Raspbian Package Auto-Building

Build log for jellyfish (2.3.0-2) on armhf

jellyfish2.3.0-2armhf → 2019-11-10 04:00:05

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+==============================================================================+
| jellyfish 2.3.0-2 (armhf)                    Sun, 10 Nov 2019 03:53:11 +0000 |
+==============================================================================+

Package: jellyfish
Version: 2.3.0-2
Source Version: 2.3.0-2
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-65180f85-605d-4b70-b213-02f460caf311' 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 [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.4 MB in 11s (2206 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: 'jellyfish' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/jellyfish.git
Please use:
git clone https://salsa.debian.org/med-team/jellyfish.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 694 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main jellyfish 2.3.0-2 (dsc) [2541 B]
Get:2 http://172.17.0.1/private bullseye-staging/main jellyfish 2.3.0-2 (tar) [679 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main jellyfish 2.3.0-2 (diff) [12.8 kB]
Fetched 694 kB in 0s (2439 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/jellyfish-y2pKzM/jellyfish-2.3.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/jellyfish-y2pKzM' 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-T3H2cl/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-T3H2cl/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-T3H2cl/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-T3H2cl/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (8952 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 36 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12235 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), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools
Filtered Build-Depends: debhelper-compat (= 12), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools
dpkg-deb: building package 'sbuild-build-depends-jellyfish-dummy' in '/<<BUILDDIR>>/resolver-T3H2cl/apt_archive/sbuild-build-depends-jellyfish-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-jellyfish-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-T3H2cl/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ Sources [574 B]
Get:5 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ Packages [655 B]
Fetched 2562 B in 0s (11.0 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install jellyfish 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 bc bsdmainutils ca-certificates
  chrpath d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism
  dos2unix dwz file gettext gettext-base groff-base intltool-debian
  libarchive-zip-perl libbrotli1 libbsd0 libcroco3 libcurl3-gnutls
  libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhogweed5
  libhts-dev libhts2 libicu63 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6
  libncursesw6 libnettle7 libnghttp2-14 libpipeline1 libprocps7 libpsl5
  libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.7
  libpython3.7-dev libpython3.7-minimal libpython3.7-stdlib librtmp1
  libruby2.5 libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libtinfo5
  libtinfo6 libtool libuchardet0 libxml2 libyaml-0-2 m4 man-db mime-support
  openssl pkg-config po-debconf procps python3 python3-all python3-all-dev
  python3-dev python3-distutils python3-lib2to3 python3-minimal python3.7
  python3.7-dev python3.7-minimal rake ruby ruby-did-you-mean ruby-minitest
  ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5
  rubygems-integration samtools sensible-utils swig swig3.0 time yaggo
  zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
  krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
  m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk
  python3-venv python3.7-venv python3.7-doc binfmt-support ri ruby-dev bundler
  swig-doc swig-examples swig3.0-examples swig3.0-doc
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev
  libmail-sendmail-perl psmisc zip fonts-lato libjs-jquery python cwltool
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bc bsdmainutils ca-certificates
  chrpath d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism
  dos2unix dwz file gettext gettext-base groff-base intltool-debian
  libarchive-zip-perl libbrotli1 libbsd0 libcroco3 libcurl3-gnutls
  libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev
  libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhogweed5
  libhts-dev libhts2 libicu63 libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6
  libnettle7 libnghttp2-14 libpipeline1 libprocps7 libpsl5 libpython3-all-dev
  libpython3-dev libpython3-stdlib libpython3.7 libpython3.7-dev
  libpython3.7-minimal libpython3.7-stdlib librtmp1 libruby2.5 libsigsegv2
  libssh2-1 libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0
  libxml2 libyaml-0-2 m4 man-db mime-support openssl pkg-config po-debconf
  procps python3 python3-all python3-all-dev python3-dev python3-distutils
  python3-lib2to3 python3-minimal python3.7 python3.7-dev python3.7-minimal
  rake ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert
  ruby-test-unit ruby-xmlrpc ruby2.5 rubygems-integration samtools
  sbuild-build-depends-jellyfish-dummy sensible-utils swig swig3.0 time yaggo
  zlib1g-dev
The following packages will be upgraded:
  libncursesw6 libtinfo6
2 upgraded, 104 newly installed, 0 to remove and 34 not upgraded.
