spoa →
3.0.2-5 →
armhf → 2020-05-09 06:03:49
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| spoa 3.0.2-5 (armhf) Sat, 09 May 2020 05:52:38 +0000 |
+==============================================================================+
Package: spoa
Version: 3.0.2-5
Source Version: 3.0.2-5
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-0a4985bf-f24e-4175-94f8-a6c7ec05f281' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 11s (2201 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'spoa' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/spoa.git
Please use:
git clone https://salsa.debian.org/med-team/spoa.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 52.1 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main spoa 3.0.2-5 (dsc) [2128 B]
Get:2 http://172.17.0.1/private bullseye-staging/main spoa 3.0.2-5 (tar) [41.2 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main spoa 3.0.2-5 (diff) [8752 B]
Fetched 52.1 kB in 0s (114 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/spoa-Wk2XBk/spoa-3.0.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/spoa-Wk2XBk' 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-DeGrhj/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-DeGrhj/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-DeGrhj/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-DeGrhj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (9184 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:
libpam-cap netbase
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 16 not upgraded.
Need to get 856 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 856 B in 0s (59.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12224 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 (= 12), cmake, d-shlibs, rename, libbioparser-dev (>= 2.0), libgtest-dev, zlib1g-dev, libsimde-dev (>= 0.0.0.git.20200421)
Filtered Build-Depends: debhelper-compat (= 12), cmake, d-shlibs, rename, libbioparser-dev (>= 2.0), libgtest-dev, zlib1g-dev, libsimde-dev (>= 0.0.0.git.20200421)
dpkg-deb: building package 'sbuild-build-depends-spoa-dummy' in '/<<BUILDDIR>>/resolver-DeGrhj/apt_archive/sbuild-build-depends-spoa-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-spoa-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-DeGrhj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ Sources [560 B]
Get:5 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ Packages [639 B]
Fetched 2532 B in 0s (10.7 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install spoa 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:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base googletest groff-base intltool-debian libarchive-zip-perl
libarchive13 libbioparser-dev libbrotli1 libbsd0 libcroco3 libcurl4
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libglib2.0-0 libgssapi-krb5-2 libgtest-dev libicu63 libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2
libsimde-dev libssh2-1 libssl1.1 libsub-override-perl libtinfo5 libtool
libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps rename
sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff lrzip krb5-doc krb5-user libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
d-shlibs debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base googletest groff-base intltool-debian libarchive-zip-perl
libarchive13 libbioparser-dev libbrotli1 libbsd0 libcroco3 libcurl4
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libglib2.0-0 libgssapi-krb5-2 libgtest-dev libicu63 libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libncurses6
libnghttp2-14 libpipeline1 libprocps8 libpsl5 librhash0 librtmp1 libsigsegv2
libsimde-dev libssh2-1 libssl1.1 libsub-override-perl libtinfo5 libtool
libuchardet0 libuv1 libxml2 m4 man-db po-debconf procps rename
sbuild-build-depends-spoa-dummy sensible-utils zlib1g-dev
0 upgraded, 65 newly installed, 0 to remove and 16 not upgraded.
Need to get 28.0 MB of archives.
After this operation, 108 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-DeGrhj/apt_archive ./ sbuild-build-depends-spoa-dummy 0.invalid.0 [924 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-4 [59.8 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-4 [238 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.16.3-2 [1628 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5 [592 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.0-2 [292 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6.1 [255 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-7+rpi1 [61.5 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-7+rpi1 [112 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1g-1 [1272 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-7+rpi1 [318 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-7+rpi1 [135 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1 [53.9 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.68.0-1 [286 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3.1 [65.8 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.3.9-1 [133 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.35.0-2 [115 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.16.3-2 [2647 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf d-shlibs all 0.91 [17.6 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13 [184 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.0-1 [14.8 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.2-1 [1158 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13 [1002 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf googletest all 1.10.0-3 [626 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libbioparser-dev all 2.1.2-1 [5692 B]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libgtest-dev armhf 1.10.0-3 [218 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libsimde-dev all 0.0.0.git.20200424-1 [87.6 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf rename all 1.10-1 [17.2 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libkrb5-3:armhf (1.17-7+rpi1) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
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Unpacking libgssapi-krb5-2:armhf (1.17-7+rpi1) ...
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Unpacking libnghttp2-14:armhf (1.40.0-1+b2) ...
Selecting previously unselected package libpsl5:armhf.
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Unpacking libpsl5:armhf (0.21.0-1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../34-librtmp1_2.4+20151223.gitfa8646d.1-2+b1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Selecting previously unselected package libssh2-1:armhf.
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Unpacking libssh2-1:armhf (1.8.0-2.1) ...
Selecting previously unselected package libcurl4:armhf.
Preparing to unpack .../36-libcurl4_7.68.0-1_armhf.deb ...
Unpacking libcurl4:armhf (7.68.0-1) ...
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Unpacking libexpat1:armhf (2.2.9-1) ...
