parsnp →
2.0.1+dfsg-1 →
armhf → 2024-01-21 05:35:30
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| parsnp 2.0.1+dfsg-1 (armhf) Sun, 21 Jan 2024 05:27:27 +0000 |
+==============================================================================+
Package: parsnp
Version: 2.0.1+dfsg-1
Source Version: 2.0.1+dfsg-1
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-aa8b6b8c-18a4-4132-ae98-97efd15b2775' 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 [14.4 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.4 MB in 10s (3030 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: '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 153 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main parsnp 2.0.1+dfsg-1 (dsc) [2242 B]
Get:2 http://172.17.4.1/private trixie-staging/main parsnp 2.0.1+dfsg-1 (tar) [141 kB]
Get:3 http://172.17.4.1/private trixie-staging/main parsnp 2.0.1+dfsg-1 (diff) [9968 B]
Fetched 153 kB in 0s (3827 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/parsnp-9QY2bx/parsnp-2.0.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/parsnp-9QY2bx' 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-3Y6Y51/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-3Y6Y51/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-3Y6Y51/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-3Y6Y51/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (9573 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 51 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (83.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12859 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-sequence-python3, python3-all-dev, python3-setuptools, cython3, libmuscle-dev
Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-all-dev, python3-setuptools, cython3, libmuscle-dev
dpkg-deb: building package 'sbuild-build-depends-parsnp-dummy' in '/<<BUILDDIR>>/resolver-3Y6Y51/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-3Y6Y51/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ Sources [536 B]
Get:5 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ Packages [614 B]
Fetched 2483 B in 0s (13.9 kB/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 packages were automatically installed and are no longer required:
krb5-locales libpam-cap sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils cython3
debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblkid1
libdebhelper-perl libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libicu72 libjs-jquery libjs-sphinxdoc
libjs-underscore libmagic-mgc libmagic1 libmount1 libmuscle-dev libmuscle1
libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib
libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
libsmartcols1 libsub-override-perl libtool libuchardet0 libuuid1 libxml2 m4
man-db media-types mount po-debconf python3 python3-all python3-all-dev
python3-dev python3-distutils python3-lib2to3 python3-minimal
python3-pkg-resources python3-setuptools python3.11 python3.11-dev
python3.11-minimal util-linux util-linux-extra zlib1g zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cython-doc dh-make flit
python3-build python3-installer python3-wheel gettext-doc libasprintf-dev
libgettextpo-dev groff cryptsetup-bin libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser nfs-common
libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc
python3.11-venv python3.11-doc binfmt-support dosfstools kbd
util-linux-locales
Recommended packages:
curl | wget | lynx libarchive-cpio-perl javascript-common libltdl-dev
uuid-runtime libmail-sendmail-perl ca-certificates
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 libicu72 libjs-jquery libjs-sphinxdoc
libjs-underscore libmagic-mgc libmagic1 libmuscle-dev libmuscle1
libpipeline1 libpython3-all-dev libpython3-dev libpython3-stdlib
libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib
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
python3.11 python3.11-dev python3.11-minimal
sbuild-build-depends-parsnp-dummy zlib1g-dev
The following packages will be upgraded:
bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 mount util-linux
util-linux-extra zlib1g
9 upgraded, 60 newly installed, 0 to remove and 42 not upgraded.
Need to get 37.1 MB of archives.
After this operation, 139 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-3Y6Y51/apt_archive ./ sbuild-build-depends-parsnp-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.3-6 [87.1 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.3-6 [102 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf util-linux-extra armhf 2.39.3-6 [135 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.3-6 [1113 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.3-6 [134 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.7-2 [801 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf zlib1g armhf 1:1.3.dfsg-3 [74.3 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.7-2 [1677 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.3-6 [28.3 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.7-2 [1694 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.7-2 [590 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
Get:17 http://172.17.4.1/private trixie-staging/main armhf python3 armhf 3.11.4-5 [26.2 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.3-6 [145 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.3-6 [168 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-6 [81.4 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-3 [1358 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf cython3 armhf 3.0.7-2 [3440 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.9 [82.3 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.9 [956 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf python3-distutils all 3.11.5-1 [131 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf python3-pkg-resources all 68.1.2-2 [241 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf python3-setuptools all 68.1.2-2 [468 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf dh-python all 6.20231223 [108 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libexpat1-dev armhf 2.5.0-2 [130 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libjs-sphinxdoc all 7.2.6-3 [149 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libmuscle1 armhf 3.7+4565-7 [202 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libmuscle-dev armhf 3.7+4565-7 [245 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libpython3.11 armhf 3.11.7-2 [1670 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg-3 [903 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-dev armhf 3.11.7-2 [3287 kB]
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Get:65 http://172.17.4.1/private trixie-staging/main armhf libpython3-all-dev armhf 3.11.4-5 [1068 B]
Get:66 http://172.17.4.1/private trixie-staging/main armhf python3-all armhf 3.11.4-5 [1060 B]
Get:67 http://172.17.4.1/private trixie-staging/main armhf python3.11-dev armhf 3.11.7-2 [508 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf python3-dev armhf 3.11.4-5 [26.2 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf python3-all-dev armhf 3.11.4-5 [1068 B]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libexpat1-dev:armhf (2.5.0-2) ...
