 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libmuscle-dev armhf 3.7+4565-7 [245 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10 armhf 3.10.4-1 [1454 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4 [183 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-dev armhf 3.10.4-1 [2984 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libpython3-dev armhf 3.10.4-1 [22.0 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.12-1+rpi1 [1611 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9 armhf 3.9.12-1+rpi1 [1419 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-dev armhf 3.9.12-1+rpi1 [3013 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libpython3-all-dev armhf 3.10.4-1 [1072 B]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf python3.9 armhf 3.9.12-1+rpi1 [492 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf python3-all armhf 3.10.4-1 [1064 B]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf python3.10-dev armhf 3.10.4-1 [508 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf python3-dev armhf 3.10.4-1 [25.4 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf python3.9-dev armhf 3.9.12-1+rpi1 [501 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf python3-all-dev armhf 3.10.4-1 [1076 B]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 59.6.0-1.2 [196 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf python3-setuptools all 59.6.0-1.2 [401 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libsub-override-perl (0.09-2) ...
Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ...
Setting up python3.9-minimal (3.9.12-1+rpi1) ...
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Setting up libxml2:armhf (2.9.13+dfsg-1) ...
Setting up libpython3.9-stdlib:armhf (3.9.12-1+rpi1) ...
Setting up libjs-underscore (1.13.2~dfsg-2) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gettext (0.21-6) ...
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Setting up libjs-sphinxdoc (4.5.0-3) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
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Setting up python3.9 (3.9.12-1+rpi1) ...
Setting up libpython3-stdlib:armhf (3.10.4-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libpython3.10:armhf (3.10.4-1) ...
Setting up python3.10 (3.10.4-1) ...
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Setting up python3 (3.10.4-1) ...
Setting up man-db (2.10.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up cython3 (0.29.28-3+rpi1) ...
Setting up libpython3.10-dev:armhf (3.10.4-1) ...
Setting up python3.10-dev (3.10.4-1) ...
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Setting up python3-pkg-resources (59.6.0-1.2) ...
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Setting up python3-setuptools (59.6.0-1.2) ...
Setting up python3-all (3.10.4-1) ...
Setting up debhelper (13.7.1) ...
Setting up libpython3-all-dev:armhf (3.10.4-1) ...
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Setting up sbuild-build-depends-parsnp-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.33-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-163-generic armhf (armv8l)
Toolchain package versions: binutils_2.38-3+rpi1 dpkg-dev_1.21.2+rpi1 g++-11_11.2.0-16+rpi1 gcc-11_11.2.0-16+rpi1 libc6-dev_2.33-7+rpi1 libstdc++-11-dev_11.2.0-16+rpi1 libstdc++6_11.2.0-16+rpi1 linux-libc-dev_5.16.14-1+rpi1
Package versions: adduser_3.120 apt_2.4.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.5.52 bash_5.1-6 binutils_2.38-3+rpi1 binutils-arm-linux-gnueabihf_2.38-3+rpi1 binutils-common_2.38-3+rpi1 bsdextrautils_2.38-4 bsdutils_1:2.37.3-1 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-16+rpi1 cython3_0.29.28-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.7.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-python_5.20220403 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3+b1 dpkg_1.21.2+rpi1 dpkg-dev_1.21.2+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.28-1 file_1:5.41-2 findutils_4.9.0-2 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-16+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-16+rpi1 gcc-11-base_11.2.0-16+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_0.21-6 gettext-base_0.21-6 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3+b1 gpg_2.2.27-3+b1 gpg-agent_2.2.27-3+b1 gpg-wks-client_2.2.27-3+b1 gpg-wks-server_2.2.27-3+b1 gpgconf_2.2.27-3+b1 gpgsm_2.2.27-3+b1 gpgv_2.2.27-3+b1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.10-4 hostname_3.23 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.4.3 libarchive-zip-perl_1.68-1 