Raspbian Package Auto-Building

Build log for bio-eagle (2.3-3) on armhf

bio-eagle2.3-3armhf → 2017-04-17 19:04:08

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02

+==============================================================================+
| bio-eagle 2.3-3 (armhf)                      Mon, 17 Apr 2017 18:55:33 +0000 |
+==============================================================================+

Package: bio-eagle
Version: 2.3-3
Source Version: 2.3-3
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-b9bc92df-79a4-40ce-9783-8bb68ad3c793' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9730 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 24s (879 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: 'bio-eagle' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/eagle.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/eagle.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1635 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main bio-eagle 2.3-3 (dsc) [2126 B]
Get:2 http://172.17.0.1/private stretch-staging/main bio-eagle 2.3-3 (tar) [1626 kB]
Get:3 http://172.17.0.1/private stretch-staging/main bio-eagle 2.3-3 (diff) [6548 B]
Fetched 1635 kB in 0s (7348 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bio-eagle-e6isst/bio-eagle-2.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bio-eagle-e6isst' 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-cWMui5/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-cWMui5/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-cWMui5/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-cWMui5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (3266 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:
  fuse2fs gnupg-l10n libfuse2 manpages
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 7 not upgraded.
Need to get 770 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 770 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13968 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper (>= 9), libopenblas-dev, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 9), libopenblas-dev, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-bio-eagle-dummy' in '/<<BUILDDIR>>/resolver-cWMui5/apt_archive/sbuild-build-depends-bio-eagle-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-bio-eagle-dummy sbuild-build-depends-core-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-cWMui5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ Sources [534 B]
Get:5 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ Packages [615 B]
Fetched 2482 B in 0s (3760 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install bio-eagle 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:
  fuse2fs gnupg-l10n libfuse2 manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils cpp debhelper
  dh-autoreconf dh-strip-nondeterminism file gcc gettext gettext-base gfortran
  gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl
  libblas-common libblas-dev libblas3 libboost-dev libboost-iostreams-dev
  libboost-iostreams1.62-dev libboost-iostreams1.62.0
  libboost-program-options-dev libboost-program-options1.62-dev
  libboost-program-options1.62.0 libboost-regex1.62-dev libboost-regex1.62.0
  libboost1.62-dev libbsd0 libcroco3 libcurl3-gnutls libffi6
  libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
  libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1 libicu-dev
  libicu57 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
  libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnettle6 libnghttp2-14
  libopenblas-base libopenblas-dev libp11-kit0 libpipeline1 libpsl5 librtmp1
  libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libtasn1-6
  libtool libunistring0 libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation cpp-doc dh-make gcc-multilib manpages-dev flex bison gdb gcc-doc
  gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-6-doc
  libgfortran3-dbg libcoarrays-dev groff liblapack-doc-man liblapack-doc
  libboost-doc libboost1.62-doc libboost-atomic1.62-dev
  libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
  libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
  libboost-filesystem1.62-dev libboost-graph1.62-dev
  libboost-graph-parallel1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
  libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev
  libboost-python1.62-dev libboost-random1.62-dev
  libboost-serialization1.62-dev libboost-signals1.62-dev
  libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
  libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
  libboost1.62-tools-dev libmpfrc++-dev libntl-dev gnutls-bin krb5-doc
  krb5-user icu-doc libtool-doc gcj-jdk m4-doc less www-browser
  libmail-box-perl
Recommended packages:
  curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
  xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev
  xml-core libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism file gettext gettext-base gfortran
  gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl
  libblas-common libblas-dev libblas3 libboost-dev libboost-iostreams-dev
  libboost-iostreams1.62-dev libboost-iostreams1.62.0
  libboost-program-options-dev libboost-program-options1.62-dev
  libboost-program-options1.62.0 libboost-regex1.62-dev libboost-regex1.62.0
  libboost1.62-dev libbsd0 libcroco3 libcurl3-gnutls libffi6
  libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
  libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1 libicu-dev
  libicu57 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
  libldap-2.4-2 libldap-common libmagic-mgc libmagic1 libnettle6 libnghttp2-14
  libopenblas-base libopenblas-dev libp11-kit0 libpipeline1 libpsl5 librtmp1
  libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.1 libtasn1-6
  libtool libunistring0 libxml2 m4 man-db po-debconf
  sbuild-build-depends-bio-eagle-dummy zlib1g-dev
The following packages will be upgraded:
  cpp gcc
2 upgraded, 76 newly installed, 0 to remove and 5 not upgraded.
Need to get 57.2 MB/57.5 MB of archives.