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Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:armhf (1:1.3.dfsg-3) ...
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Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
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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 libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up python3.11 (3.11.7-2) ...
Setting up gettext (0.21-14) ...
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Setting up libtool (2.4.7-7) ...
Setting up python3 (3.11.4-5) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
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Setting up cython3 (3.0.7-2) ...
Setting up libjs-sphinxdoc (7.2.6-3) ...
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Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython3-all-dev:armhf (3.11.4-5) ...
Setting up python3-dev (3.11.4-5) ...
Setting up dh-python (6.20231223) ...
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Setting up debhelper (13.11.9) ...
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Processing triggers for libc-bin (2.37-12+rpi2) ...
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_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-7+rpi1 cython3_3.0.7-2 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.9 debianutils_5.14 dh-autoreconf_20 dh-python_6.20231223 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 gcc-13-base_13.2.0-7+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_0.21-14 gettext-base_0.21-14 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_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-5 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-7+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-7+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-6 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-3 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_13.2.0-7+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.11.9 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libexpat1-dev_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.2-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-7+rpi1 libgcc-s1_13.2.0-7+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.2-1 libgomp1_13.2.0-7+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjs-jquery_3.6.1+dfsg+~3.5.14-1 libjs-sphinxdoc_7.2.6-3 libjs-underscore_1.13.4~dfsg+~1.11.4-3 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.3-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libmuscle-dev_3.7+4565-7 libmuscle1_3.7+4565-7 libncursesw6_6.4+20231209-1 libnettle8_3.9.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-2 libpam-cap_1:2.66-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.36_5.36.0-10 libpipeline1_1.5.7-1 libpython3-all-dev_3.11.4-5 libpython3-dev_3.11.4-5 libpython3-stdlib_3.11.4-5 libpython3.11_3.11.7-2 libpython3.11-dev_3.11.7-2 libpython3.11-minimal_3.11.7-2 libpython3.11-stdlib_3.11.7-2 libreadline8_8.2-3 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol1_3.1-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-6 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssl1.1_1.1.1o-1 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-7+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-6 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 media-types_10.1.0 mount_2.39.3-6 nano_7.2-1 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 netbase_6.4 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-10 perl-base_5.36.0-10 perl-modules-5.36_5.36.0-10 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-all_3.11.4-5 python3-all-dev_3.11.4-5 python3-dev_3.11.4-5 python3-distutils_3.11.5-1 python3-lib2to3_3.11.5-1 python3-minimal_3.11.4-5 python3-pkg-resources_68.1.2-2 python3-setuptools_68.1.2-2 python3.11_3.11.7-2 python3.11-dev_3.11.7-2 python3.11-minimal_3.11.7-2 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-parsnp-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.08-5 tar_1.34+dfsg-1.3 tzdata_2023c-11 usrmerge_38 util-linux_2.39.3-6 util-linux-extra_2.39.3-6 xz-utils_5.4.5-0.1 zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Thu Jan 18 19:32:55 2024 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./parsnp_2.0.1+dfsg-1.dsc: no acceptable signature found
dpkg-source: info: extracting parsnp in /<<BUILDDIR>>/parsnp-2.0.1+dfsg
dpkg-source: info: unpacking parsnp_2.0.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking parsnp_2.0.1+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
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-aa8b6b8c-18a4-4132-ae98-97efd15b2775
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package parsnp
dpkg-buildpackage: info: source version 2.0.1+dfsg-1
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
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-2.0.1+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... /usr/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-2.0.1+dfsg'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
Making all in src
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+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-2.0.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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-2.0.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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-2.0.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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-2.0.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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-2.0.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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-2.0.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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-2.0.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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:955:28: warning: '%d' directive writing between 1 and 11 bytes into a region of size 9 [-Wformat-overflow=]
955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null
| ^~
parsnp.cpp:955:27: note: directive argument in the range [-2147483647, 2147483647]
955 | sprintf(b,"%d",(int)z+1);// C-style string formed without null
| ^~~~
In file included from /usr/include/stdio.h:906,
from /usr/include/c++/13/cstdio:42,
from /usr/include/c++/13/ext/string_conversions.h:45,
from /usr/include/c++/13/bits/basic_string.h:4109,
from /usr/include/c++/13/string:54,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from parsnp.hh:14,
from parsnp.cpp:54:
In function 'int sprintf(char*, const char*, ...)',
inlined from 'void Aligner::writeOutput(std::string, std::vector<float>&)' at parsnp.cpp:955:24:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 2 and 12 bytes into a destination of size 9
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __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-2.0.1+dfsg=. -fstack-protector-strong -fstack-clash-protection -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-2.0.1+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
dh_auto_test -a
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
Making check in src
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install --destdir=debian/parsnp/ -a
make -j4 install DESTDIR=/<<BUILDDIR>>/parsnp-2.0.1\+dfsg/debian/parsnp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
Making install in src
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg/src'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/<<BUILDDIR>>/parsnp-2.0.1+dfsg/debian/parsnp../bin'
/usr/bin/install -c parsnp_core '/<<BUILDDIR>>/parsnp-2.0.1+dfsg/debian/parsnp../bin'
make[3]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg/src'
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/parsnp-2.0.1+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-2.0.1+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+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-2.0.1+dfsg'
dh_fixperms
chmod -x debian/parsnp/usr/share/parsnp/template.ini
make[1]: Leaving directory '/<<BUILDDIR>>/parsnp-2.0.1+dfsg'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/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_2.0.1+dfsg-1_armhf.deb'.