Selecting previously unselected package libjsoncpp1:armhf.
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Unpacking libjsoncpp1:armhf (1.7.4-3.1) ...
Selecting previously unselected package librhash0:armhf.
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Unpacking librhash0:armhf (1.3.9-1) ...
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Unpacking libuv1:armhf (1.35.0-2) ...
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Unpacking cmake (3.16.3-2) ...
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Unpacking d-shlibs (0.91) ...
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Unpacking libtool (2.4.6-14) ...
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Unpacking dh-autoreconf (19) ...
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Unpacking libdebhelper-perl (13) ...
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Unpacking libarchive-zip-perl (1.68-1) ...
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Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
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Unpacking libfile-stripnondeterminism-perl (1.8.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
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Unpacking dh-strip-nondeterminism (1.8.0-1) ...
Selecting previously unselected package libelf1:armhf.
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Unpacking dwz (0.13-5) ...
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Unpacking libglib2.0-0:armhf (2.64.2-1) ...
Selecting previously unselected package libcroco3:armhf.
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Unpacking libcroco3:armhf (0.6.13-1) ...
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Unpacking gettext (0.19.8.1-10) ...
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Unpacking debhelper (13) ...
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Unpacking googletest (1.10.0-3) ...
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Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libbioparser-dev.
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Unpacking libbioparser-dev (2.1.2-1) ...
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Unpacking libsimde-dev (0.0.0.git.20200424-1) ...
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Unpacking rename (1.10-1) ...
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Unpacking sbuild-build-depends-spoa-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.9-1) ...
Setting up libpipeline1:armhf (1.5.2-2) ...
Setting up libsimde-dev (0.0.0.git.20200424-1) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1) ...
Setting up libmagic-mgc (1:5.38-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.2-1) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1g-1) ...
Setting up libdebhelper-perl (13) ...
Setting up libbrotli1:armhf (1.0.7-6.1) ...
Setting up libnghttp2-14:armhf (1.40.0-1+b2) ...
Setting up libmagic1:armhf (1:5.38-4) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up rename (1.10-1) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Setting up file (1:5.38-4) ...
Setting up googletest (1.10.0-3) ...
Setting up libicu63:armhf (63.2-3) ...
Setting up libkrb5support0:armhf (1.17-7+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libuv1:armhf (1.35.0-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.2-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up d-shlibs (0.91) ...
Setting up libk5crypto3:armhf (1.17-7+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libbioparser-dev (2.1.2-1) ...
Setting up librhash0:armhf (1.3.9-1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up cmake-data (3.16.3-2) ...
Setting up libkrb5-3:armhf (1.17-7+rpi1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5) ...
Setting up libprocps8:armhf (2:3.3.16-4) ...
Setting up libjsoncpp1:armhf (1.7.4-3.1) ...
Setting up libfile-stripnondeterminism-perl (1.8.0-1) ...
Setting up libgtest-dev:armhf (1.10.0-3) ...
Setting up libtool (2.4.6-14) ...
Setting up libarchive13:armhf (3.4.0-2) ...
Setting up m4 (1.4.18-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-7+rpi1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.8.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up procps (2:3.3.16-4) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libcurl4:armhf (7.68.0-1) ...
Setting up automake (1:1.16.2-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up cmake (3.16.3-2) ...
Setting up po-debconf (1.0.21) ...
Setting up debhelper (13) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-spoa-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.34-5+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-10+rpi1 gcc-9_9.3.0-10+rpi1 libc6-dev_2.30-4+rpi1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200418-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-5+rpi1 binutils-arm-linux-gnueabihf_2.34-5+rpi1 binutils-common_2.34-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 cmake_3.16.3-2 cmake-data_3.16.3-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-10+rpi1 d-shlibs_0.91 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-10+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10-20200418-1+rpi1 gcc-9_9.3.0-10+rpi1 gcc-9-base_9.3.0-10+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 googletest_1.10.0-3 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-6 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libarchive13_3.4.0-2 libasan5_9.3.0-10+rpi1 libassuan0_2.5.3-7 libatomic1_10-20200418-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-5+rpi1 libbioparser-dev_2.1.2-1 libblkid1_2.34-0.1 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4+rpi1 libc-dev-bin_2.30-4+rpi1 libc6_2.30-4+rpi1 libc6-dev_2.30-4+rpi1 libcap-ng0_0.7.9-2.1+b1 libcap2_1:2.33-1 libcap2-bin_1:2.33-1 libcc1-0_10-20200418-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-5+rpi1 libctf0_2.34-5+rpi1 libcurl4_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgcc-9-dev_9.3.0-10+rpi1 libgcc-s1_10-20200418-1+rpi1 libgcc1_1:10-20200418-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200418-1+rpi1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7+rpi1 libgtest-dev_1.10.0-3 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-7+rpi1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7+rpi1 libkrb5support0_1.17-7+rpi1 libksba8_1.3.5-2 libldap-2.4-2_2.4.49+dfsg-4+rpi1 libldap-common_2.4.49+dfsg-4+rpi1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.33-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libprocps8_2:3.3.16-4 libpsl5_0.21.0-1 libreadline7_7.0-5 libreadline8_8.0-4 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsimde-dev_0.0.0.git.20200424-1 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200418-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.5-1+rpi1 libtasn1-6_4.16.0-2 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10-20200418-1+rpi1 libuchardet0_0.0.6-3 libudev1_245.5-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.35.0-2 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-3 po-debconf_1.0.21 procps_2:3.3.16-4 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 rename_1.10-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-spoa-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu May 7 12:23:21 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./spoa_3.0.2-5.dsc