libasan6_11.2.0-16+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-16+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38-3+rpi1 libblkid1_2.37.3-1 libbz2-1.0_1.0.8-5 libc-bin_2.33-7+rpi1 libc-dev-bin_2.33-7+rpi1 libc6_2.33-7+rpi1 libc6-dev_2.33-7+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-16+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-3+rpi1 libctf0_2.38-3+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.7.1 libdpkg-perl_1.21.2+rpi1 libelf1_0.186-1 libexpat1_2.4.8-1 libexpat1-dev_2.4.8-1 libext2fs2_1.46.5-2 libfakeroot_1.28-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.2.0-16+rpi1 libgcc-s1_11.2.0-16+rpi1 libgcrypt20_1.9.4-5 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.3-4 libgomp1_11.2.0-16+rpi1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.19.2-2+b1 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjs-jquery_3.6.0+dfsg+~3.5.13-1 libjs-sphinxdoc_4.5.0-3 libjs-underscore_1.13.2~dfsg-2 libk5crypto3_1.19.2-2+b1 libkeyutils1_1.6.1-3+rpi1 libkrb5-3_1.19.2-2+b1 libkrb5support0_1.19.2-2+b1 libksba8_1.6.0-2 libldap-2.5-0_2.5.11+dfsg-1+rpi1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmount1_2.37.3-1 libmpc3_1.2.1-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libmuscle-dev_3.7+4565-7 libmuscle1_3.7+4565-7 libncursesw6_6.3-2 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.34_5.34.0-3 libpipeline1_1.5.5-1 libpython3-all-dev_3.10.4-1 libpython3-dev_3.10.4-1 libpython3-stdlib_3.10.4-1 libpython3.10_3.10.4-1 libpython3.10-dev_3.10.4-1 libpython3.10-minimal_3.10.4-1 libpython3.10-stdlib_3.10.4-1 libpython3.9_3.9.12-1+rpi1 libpython3.9-dev_3.9.12-1+rpi1 libpython3.9-minimal_3.9.12-1+rpi1 libpython3.9-stdlib_3.9.12-1+rpi1 libreadline8_8.1.2-1 libsasl2-2_2.1.28+dfsg-2+b1 libsasl2-modules-db_2.1.28+dfsg-2+b1 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.38-4 libsqlite3-0_3.38.1-1 libss2_1.46.5-2 libssl1.1_1.1.1n-1 libstdc++-11-dev_11.2.0-16+rpi1 libstdc++6_11.2.0-16+rpi1 libsub-override-perl_0.09-2 libsystemd0_250.4-1+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-3 libubsan1_11.2.0-16+rpi1 libuchardet0_0.0.7-1 libudev1_250.4-1+rpi1 libunistring2_1.0-1 libuuid1_2.37.3-1 libxml2_2.9.13+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.4.9+dfsg-1+rpi1 linux-libc-dev_5.16.14-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 media-types_7.1.0 mount_2.37.3-1 ncurses-base_6.3-2 ncurses-bin_6.3-2 netbase_6.3 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-3 perl-base_5.34.0-3 perl-modules-5.34_5.34.0-3 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.10.4-1 python3-all_3.10.4-1 python3-all-dev_3.10.4-1 python3-dev_3.10.4-1 python3-distutils_3.9.12-1 python3-lib2to3_3.9.12-1 python3-minimal_3.10.4-1 python3-pkg-resources_59.6.0-1.2 python3-setuptools_59.6.0-1.2 python3.10_3.10.4-1 python3.10-dev_3.10.4-1 python3.10-minimal_3.10.4-1 python3.9_3.9.12-1+rpi1 python3.9-dev_3.9.12-1+rpi1 python3.9-minimal_3.9.12-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-parsnp-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.01-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.3-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-4 zlib1g-dev_1:1.2.11.dfsg-4
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.DCTOAPH5/trustedkeys.kbx': General error
gpgv: Signature made Thu Apr 14 15:42:20 2022 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./parsnp_1.7.2+dfsg-1.dsc
dpkg-source: info: extracting parsnp in /<<BUILDDIR>>/parsnp-1.7.2+dfsg
dpkg-source: info: unpacking parsnp_1.7.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking parsnp_1.7.2+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying add_missing_interpreter_line.patch
dpkg-source: info: applying proper_calls_to_tools.patch
dpkg-source: info: applying drop_m64.patch
dpkg-source: info: applying fix_build_with_as-needed.patch
dpkg-source: info: applying non-versioned-libs.patch
dpkg-source: info: applying blhc-fix.patch
dpkg-source: info: applying py3-parsnp-libs.patch
dpkg-source: info: applying typos.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.7.2+dfsg-1+b8
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-f6768967-ce7c-489f-92f8-6f3f10383b11
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package parsnp
dpkg-buildpackage: info: source version 1.7.2+dfsg-1+b8
dpkg-buildpackage: info: source distribution bookworm-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3
dh_clean
debian/rules binary-arch
dh binary-arch --with python3
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:23: warning: AC_OUTPUT should be used without arguments.
configure.ac:23: You should run autoupdate.