dpkg-deb: building package 'parsnp' in '../parsnp_2.0.1+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../parsnp_2.0.1+dfsg-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../parsnp_2.0.1+dfsg-1_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 2024-01-21T05:35:23Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
parsnp_2.0.1+dfsg-1_armhf.changes:
----------------------------------
Format: 1.8
Date: Thu, 18 Jan 2024 20:07:57 +0100
Source: parsnp
Binary: parsnp parsnp-dbgsym
Architecture: armhf
Version: 2.0.1+dfsg-1
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Étienne Mollier <emollier@debian.org>
Description:
parsnp - rapid core genome multi-alignment
Changes:
parsnp (2.0.1+dfsg-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
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56a82e55ea4a671c478c58863df88adbd0ca4d86 182504 parsnp_2.0.1+dfsg-1_armhf.deb
Checksums-Sha256:
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bff106e11fb541221cbbcdb3e1b14fed0212d2e5ffedaec6dd0672f1f2609680 6282 parsnp_2.0.1+dfsg-1_armhf.buildinfo
22541406f09d202635a7fe42fcf1c25df8cbd9b6b764399f51936af1f2097f6a 182504 parsnp_2.0.1+dfsg-1_armhf.deb
Files:
c036bf258fa4c52d924ab01c82bf9bb5 1226332 debug optional parsnp-dbgsym_2.0.1+dfsg-1_armhf.deb
06b55f9941f12fd1f71d46933a7acf0b 6282 science optional parsnp_2.0.1+dfsg-1_armhf.buildinfo
e39a25129fefd354b22f3582364ad56a 182504 science optional parsnp_2.0.1+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
parsnp-dbgsym_2.0.1+dfsg-1_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 1226332 bytes: control archive=536 bytes.
377 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: parsnp-dbgsym
Source: parsnp
Version: 2.0.1+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1241
Depends: parsnp (= 2.0.1+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for parsnp
Build-Ids: 36860a4d1e17efd70ee76d9b9d8b69a321e59c1b
drwxr-xr-x root/root 0 2024-01-18 19:07 ./
drwxr-xr-x root/root 0 2024-01-18 19:07 ./usr/
drwxr-xr-x root/root 0 2024-01-18 19:07 ./usr/lib/
drwxr-xr-x root/root 0 2024-01-18 19:07 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-01-18 19:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-01-18 19:07 ./usr/lib/debug/.build-id/36/
-rw-r--r-- root/root 1259876 2024-01-18 19:07 ./usr/lib/debug/.build-id/36/860a4d1e17efd70ee76d9b9d8b69a321e59c1b.debug
drwxr-xr-x root/root 0 2024-01-18 19:07 ./usr/share/
drwxr-xr-x root/root 0 2024-01-18 19:07 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-01-18 19:07 ./usr/share/doc/parsnp-dbgsym -> parsnp
parsnp_2.0.1+dfsg-1_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 182504 bytes: control archive=2852 bytes.
1076 bytes, 18 lines control
5748 bytes, 61 lines md5sums
259 bytes, 12 lines * postinst #!/bin/sh
372 bytes, 12 lines * prerm #!/bin/sh
Package: parsnp
Version: 2.0.1+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1889
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libmuscle1 (>= 3.7+4565), libstdc++6 (>= 13.1), python3:any, python3-biopython, python3-numpy, python3-tqdm, fasttree, harvest-tools, mummer, phipack, python3, raxml, time
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.
drwxr-xr-x root/root 0 2024-01-18 19:07 ./
drwxr-xr-x root/root 0 2024-01-18 19:07 ./usr/
drwxr-xr-x root/root 0 2024-01-18 19:07 ./usr/bin/
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 22124
Build-Time: 69
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 389
Job: parsnp_2.0.1+dfsg-1
Machine Architecture: armhf
Package: parsnp
Package-Time: 476
Source-Version: 2.0.1+dfsg-1
Space: 22124
Status: successful
Version: 2.0.1+dfsg-1
--------------------------------------------------------------------------------
Finished at 2024-01-21T05:35:23Z
Build needed 00:07:56, 22124k disk space