dpkg-source: info: extracting spoa in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking spoa_3.0.2.orig.tar.gz
dpkg-source: info: unpacking spoa_3.0.2-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix-ftbfs-gcc-10.patch
dpkg-source: info: applying use_debian_packaged_libs.patch
dpkg-source: info: applying shared_and_static.patch
dpkg-source: info: applying fix_soversion.patch
dpkg-source: info: applying simde
dpkg-source: info: applying getopt.patch
dpkg-source: info: applying fix-959880.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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-0a4985bf-f24e-4175-94f8-a6c7ec05f281
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package spoa
dpkg-buildpackage: info: source version 3.0.2-5
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- -DCMAKE_BUILD_TYPE=Release -Dspoa_build_executable=ON -Dspoa_build_tests=ON -Dspoa_optimize_for_native=FALSE
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_AUTOGEN_VERBOSE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DCMAKE_BUILD_TYPE=Release -Dspoa_build_executable=ON -Dspoa_build_tests=ON -Dspoa_optimize_for_native=FALSE ..
-- The CXX compiler identification is GNU 9.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_AUTOGEN_VERBOSE
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
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make -f CMakeFiles/Makefile2 all
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Scanning dependencies of target spoa
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[ 25%] Building CXX object CMakeFiles/spoa_static.dir/src/alignment_engine.cpp.o
[ 25%] Building CXX object CMakeFiles/spoa_static.dir/src/graph.cpp.o
[ 25%] Building CXX object CMakeFiles/spoa.dir/src/graph.cpp.o
[ 25%] Building CXX object CMakeFiles/spoa.dir/src/alignment_engine.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/config -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -std=c++11 -o CMakeFiles/spoa_static.dir/src/alignment_engine.cpp.o -c /<<PKGBUILDDIR>>/src/alignment_engine.cpp
/usr/bin/c++ -Dspoa_EXPORTS -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/config -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -fPIC -std=c++11 -o CMakeFiles/spoa.dir/src/graph.cpp.o -c /<<PKGBUILDDIR>>/src/graph.cpp
/usr/bin/c++ -Dspoa_EXPORTS -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/config -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -fPIC -std=c++11 -o CMakeFiles/spoa.dir/src/alignment_engine.cpp.o -c /<<PKGBUILDDIR>>/src/alignment_engine.cpp
/usr/bin/c++ -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/config -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -std=c++11 -o CMakeFiles/spoa_static.dir/src/graph.cpp.o -c /<<PKGBUILDDIR>>/src/graph.cpp
[ 31%] Building CXX object CMakeFiles/spoa_static.dir/src/simd_alignment_engine.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/config -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -std=c++11 -o CMakeFiles/spoa_static.dir/src/simd_alignment_engine.cpp.o -c /<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp
[ 37%] Building CXX object CMakeFiles/spoa_static.dir/src/sisd_alignment_engine.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/config -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -std=c++11 -o CMakeFiles/spoa_static.dir/src/sisd_alignment_engine.cpp.o -c /<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp: In member function 'void spoa::SisdAlignmentEngine::initialize(const char*, uint32_t, const std::unique_ptr<spoa::Graph>&)':
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp:136:13: warning: this statement may fall through [-Wimplicit-fallthrough=]
136 | }
| ^
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp:137:9: note: here
137 | case AlignmentSubtype::kAffine:
| ^~~~
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp:156:13: warning: this statement may fall through [-Wimplicit-fallthrough=]
156 | }
| ^
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp:157:9: note: here
157 | case AlignmentSubtype::kLinear:
| ^~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:215:30: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
215 | std::unique_ptr<__mxxxi[]> sequence_profile_storage;
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:220:30: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
220 | std::unique_ptr<__mxxxi[]> M_storage;
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:228:30: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
228 | std::unique_ptr<__mxxxi[]> masks_storage;
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:232:30: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
232 | std::unique_ptr<__mxxxi[]> penalties_storage;
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function 'void spoa::SimdAlignmentEngine::realloc(uint32_t, uint32_t, uint32_t)':
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:288:69: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
288 | pimpl_->sequence_profile_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:300:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
300 | pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:314:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
314 | pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:330:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
330 | pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:339:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
339 | pimpl_->masks_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:347:62: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
347 | pimpl_->penalties_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function 'void spoa::SimdAlignmentEngine::initialize(const char*, const std::unique_ptr<spoa::Graph>&, uint32_t, uint32_t, uint32_t) [with T = spoa::InstructionSet<short int>]':