configure.ac:3: installing './compile'
configure.ac:2: installing './install-sh'
configure.ac:2: installing './missing'
src/Makefile.am:4: warning: source file './ext/iniFile.cpp' is in a subdirectory,
src/Makefile.am:4: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least one source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However, this
automake: behavior may change in a future Automake major version, with object
automake: files being placed in the same subdirectory as the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
src/Makefile.am: installing './depcomp'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
dh_auto_configure -- --with-libmuscle=/usr/include/libMUSCLE-3.7
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-libmuscle=/usr/include/libMUSCLE-3.7
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... none
checking for g++... g++
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking dependency style of g++... none
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for libMUSCLE/muscle.h... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: executing depfiles commands
make[1]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
Making all in src
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/src'
g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/parsnp-1.7.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-MuscleInterface.o `test -f 'MuscleInterface.cpp' || echo './'`MuscleInterface.cpp
g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/parsnp-1.7.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-parsnp.o `test -f 'parsnp.cpp' || echo './'`parsnp.cpp
g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/parsnp-1.7.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-LCB.o `test -f 'LCB.cpp' || echo './'`LCB.cpp
g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/parsnp-1.7.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-LCR.o `test -f 'LCR.cpp' || echo './'`LCR.cpp
g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/parsnp-1.7.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-TMum.o `test -f 'TMum.cpp' || echo './'`TMum.cpp
g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/parsnp-1.7.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-Converter.o `test -f 'Converter.cpp' || echo './'`Converter.cpp
g++ -DPACKAGE_NAME=\"parsnp\" -DPACKAGE_TARNAME=\"parsnp\" -DPACKAGE_VERSION=\"1.6.1\" -DPACKAGE_STRING=\"parsnp\ 1.6.1\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"parsnp\" -DVERSION=\"1.6.1\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -I. -I/usr/include/libMUSCLE-3.7 -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/parsnp-1.7.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parsnp_core-iniFile.o `test -f './ext/iniFile.cpp' || echo './'`./ext/iniFile.cpp
parsnp.cpp: In member function 'void Aligner::writeOutput(std::string, std::vector<float>&)':
parsnp.cpp:925:24: warning: '%d' directive writing between 1 and 11 bytes into a region of size 9 [-Wformat-overflow=]
925 | sprintf(b,"%d",(int)z+1);// C-style string formed without null
| ^~
parsnp.cpp:925:23: note: directive argument in the range [-2147483647, 2147483647]
925 | sprintf(b,"%d",(int)z+1);// C-style string formed without null
| ^~~~
In file included from /usr/include/stdio.h:866,
from /usr/include/c++/11/cstdio:42,
from /usr/include/c++/11/ext/string_conversions.h:43,
from /usr/include/c++/11/bits/basic_string.h:6608,
from /usr/include/c++/11/string:55,
from /usr/include/c++/11/bits/locale_classes.h:40,
from /usr/include/c++/11/bits/ios_base.h:41,
from /usr/include/c++/11/ios:42,
from /usr/include/c++/11/ostream:38,
from /usr/include/c++/11/iostream:39,
from parsnp.hh:14,
from parsnp.cpp:54:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:38:34: note: '__builtin___sprintf_chk' output between 2 and 12 bytes into a destination of size 9
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
40 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
g++ -fopenmp -O2 -funroll-all-loops -fomit-frame-pointer -ftree-vectorize -std=gnu++0x -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/parsnp-1.7.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o parsnp_core parsnp_core-MuscleInterface.o parsnp_core-parsnp.o parsnp_core-LCB.o parsnp_core-LCR.o parsnp_core-TMum.o parsnp_core-Converter.o parsnp_core-iniFile.o -fopenmp -lstdc++ -lpthread -L/usr/include/libMUSCLE-3.7/lib -lMUSCLE
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
dh_auto_test -a
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
Making check in src
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install --destdir=debian/parsnp/ -a
make -j4 install DESTDIR=/<<BUILDDIR>>/parsnp-1.7.2\+dfsg/debian/parsnp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
Making install in src
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/src'
/bin/mkdir -p '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/debian/parsnp../bin'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/install -c parsnp_core '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/debian/parsnp../bin'
make[3]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_python3 -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
dh_fixperms
chmod -x debian/parsnp/usr/share/parsnp/template.ini
make[1]: Leaving directory '/<<BUILDDIR>>/parsnp-1.7.2+dfsg'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/parsnp/usr/lib/parsnp/parsnp_core contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/parsnp/usr/lib/parsnp/parsnp_core 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 'parsnp-dbgsym' in '../parsnp-dbgsym_1.7.2+dfsg-1+b8_armhf.deb'.
dpkg-deb: building package 'parsnp' in '../parsnp_1.7.2+dfsg-1+b8_armhf.deb'.