Need to get 81.7 MB of archives.
After this operation, 202 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-T3H2cl/apt_archive ./ sbuild-build-depends-jellyfish-dummy 0.invalid.0 [944 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 6.1+20191019-1 [316 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 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-1 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.5-2 [584 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.5-2 [1527 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-1 [36.6 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.1+20191019-1 [320 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.1+20191019-1 [104 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.5-2 [1668 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.5-2 [347 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-1 [20.1 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-1 [61.5 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libprocps7 armhf 2:3.3.15-2 [58.9 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.15-2 [235 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf bc armhf 1.07.1-2+b1 [101 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf time armhf 1.7-25.1 [30.8 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1d-2 [806 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20190110 [157 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf d-shlibs all 0.88 [17.4 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.1-1 [23.5 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.1-1 [14.4 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-1 [69.7 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.1 [173 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.2-3 [1137 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.1 [997 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.0-1 [78.3 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.0-1 [145 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20191017 [94.4 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf dos2unix armhf 7.4.0-2 [386 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-4 [266 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libnettle7 armhf 3.5.1+really3.5.1-2 [232 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.39.2-1 [71.3 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libhogweed5 armhf 3.5.1+really3.5.1-2 [127 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.66.0-1+b1 [295 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.3-3 [76.4 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libexpat1-dev armhf 2.2.9-1 [119 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-11 [255 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.9-11 [4286 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7 armhf 3.7.5-2 [1252 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-dev armhf 3.7.5-2 [40.2 MB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libpython3-dev armhf 3.7.5-1 [20.1 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libpython3-all-dev armhf 3.7.5-1 [1068 B]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf rubygems-integration all 1.12 [5160 B]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf ruby2.5 armhf 2.5.7-1 [375 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf ruby armhf 1:2.5.2 [11.5 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf rake all 12.3.3-1 [67.3 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf ruby-did-you-mean all 1.2.1-1 [14.4 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf ruby-minitest all 5.11.3-1 [54.8 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf ruby-power-assert all 1.1.1-1 [10.9 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf ruby-test-unit all 3.2.9-1 [74.1 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libyaml-0-2 armhf 0.2.2-1 [40.0 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libruby2.5 armhf 2.5.7-1 [3128 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf python3-all armhf 3.7.5-1 [1064 B]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf python3.7-dev armhf 3.7.5-2 [513 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf python3-dev armhf 3.7.5-1 [1272 B]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf python3-all-dev armhf 3.7.5-1 [1064 B]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.9-5 [397 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf swig3.0 armhf 3.0.12-2.2 [1242 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf swig armhf 3.0.12-2.2 [310 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf yaggo all 1.5.10-2 [18.9 kB]
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Setting up libncurses6:armhf (6.1+20191019-1) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up pkg-config (0.29-6) ...
Setting up d-shlibs (0.88) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libnettle7:armhf (3.5.1+really3.5.1-2) ...
Setting up sensible-utils (0.0.12) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up procps (2:3.3.15-2) ...
update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up dos2unix (7.4.0-2) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up ruby-did-you-mean (1.2.1-1) ...
Setting up openssl (1.1.1d-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up ruby-xmlrpc (0.3.0-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Setting up chrpath (0.16-2) ...
Setting up libfile-stripnondeterminism-perl (1.6.1-1) ...
Setting up libpython3.7-stdlib:armhf (3.7.5-2) ...
Setting up swig (3.0.12-2.2) ...
Setting up libhogweed5:armhf (3.5.1+really3.5.1-2) ...
Setting up libpython3.7:armhf (3.7.5-2) ...