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:402:13: warning: this statement may fall through [-Wimplicit-fallthrough=]
402 | for (std::uint32_t i = 1; i < matrix_height; ++i) {
| ^~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:414:9: note: here
414 | case AlignmentSubtype::kAffine:
| ^~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function 'void spoa::SimdAlignmentEngine::initialize(const char*, const std::unique_ptr<spoa::Graph>&, uint32_t, uint32_t, uint32_t) [with T = spoa::InstructionSet<int>]':
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:402:13: warning: this statement may fall through [-Wimplicit-fallthrough=]
402 | for (std::uint32_t i = 1; i < matrix_height; ++i) {
| ^~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:414:9: note: here
414 | case AlignmentSubtype::kAffine:
| ^~~~
[ 43%] Building CXX object CMakeFiles/spoa.dir/src/simd_alignment_engine.cpp.o
/usr/bin/c++ -Dspoa_EXPORTS -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/config -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -fPIC -std=c++11 -o CMakeFiles/spoa.dir/src/simd_alignment_engine.cpp.o -c /<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:215:30: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
215 | std::unique_ptr<__mxxxi[]> sequence_profile_storage;
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:220:30: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
220 | std::unique_ptr<__mxxxi[]> M_storage;
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:228:30: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
228 | std::unique_ptr<__mxxxi[]> masks_storage;
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:232:30: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
232 | std::unique_ptr<__mxxxi[]> penalties_storage;
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function 'void spoa::SimdAlignmentEngine::realloc(uint32_t, uint32_t, uint32_t)':
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:288:69: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
288 | pimpl_->sequence_profile_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:300:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
300 | pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:314:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
314 | pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:330:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
330 | pimpl_->M_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:339:58: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
339 | pimpl_->masks_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:347:62: warning: ignoring attributes on template argument 'spoa::__mxxxi []' {aka '__vector(8) int []'} [-Wignored-attributes]
347 | pimpl_->penalties_storage = std::unique_ptr<__mxxxi[]>(storage);
| ^
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function 'void spoa::SimdAlignmentEngine::initialize(const char*, const std::unique_ptr<spoa::Graph>&, uint32_t, uint32_t, uint32_t) [with T = spoa::InstructionSet<short int>]':
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:402:13: warning: this statement may fall through [-Wimplicit-fallthrough=]
402 | for (std::uint32_t i = 1; i < matrix_height; ++i) {
| ^~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:414:9: note: here
414 | case AlignmentSubtype::kAffine:
| ^~~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp: In member function 'void spoa::SimdAlignmentEngine::initialize(const char*, const std::unique_ptr<spoa::Graph>&, uint32_t, uint32_t, uint32_t) [with T = spoa::InstructionSet<int>]':
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:402:13: warning: this statement may fall through [-Wimplicit-fallthrough=]
402 | for (std::uint32_t i = 1; i < matrix_height; ++i) {
| ^~~
/<<PKGBUILDDIR>>/src/simd_alignment_engine.cpp:414:9: note: here
414 | case AlignmentSubtype::kAffine:
| ^~~~
[ 50%] Building CXX object CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o
/usr/bin/c++ -Dspoa_EXPORTS -I/<<PKGBUILDDIR>>/include -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/config -I/<<PKGBUILDDIR>>/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -fPIC -std=c++11 -o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o -c /<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp: In member function 'void spoa::SisdAlignmentEngine::initialize(const char*, uint32_t, const std::unique_ptr<spoa::Graph>&)':
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp:136:13: warning: this statement may fall through [-Wimplicit-fallthrough=]
136 | }
| ^
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp:137:9: note: here
137 | case AlignmentSubtype::kAffine:
| ^~~~
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp:156:13: warning: this statement may fall through [-Wimplicit-fallthrough=]
156 | }
| ^
/<<PKGBUILDDIR>>/src/sisd_alignment_engine.cpp:157:9: note: here
157 | case AlignmentSubtype::kLinear:
| ^~~~
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[ 87%] Building CXX object CMakeFiles/spoa_bin.dir/src/sequence.cpp.o
[ 87%] Building CXX object CMakeFiles/spoa_test.dir/src/sequence.cpp.o
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[ 87%] Building CXX object CMakeFiles/spoa_bin.dir/src/main.cpp.o
/usr/bin/c++ -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/config -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -std=c++11 -o CMakeFiles/spoa_test.dir/test/spoa_test.cpp.o -c /<<PKGBUILDDIR>>/test/spoa_test.cpp
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[ 93%] Linking CXX executable bin/spoa
/usr/bin/cmake -E cmake_link_script CMakeFiles/spoa_bin.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spoa_bin.dir/src/sequence.cpp.o CMakeFiles/spoa_bin.dir/src/main.cpp.o -o bin/spoa -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/lib: lib/libspoa.so.3 -lz
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 93%] Built target spoa_bin
[100%] Linking CXX executable bin/spoa_test
/usr/bin/cmake -E cmake_link_script CMakeFiles/spoa_test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/spoa_test.dir/src/sequence.cpp.o CMakeFiles/spoa_test.dir/test/spoa_test.cpp.o -o bin/spoa_test -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/lib lib/libspoa.so.3 -lgtest_main -lgtest -lz -lpthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target spoa_test
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
`find . -name spoa_test`
Running main() from /build/googletest-o5PlHZ/googletest-1.10.0/googletest/src/gtest_main.cc
[==========] Running 39 tests from 2 test suites.