dpkg-genbuildinfo --build=any -O../parsnp_1.7.2+dfsg-1+b8_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../parsnp_1.7.2+dfsg-1+b8_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 2022-04-22T22:46:50Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
parsnp_1.7.2+dfsg-1+b8_armhf.changes:
-------------------------------------
Format: 1.8
Date: Thu, 14 Apr 2022 17:22:39 +0200
Source: parsnp (1.7.2+dfsg-1)
Binary: parsnp parsnp-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 1.7.2+dfsg-1+b8
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
parsnp - rapid core genome multi-alignment
Changes:
parsnp (1.7.2+dfsg-1+b8) bookworm-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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e5ca7d57a63c3b04cda3fba65b14fb5e24e52145 6583 parsnp_1.7.2+dfsg-1+b8_armhf.buildinfo
950a8c402b9fe7085c15e097308e61197e153c19 172708 parsnp_1.7.2+dfsg-1+b8_armhf.deb
Checksums-Sha256:
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6927d0e577a8943da45f1be011319f973b6b42d20a0d114b4f4f091b8994c258 6583 parsnp_1.7.2+dfsg-1+b8_armhf.buildinfo
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Files:
48c410944f1cc9fa233836be7cb853ff 1280276 debug optional parsnp-dbgsym_1.7.2+dfsg-1+b8_armhf.deb
b60cb207fef82df748eeb51d84bd8aca 6583 science optional parsnp_1.7.2+dfsg-1+b8_armhf.buildinfo
a60b88c3c5a2c98088bb65862c0ed137 172708 science optional parsnp_1.7.2+dfsg-1+b8_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
parsnp-dbgsym_1.7.2+dfsg-1+b8_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 1280276 bytes: control archive=540 bytes.
398 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: parsnp-dbgsym
Source: parsnp (1.7.2+dfsg-1)
Version: 1.7.2+dfsg-1+b8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1297
Depends: parsnp (= 1.7.2+dfsg-1+b8)
Section: debug
Priority: optional
Description: debug symbols for parsnp
Build-Ids: 45c6076c817e86d373c925edec01dcb8983646d4
drwxr-xr-x root/root 0 2022-04-14 15:22 ./
drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/
drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/lib/
drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/lib/debug/.build-id/45/
-rw-r--r-- root/root 1316884 2022-04-14 15:22 ./usr/lib/debug/.build-id/45/c6076c817e86d373c925edec01dcb8983646d4.debug
drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/share/
drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-04-14 15:22 ./usr/share/doc/parsnp-dbgsym -> parsnp
parsnp_1.7.2+dfsg-1+b8_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 172708 bytes: control archive=2876 bytes.
1087 bytes, 19 lines control
5815 bytes, 62 lines md5sums
259 bytes, 12 lines * postinst #!/bin/sh
403 bytes, 12 lines * prerm #!/bin/sh
Package: parsnp
Source: parsnp (1.7.2+dfsg-1)
Version: 1.7.2+dfsg-1+b8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1851
Depends: libc6 (>= 2.27), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libmuscle1 (>= 3.7+4565), libstdc++6 (>= 11), python3:any, python3-biopython, python3-numpy, fasttree, harvest-tools, mummer, phipack, python3, raxml
Recommends: python3-dendropy
Section: science
Priority: optional
Homepage: https://harvest.readthedocs.org/en/latest/content/parsnp.html
Description: rapid core genome multi-alignment
Parsnp was designed to align the core genome of hundreds to thousands of
bacterial genomes within a few minutes to few hours. Input can be both
draft assemblies and finished genomes, and output includes variant (SNP)
calls, core genome phylogeny and multi-alignments. Parsnp leverages
contextual information provided by multi-alignments surrounding SNP
sites for filtration/cleaning, in addition to existing tools for
recombination detection/filtration and phylogenetic reconstruction.
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drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/bin/
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drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/share/doc/parsnp/
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drwxr-xr-x root/root 0 2022-04-14 15:22 ./usr/share/doc/parsnp/examples/
drwxr-xr-x root/root 0 2022-03-31 16:16 ./usr/share/doc/parsnp/examples/mers_virus/
drwxr-xr-x root/root 0 2022-03-31 16:16 ./usr/share/doc/parsnp/examples/mers_virus/genomes/
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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Build Architecture: armhf
Build-Space: 22840
Build-Time: 95
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 264
Job: parsnp_1.7.2+dfsg-1
Machine Architecture: armhf
Package: parsnp
Package-Time: 382
Source-Version: 1.7.2+dfsg-1
Space: 22840
Status: successful
Version: 1.7.2+dfsg-1+b8
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Finished at 2022-04-22T22:46:50Z
Build needed 00:06:22, 22840k disk space