Setting up libtool (2.4.6-11) ...
Setting up libpython3.7-dev:armhf (3.7.5-2) ...
Setting up bc (1.07.1-2+b1) ...
Setting up m4 (1.4.18-4) ...
Setting up ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
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 (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.13-1) ...
Setting up groff-base (1.22.4-3) ...
Setting up libpython3-stdlib:armhf (3.7.5-1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.7 (3.7.5-2) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libpython3-dev:armhf (3.7.5-1) ...
Setting up libcurl3-gnutls:armhf (7.66.0-1+b1) ...
Setting up python3 (3.7.5-1) ...
Setting up rubygems-integration (1.12) ...
Setting up man-db (2.9.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up python3.7-dev (3.7.5-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libpython3-all-dev:armhf (3.7.5-1) ...
Setting up python3-lib2to3 (3.8.0-1) ...
Setting up python3-distutils (3.8.0-1) ...
Setting up dh-python (4.20191017) ...
Setting up libhts2:armhf (1.9-11) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.9-11) ...
Setting up python3-all (3.7.5-1) ...
Setting up samtools (1.9-5) ...
Setting up python3-dev (3.7.5-1) ...
Setting up python3-all-dev (3.7.5-1) ...
Setting up dh-autoreconf (19) ...
Setting up rake (12.3.3-1) ...
Setting up libruby2.5:armhf (2.5.7-1) ...
Setting up debhelper (12.7.1) ...
Setting up dh-strip-nondeterminism (1.6.1-1) ...
Setting up ruby2.5 (2.5.7-1) ...
Setting up ruby (1:2.5.2) ...
Setting up yaggo (1.5.10-2) ...
Setting up sbuild-build-depends-jellyfish-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-2+rpi1) ...
Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.15.0-58-generic armhf (armv8l)
Toolchain package versions: binutils_2.32.51.20190909-1+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-8+rpi1 gcc-9_9.2.1-8+rpi1 libc6-dev_2.29-2+rpi1 libstdc++-9-dev_9.2.1-8+rpi1 libstdc++6_9.2.1-8+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-4 bc_1.07.1-2+b1 binutils_2.32.51.20190909-1+rpi1 binutils-arm-linux-gnueabihf_2.32.51.20190909-1+rpi1 binutils-common_2.32.51.20190909-1+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 chrpath_0.16-2 coreutils_8.30-3 cpp_4:9.2.1-3+rpi1 cpp-9_9.2.1-8+rpi1 d-shlibs_0.88 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1 debianutils_4.9 dh-autoreconf_19 dh-python_4.20191017 dh-strip-nondeterminism_1.6.1-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dos2unix_7.4.0-2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3+rpi1 g++-9_9.2.1-8+rpi1 gcc_4:9.2.1-3+rpi1 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b3 gcc-7-base_7.4.0-14 gcc-9_9.2.1-8+rpi1 gcc-9-base_9.2.1-8+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.22 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-8+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-8+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.32.51.20190909-1+rpi1 libblkid1_2.34-0.1 libbrotli1_1.0.7-4 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-2+rpi1 libc-dev-bin_2.29-2+rpi1 libc6_2.29-2+rpi1 libc6-dev_2.29-2+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcap2-bin_1:2.25-2 libcc1-0_9.2.1-8+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcurl3-gnutls_7.66.0-1+b1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.249 libdebhelper-perl_12.7.1 libdeflate0_1.3-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.1-1 libgcc-9-dev_9.2.1-8+rpi1 libgcc1_1:9.2.1-8+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-5 libgomp1_9.2.1-8+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.9-11 libhts2_1.9-11 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl19_0.20-2 libisl21_0.21-2 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b1 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.1-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.39.2-1 libnpth0_1.6-1 libp11-kit0_0.23.17-2 libpam-cap_1:2.25-2 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_10.32-5 libpcre3_2:8.39-12 libperl5.30_5.30.0-7 libpipeline1_1.5.1-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython3-all-dev_3.7.5-1 libpython3-dev_3.7.5-1 libpython3-stdlib_3.7.5-1 libpython3.7_3.7.5-2 libpython3.7-dev_3.7.5-2 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libruby2.5_2.5.7-1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.1-2+rpi1 