[----------] Global test environment set-up.
[----------] 2 tests from SpoaTest
[ RUN ] SpoaTest.AlignmentTypeError
[ OK ] SpoaTest.AlignmentTypeError (0 ms)
[ RUN ] SpoaTest.EmptyInputError
[ OK ] SpoaTest.EmptyInputError (1 ms)
[----------] 2 tests from SpoaTest (1 ms total)
[----------] 37 tests from SpoaAlignmentTest
[ RUN ] SpoaAlignmentTest.GraphClear
[ OK ] SpoaAlignmentTest.GraphClear (6598 ms)
[ RUN ] SpoaAlignmentTest.LocalConsensus
[ OK ] SpoaAlignmentTest.LocalConsensus (3290 ms)
[ RUN ] SpoaAlignmentTest.LocalAffineConsensus
[ OK ] SpoaAlignmentTest.LocalAffineConsensus (4307 ms)
[ RUN ] SpoaAlignmentTest.LocalConvexConsensus
[ OK ] SpoaAlignmentTest.LocalConvexConsensus (7342 ms)
[ RUN ] SpoaAlignmentTest.LocalConsensusWithQualities
[ OK ] SpoaAlignmentTest.LocalConsensusWithQualities (3292 ms)
[ RUN ] SpoaAlignmentTest.LocalAffineConsensusWithQualities
[ OK ] SpoaAlignmentTest.LocalAffineConsensusWithQualities (4316 ms)
[ RUN ] SpoaAlignmentTest.LocalConvexConsensusWithQualities
[ OK ] SpoaAlignmentTest.LocalConvexConsensusWithQualities (7327 ms)
[ RUN ] SpoaAlignmentTest.GlobalConsensus
[ OK ] SpoaAlignmentTest.GlobalConsensus (3155 ms)
[ RUN ] SpoaAlignmentTest.GlobalAffineConsensus
[ OK ] SpoaAlignmentTest.GlobalAffineConsensus (4139 ms)
[ RUN ] SpoaAlignmentTest.GlobalConvexConsensus
[ OK ] SpoaAlignmentTest.GlobalConvexConsensus (7166 ms)
[ RUN ] SpoaAlignmentTest.GlobalConsensusWithQualities
[ OK ] SpoaAlignmentTest.GlobalConsensusWithQualities (3155 ms)
[ RUN ] SpoaAlignmentTest.GlobalAffineConsensusWithQualities
[ OK ] SpoaAlignmentTest.GlobalAffineConsensusWithQualities (4140 ms)
[ RUN ] SpoaAlignmentTest.GlobalConvexConsensusWithQualities
[ OK ] SpoaAlignmentTest.GlobalConvexConsensusWithQualities (7162 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalConsensus
[ OK ] SpoaAlignmentTest.SemiGlobalConsensus (3133 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalAffineConsensus
[ OK ] SpoaAlignmentTest.SemiGlobalAffineConsensus (4116 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalConvexConsensus
[ OK ] SpoaAlignmentTest.SemiGlobalConvexConsensus (7178 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalConsensusWithQualities
[ OK ] SpoaAlignmentTest.SemiGlobalConsensusWithQualities (3133 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalAffineConsensusWithQualities
[ OK ] SpoaAlignmentTest.SemiGlobalAffineConsensusWithQualities (4117 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalConvexConsensusWithQualities
[ OK ] SpoaAlignmentTest.SemiGlobalConvexConsensusWithQualities (7194 ms)
[ RUN ] SpoaAlignmentTest.LocalMSA
[ OK ] SpoaAlignmentTest.LocalMSA (3294 ms)
[ RUN ] SpoaAlignmentTest.LocalAffineMSA
[ OK ] SpoaAlignmentTest.LocalAffineMSA (4387 ms)
[ RUN ] SpoaAlignmentTest.LocalConvexMSA
[ OK ] SpoaAlignmentTest.LocalConvexMSA (7417 ms)
[ RUN ] SpoaAlignmentTest.LocalMSAWithQualities
[ OK ] SpoaAlignmentTest.LocalMSAWithQualities (3345 ms)
[ RUN ] SpoaAlignmentTest.LocalAffineMSAWithQualities
[ OK ] SpoaAlignmentTest.LocalAffineMSAWithQualities (4367 ms)
[ RUN ] SpoaAlignmentTest.LocalConvexMSAWithQualities
[ OK ] SpoaAlignmentTest.LocalConvexMSAWithQualities (7433 ms)
[ RUN ] SpoaAlignmentTest.GlobalMSA
[ OK ] SpoaAlignmentTest.GlobalMSA (3229 ms)
[ RUN ] SpoaAlignmentTest.GlobalAffineMSA
[ OK ] SpoaAlignmentTest.GlobalAffineMSA (4233 ms)
[ RUN ] SpoaAlignmentTest.GlobalConvexMSA
[ OK ] SpoaAlignmentTest.GlobalConvexMSA (7304 ms)
[ RUN ] SpoaAlignmentTest.GlobalMSAWithQualities
[ OK ] SpoaAlignmentTest.GlobalMSAWithQualities (3227 ms)
[ RUN ] SpoaAlignmentTest.GlobalAffineMSAWithQualities
[ OK ] SpoaAlignmentTest.GlobalAffineMSAWithQualities (4185 ms)
[ RUN ] SpoaAlignmentTest.GlobalConvexMSAWithQualities
[ OK ] SpoaAlignmentTest.GlobalConvexMSAWithQualities (7309 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalMSA
[ OK ] SpoaAlignmentTest.SemiGlobalMSA (3184 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalAffineMSA
[ OK ] SpoaAlignmentTest.SemiGlobalAffineMSA (4213 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalConvexMSA
[ OK ] SpoaAlignmentTest.SemiGlobalConvexMSA (7250 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalMSAWithQualities
[ OK ] SpoaAlignmentTest.SemiGlobalMSAWithQualities (3161 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalAffineMSAWithQualities
[ OK ] SpoaAlignmentTest.SemiGlobalAffineMSAWithQualities (4156 ms)
[ RUN ] SpoaAlignmentTest.SemiGlobalConvexMSAWithQualities
[ OK ] SpoaAlignmentTest.SemiGlobalConvexMSAWithQualities (7236 ms)
[----------] 37 tests from SpoaAlignmentTest (183197 ms total)
[----------] Global test environment tear-down
[==========] 39 tests from 2 test suites ran. (183198 ms total)
[ PASSED ] 39 tests.
`find . -name spoa | grep bin` test/data/sample.fastq
Consensus (495)
AATGATGCGCTTTGTTGGCGCGGTGGCTTGATGCAGGGGCTAATCGACCTCTGGCAACCACTTTTCCATGACAGGAGTTGAATATGGCATTCAGTAATCCCTTCGATGATCCGCAGGGAGCGTTTTACATATTGCGCAATGCGCAGGGCAATTCAGTCTGTGGCCGCAACAATGCGTCTTACCGGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGAAGCCCACTGGCGTACTCTGACACCGACGAATTTTACCCAGTTGCAGGAGGCACAATGAGCCAGCATTTACCTTTGGTCGCCGCACAGCCCGGCATCTGGATGGCAGAAAAACTGTCAGAATTACCCTCCGCCTGGAGCGTGGCGCATTACGTTGAGTTAACCGGAGAGGTTGATTCGCCATTACTGGCCCGCGCGGTGGTTGCCGGACTAGCGCAAGCAGATACGCTTTACACGCGCAACCAAGGATTTCGG
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
dh_auto_install -a
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/spoa.dir/build.make CMakeFiles/spoa.dir/depend
make -f CMakeFiles/spoa_static.dir/build.make CMakeFiles/spoa_static.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/spoa.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/spoa_static.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/spoa_static.dir/build.make CMakeFiles/spoa_static.dir/build
make -f CMakeFiles/spoa.dir/build.make CMakeFiles/spoa.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'CMakeFiles/spoa_static.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'CMakeFiles/spoa.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 62%] Built target spoa_static
[ 62%] Built target spoa
make -f CMakeFiles/spoa_bin.dir/build.make CMakeFiles/spoa_bin.dir/depend
make -f CMakeFiles/spoa_test.dir/build.make CMakeFiles/spoa_test.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/spoa_bin.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/spoa_test.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/spoa_test.dir/build.make CMakeFiles/spoa_test.dir/build
make -f CMakeFiles/spoa_bin.dir/build.make CMakeFiles/spoa_bin.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'CMakeFiles/spoa_test.dir/build'.