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-8+rpi1 libstdc++6_9.2.1-8+rpi1 libsub-override-perl_0.09-2 libsystemd0_242-7+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-8+rpi1 libuchardet0_0.0.6-3 libudev1_242-7+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-7+b2 libyaml-0-2_0.2.2-1 libzstd1_1.4.3+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20190803-1 ncurses-bin_6.1+20190803-1 netbase_5.6 openssl_1.1.1d-2 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-7 perl-base_5.30.0-7 perl-modules-5.30_5.30.0-7 pinentry-curses_1.1.0-3 pkg-config_0.29-6 po-debconf_1.0.21 procps_2:3.3.15-2 python3_3.7.5-1 python3-all_3.7.5-1 python3-all-dev_3.7.5-1 python3-dev_3.7.5-1 python3-distutils_3.8.0-1 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-1 python3.7_3.7.5-2 python3.7-dev_3.7.5-2 python3.7-minimal_3.7.5-2 rake_12.3.3-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 ruby_1:2.5.2 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.11.3-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.1-1 ruby-test-unit_3.2.9-1 ruby-xmlrpc_0.3.0-2 ruby2.5_2.5.7-1 rubygems-integration_1.12 samtools_1.9-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-jellyfish-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 swig_3.0.12-2.2 swig3.0_3.0.12-2.2 sysvinit-utils_2.96~beta-3 tar_1.30+dfsg-6 time_1.7-25.1 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 yaggo_1.5.10-2 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Oct  1 09:08:07 2019 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./jellyfish_2.3.0-2.dsc
dpkg-source: info: extracting jellyfish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking jellyfish_2.3.0.orig.tar.gz
dpkg-source: info: unpacking jellyfish_2.3.0-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying manpage_whatis_entry.patch
dpkg-source: info: applying reproducible.patch
dpkg-source: info: applying portability.patch
dpkg-source: info: applying fix_replacement_of_-L_option.patch
dpkg-source: info: applying test_needs_bash
dpkg-source: info: applying python3

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-65180f85-605d-4b70-b213-02f460caf311
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package jellyfish
dpkg-buildpackage: info: source version 2.3.0-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean --with python3
   debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
if [ -d debian/tmp_save_tests ] ; then \
    mv debian/tmp_save_tests/* tests ; \
    rmdir debian/tmp_save_tests ; \
fi
rm -f tests/compat.sh
rm -f swig/python/jellyfish* # swig/python/dna_jellyfish.py
rm -f swig/perl5/blib/arch/auto/jellyfish/jellyfish.so
rm -f swig/perl5/blib/bin/.exists
rm -f swig/perl5/blib/lib/.exists
rm -f swig/perl5/blib/lib/auto/jellyfish/.exists
rm -f swig/perl5/blib/man1/.exists
rm -f swig/perl5/blib/man3/.exists
rm -f swig/perl5/blib/script/.exists
rm -f swig/perl5/jellyfish.bs
rm -f swig/perl5/pm_to_blib
rm -rf swig/perl5/MYMETA.json swig/perl5/MYMETA.yml swig/perl5/Makefile swig/perl5/blib/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
 debian/rules build-arch
dh build-arch --with python3
   dh_update_autotools_config -a
   dh_autoreconf -a
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:8: installing './compile'
configure.ac:2: installing './config.guess'
configure.ac:2: installing './config.sub'
configure.ac:4: installing './install-sh'
configure.ac:4: installing './missing'
Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3
	./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3
configure: WARNING: unrecognized options: --disable-maintainer-mode
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
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 we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for shared library run path origin... done
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for HTSLIB... yes
checking for samtools... /usr/bin/samtools
checking for unix2dos... /usr/bin/unix2dos
checking for md5sum... md5sum
checking for yaggo... /usr/bin/yaggo
checking for x86 cpuid  output... unknown
checking for x86-AVX xgetbv  output... unknown
checking for __int128... no
checking for std::numeric_limits<__int128>... no
checking for _NSGetExecutablePath... no