make[3]: Nothing to be done for 'CMakeFiles/spoa_bin.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target spoa_bin
[100%] Built target spoa_test
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Release"
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libspoa.so.3
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libspoa.so
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libspoa_static.a
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/spoa
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/spoa/alignment_engine.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/spoa/graph.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/spoa/spoa.hpp
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/spoa-1.pc
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/bin/spoa
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/tmp/usr/bin/spoa" to ""
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
file-rename 's/_static\.a/.a/' `find debian -name libspoa_static.a`
d-shlibmove --commit \
--multiarch \
--devunversioned \
--exclude-la \
--movedev debian/tmp/usr/include/* usr/include \
--movedev debian/tmp/usr/lib/*/pkgconfig usr/lib/arm-linux-gnueabihf \
debian/tmp/usr/lib/*/*.so
Library package automatic movement utility
set -e
install -d -m 755 debian/libspoa-dev/usr/lib/arm-linux-gnueabihf
install -d -m 755 debian/libspoa3/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libspoa.a debian/libspoa-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/libspoa.so debian/libspoa-dev/usr/lib/arm-linux-gnueabihf
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/arm-linux-gnueabihf/libspoa.so.3 debian/libspoa3/usr/lib/arm-linux-gnueabihf
PKGDEV=libspoa-dev
PKGSHL=libspoa3
install -d -m 755 debian/libspoa-dev/usr/include
mv debian/tmp/usr/include/spoa debian/libspoa-dev/usr/include
install -d -m 755 debian/libspoa-dev/usr/lib/arm-linux-gnueabihf
mv debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig debian/libspoa-dev/usr/lib/arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/spoa/usr/bin/spoa 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/spoa/usr/bin/spoa was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libspoa3/usr/lib/arm-linux-gnueabihf/libspoa.so.3 found in none of the libraries
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: Depends field of package libspoa-dev: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'spoa' in '../spoa_3.0.2-5_armhf.deb'.
dpkg-deb: building package 'libspoa3' in '../libspoa3_3.0.2-5_armhf.deb'.
dpkg-deb: building package 'libspoa-dev' in '../libspoa-dev_3.0.2-5_armhf.deb'.
dpkg-deb: building package 'spoa-dbgsym' in '../spoa-dbgsym_3.0.2-5_armhf.deb'.
dpkg-deb: building package 'libspoa3-dbgsym' in '../libspoa3-dbgsym_3.0.2-5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../spoa_3.0.2-5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-05-09T06:03:46Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
spoa_3.0.2-5_armhf.changes:
---------------------------
Format: 1.8
Date: Thu, 07 May 2020 14:07:13 +0200
Source: spoa
Binary: libspoa-dev libspoa3 libspoa3-dbgsym spoa spoa-dbgsym
Architecture: armhf
Version: 3.0.2-5
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Frédéric Bonnard <frediz@debian.org>
Description:
libspoa-dev - SIMD partial order alignment library (development files)
libspoa3 - SIMD partial order alignment library
spoa - SIMD partial order alignment tool
Closes: 959880
Changes:
spoa (3.0.2-5) unstable; urgency=medium
.
* Team upload
* Fix ppc64el FTBFS with altivec and c++ (Closes: #959880)
Checksums-Sha1:
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0e51c82c2d4889d11d7c378b7ff21574d0aa25ff 145680 spoa-dbgsym_3.0.2-5_armhf.deb
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Checksums-Sha256:
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Files:
4ad0668f1e4f14f4392cc708052d20c0 76528 libdevel optional libspoa-dev_3.0.2-5_armhf.deb
b9cfeacd8cb5dfe0ed356126b1b635c6 643264 debug optional libspoa3-dbgsym_3.0.2-5_armhf.deb
3c01c063ce51477254862d519a6d4bdc 71468 libs optional libspoa3_3.0.2-5_armhf.deb
a4512a887d6e25a0927ac7d90e5a8055 145680 debug optional spoa-dbgsym_3.0.2-5_armhf.deb
b233fa82c10c9df1137e615c0cefa184 7248 science optional spoa_3.0.2-5_armhf.buildinfo
d5bad8730bd5e5490ce68a9f985e062a 27468 science optional spoa_3.0.2-5_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libspoa-dev_3.0.2-5_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 76528 bytes: control archive=1012 bytes.
798 bytes, 20 lines control
497 bytes, 7 lines md5sums
Package: libspoa-dev
Source: spoa
Version: 3.0.2-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 293
Depends: libspoa3 (= 3.0.2-5)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/rvaser/spoa
Description: SIMD partial order alignment library (development files)
Spoa (SIMD POA) is a c++ implementation of the partial order alignment
(POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
is used to generate consensus sequences (as described in
10.1093/bioinformatics/btg109). It supports three alignment modes: local
(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
(overlap).
.
This package contains the static library and the header files.
drwxr-xr-x root/root 0 2020-05-07 12:07 ./
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/include/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/include/spoa/
-rw-r--r-- root/root 1834 2020-03-04 11:17 ./usr/include/spoa/alignment_engine.hpp
-rw-r--r-- root/root 5503 2020-03-04 11:17 ./usr/include/spoa/graph.hpp
-rw-r--r-- root/root 162 2020-03-04 11:17 ./usr/include/spoa/spoa.hpp
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 273134 2020-05-07 12:07 ./usr/lib/arm-linux-gnueabihf/libspoa.a
lrwxrwxrwx root/root 0 2020-05-07 12:07 ./usr/lib/arm-linux-gnueabihf/libspoa.so -> libspoa.so.3
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 233 2020-05-07 12:07 ./usr/lib/arm-linux-gnueabihf/pkgconfig/spoa-1.pc
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/doc/libspoa-dev/
-rw-r--r-- root/root 1203 2020-05-07 12:07 ./usr/share/doc/libspoa-dev/changelog.Debian.gz
-rw-r--r-- root/root 1353 2020-05-07 12:07 ./usr/share/doc/libspoa-dev/copyright
libspoa3-dbgsym_3.0.2-5_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 643264 bytes: control archive=552 bytes.
387 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libspoa3-dbgsym
Source: spoa
Version: 3.0.2-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 655
Depends: libspoa3 (= 3.0.2-5)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libspoa3
Build-Ids: 99caaea57cf52dfd9d3ecc8507959699c0ce8bb8
drwxr-xr-x root/root 0 2020-05-07 12:07 ./
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/debug/.build-id/99/
-rw-r--r-- root/root 659716 2020-05-07 12:07 ./usr/lib/debug/.build-id/99/caaea57cf52dfd9d3ecc8507959699c0ce8bb8.debug
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-05-07 12:07 ./usr/share/doc/libspoa3-dbgsym -> libspoa3
libspoa3_3.0.2-5_armhf.deb
--------------------------
new Debian package, version 2.0.
size 71468 bytes: control archive=968 bytes.
785 bytes, 20 lines control
219 bytes, 3 lines md5sums
30 bytes, 1 lines shlibs
63 bytes, 2 lines triggers
Package: libspoa3
Source: spoa
Version: 3.0.2-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 216
Depends: libc6 (>= 2.4), libgcc-s1 (>= 3.5), libstdc++6 (>= 5.2)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/rvaser/spoa
Description: SIMD partial order alignment library
Spoa (SIMD POA) is a c++ implementation of the partial order alignment
(POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
is used to generate consensus sequences (as described in
10.1093/bioinformatics/btg109). It supports three alignment modes: local
(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
(overlap).
.
This package contains the shared library.
drwxr-xr-x root/root 0 2020-05-07 12:07 ./
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 206240 2020-05-07 12:07 ./usr/lib/arm-linux-gnueabihf/libspoa.so.3
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/doc/libspoa3/
-rw-r--r-- root/root 1203 2020-05-07 12:07 ./usr/share/doc/libspoa3/changelog.Debian.gz
-rw-r--r-- root/root 1353 2020-05-07 12:07 ./usr/share/doc/libspoa3/copyright
spoa-dbgsym_3.0.2-5_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 145680 bytes: control archive=532 bytes.
358 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: spoa-dbgsym
Source: spoa
Version: 3.0.2-5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 161
Depends: spoa (= 3.0.2-5)
Section: debug
Priority: optional
Description: debug symbols for spoa
Build-Ids: 4a4cb1ef6ff1b9a7603d3581c370088743669105
drwxr-xr-x root/root 0 2020-05-07 12:07 ./
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/lib/debug/.build-id/4a/
-rw-r--r-- root/root 154348 2020-05-07 12:07 ./usr/lib/debug/.build-id/4a/4cb1ef6ff1b9a7603d3581c370088743669105.debug
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-05-07 12:07 ./usr/share/doc/spoa-dbgsym -> spoa
spoa_3.0.2-5_armhf.deb
----------------------
new Debian package, version 2.0.
size 27468 bytes: control archive=928 bytes.
746 bytes, 16 lines control
388 bytes, 6 lines md5sums
Package: spoa
Version: 3.0.2-5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 93
Depends: libc6 (>= 2.4), libgcc-s1 (>= 3.5), libspoa3 (>= 3.0.2), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: https://github.com/rvaser/spoa
Description: SIMD partial order alignment tool
Spoa (SIMD POA) is a c++ implementation of the partial order alignment
(POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which
is used to generate consensus sequences (as described in
10.1093/bioinformatics/btg109). It supports three alignment modes: local
(Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment
(overlap).
drwxr-xr-x root/root 0 2020-05-07 12:07 ./
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/bin/
-rwxr-xr-x root/root 26216 2020-05-07 12:07 ./usr/bin/spoa
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/doc/spoa/
-rw-r--r-- root/root 1203 2020-05-07 12:07 ./usr/share/doc/spoa/changelog.Debian.gz
-rw-r--r-- root/root 1353 2020-05-07 12:07 ./usr/share/doc/spoa/copyright
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/doc/spoa/examples/
-rw-r--r-- root/root 51678 2020-03-04 11:17 ./usr/share/doc/spoa/examples/sample.fastq
-rw-r--r-- root/root 294 2020-05-07 12:07 ./usr/share/doc/spoa/run-unit-test
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/man/
drwxr-xr-x root/root 0 2020-05-07 12:07 ./usr/share/man/man1/
-rw-r--r-- root/root 700 2020-05-07 12:07 ./usr/share/man/man1/spoa.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 26772
Build-Time: 302
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 347
Job: spoa_3.0.2-5
Machine Architecture: armhf
Package: spoa
Package-Time: 668
Source-Version: 3.0.2-5
Space: 26772
Status: successful
Version: 3.0.2-5
--------------------------------------------------------------------------------
Finished at 2020-05-09T06:03:46Z
Build needed 00:11:08, 26772k disk space