checking for execinfo.h... yes
checking for ext/stdio_filebuf.h... yes
checking for sys/syscall.h... yes
checking for siginfo_t.si_int... yes
checking for swig... /usr/bin/swig
checking SWIG version... 3.0.12
checking for SWIG library... /usr/share/swig3.0
checking for python... /usr/bin/python3
checking for a version of Python >= '2.1.0'... yes
checking for the distutils Python package... yes
checking for Python include path... -I/usr/include/python3.7m
checking for Python library path... -L/usr/lib -lpython3.7m
checking for Python site-packages path... /usr/lib/python3/dist-packages
checking python extra libraries... -lcrypt -lpthread -ldl  -lutil -lm
checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
checking consistency of all components of python development environment... yes
checking for perl... /usr/bin/perl
checking for Perl prefix... /usr
checking for Perl extension include path... /usr/lib/arm-linux-gnueabihf/perl/5.30/CORE
checking for Perl extension target directory... /usr/lib/perl/5.30.0
checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include
checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong
checking for posix_memalign... yes
checking for aligned_alloc... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating compat.sh
config.status: creating jellyfish-2.0.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
dh_auto_configure --sourcedirectory=swig/perl5
	cd swig/perl5 && perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -lpthread"
-I/<<PKGBUILDDIR>>/debian/tmp//usr/include/jellyfish-2.3.0
-L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -lpthread
-L/<<PKGBUILDDIR>>/debian/tmp//usr/lib/arm-linux-gnueabihf
Warning (mostly harmless): No library found for -ljellyfish-2.0
Generating a Unix-style Makefile
Writing Makefile for jellyfish
Writing MYMETA.yml and MYMETA.json
dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild
I: pybuild base:217: python3.7 setup.py config 
running config
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p debian/tmp_save_tests
cp -a tests/* debian/tmp_save_tests
dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam
	make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam
make[2]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo
/usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo
/usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i
/usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i
make  all-am
make[3]: Entering directory '/<<PKGBUILDDIR>>'
g++ -DHAVE_CONFIG_H -I.  -Wall -Wnon-virtual-dtor -I. -I./include  -Wdate-time -D_FORTIFY_SOURCE=2   -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc
g++ -DHAVE_CONFIG_H -I.  -Wall -Wnon-virtual-dtor -I. -I./include  -Wdate-time -D_FORTIFY_SOURCE=2   -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/count_main.o sub_commands/count_main.cc
In file included from ./include/jellyfish/large_hash_array.hpp:19,
                 from ./include/jellyfish/hash_counter.hpp:14,
                 from sub_commands/count_main.cc:38:
./include/jellyfish/rectangular_binary_matrix.hpp: In member function 'bool jellyfish::RectangularBinaryMatrix::is_zero() const':
./include/jellyfish/rectangular_binary_matrix.hpp:121:29: error: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Werror=sign-compare]
  121 |       return (p - _columns) == _c;
      |              ~~~~~~~~~~~~~~~^~~~~
cc1plus: all warnings being treated as errors
make[3]: *** [Makefile:1710: sub_commands/count_main.o] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: *** [Makefile:1025: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam returned exit code 2
make[1]: *** [debian/rules:75: override_dh_auto_build] Error 255
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:21: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-11-10T04:00:04Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 8968
Build-Time: 75
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 320
Job: jellyfish_2.3.0-2
Machine Architecture: armhf
Package: jellyfish
Package-Time: 413
Source-Version: 2.3.0-2
Space: 8968
Status: attempted
Version: 2.3.0-2
--------------------------------------------------------------------------------
Finished at 2019-11-10T04:00:04Z
Build needed 00:06:53, 8968k disk space