After this operation, 317 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-cWMui5/apt_archive ./ sbuild-build-depends-bio-eagle-dummy 0.invalid.0 [818 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libssl1.1 armhf 1.1.0e-1 [1103 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-3 [221 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-3 [104 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-3 [63.2 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-2 [116 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.3-2 [94.4 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.10-1 [45.3 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.5.8-5 [824 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.15-1 [57.9 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.15-1 [115 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.15-1 [262 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.15-1 [132 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3 [66.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3 [98.1 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libldap-common all 2.4.44+dfsg-3 [84.5 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-3 [194 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.2 [806 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-6 [733 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf cpp armhf 4:6.3.0-4 [18.7 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf gcc armhf 4:6.3.0-4 [5212 B]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.032-1 [15.8 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.032-1 [9888 B]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.3-2 [2527 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-2 [1434 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.3.0-11+rpi1 [166 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.3.0-11+rpi1 [200 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.3.0-11+rpi1 [5414 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.3.0-4 [1352 B]
Get:50 http://172.17.0.1/private stretch-staging/main armhf icu-devtools armhf 57.1-5 [156 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.7.0-1 [14.0 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.7.0-1 [107 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.7.0-1 [19.0 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.62.0.1+b4 [3920 B]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-4 [232 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libicu-dev armhf 57.1-5 [15.8 MB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-4 [325 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-4 [48.7 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-4 [57.7 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b4 [3694 B]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.62.0 armhf 1.62.0+dfsg-4 [136 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.62-dev armhf 1.62.0+dfsg-4 [178 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options-dev armhf 1.62.0.1+b4 [3716 B]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libidn2-0 armhf 0.16-1 [59.3 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.18.1-1 [68.0 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libpsl5 armhf 0.17.0-3 [40.8 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.52.1-4 [259 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.2-2+rpi1 [215 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3.2-2+rpi1 [270 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libopenblas-base armhf 0.2.19-2+rpi1 [1980 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libopenblas-dev armhf 0.2.19-2+rpi1 [1847 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 57.2 MB in 5s (9779 kB/s)
Selecting previously unselected package groff-base.
(Reading database ... 13968 files and directories currently installed.)
Preparing to unpack .../00-groff-base_1.22.3-9_armhf.deb ...
Unpacking groff-base (1.22.3-9) ...
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Unpacking libbsd0:armhf (0.8.3-1) ...
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Preparing to unpack .../03-libpipeline1_1.4.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.4.1-2) ...
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Preparing to unpack .../04-man-db_2.7.6.1-2_armhf.deb ...
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Unpacking libssl1.1:armhf (1.1.0e-1) ...
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Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-3) ...
Setting up gettext-base (0.19.8.1-2) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up gcc (4:6.3.0-4) ...
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Setting up libxml2:armhf (2.9.4+dfsg1-2.2) ...
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Setting up libmagic-mgc (1:5.29-3) ...
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Setting up libboost-iostreams1.62.0:armhf (1.62.0+dfsg-4) ...
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update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libssh2-1:armhf (1.7.0-1) ...
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Setting up libssl1.1:armhf (1.1.0e-1) ...
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Setting up libboost-dev:armhf (1.62.0.1+b4) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.12) ...
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
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Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
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Setting up libopenblas-base (0.2.19-2+rpi1) ...
update-alternatives: using /usr/lib/openblas-base/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
update-alternatives: using /usr/lib/openblas-base/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up gfortran-6 (6.3.0-11+rpi1) ...
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Setting up libpsl5:armhf (0.17.0-3) ...
Setting up libglib2.0-0:armhf (2.50.3-2) ...
No schema files found: doing nothing.
Setting up libboost-regex1.62.0:armhf (1.62.0+dfsg-4) ...
Setting up autoconf (2.69-10) ...
Setting up libicu-dev (57.1-5) ...
Setting up file (1:5.29-3) ...
Setting up libkrb5support0:armhf (1.15-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libp11-kit0:armhf (0.23.3-2) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up gfortran (4:6.3.0-4) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libk5crypto3:armhf (1.15-1) ...
Setting up gettext (0.19.8.1-2) ...
Setting up libblas-dev (3.7.0-1) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libboost-regex1.62-dev:armhf (1.62.0+dfsg-4) ...
Setting up libboost-iostreams1.62-dev:armhf (1.62.0+dfsg-4) ...
Setting up libgnutls30:armhf (3.5.8-5) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libldap-2.4-2:armhf (2.4.44+dfsg-3) ...
Setting up libboost-iostreams-dev:armhf (1.62.0.1+b4) ...
Setting up libkrb5-3:armhf (1.15-1) ...
Setting up libopenblas-dev (0.2.19-2+rpi1) ...
update-alternatives: using /usr/lib/openblas-base/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
update-alternatives: using /usr/lib/openblas-base/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up po-debconf (1.0.20) ...
Setting up libgssapi-krb5-2:armhf (1.15-1) ...
Setting up libcurl3-gnutls:armhf (7.52.1-4) ...
Setting up libhts1:armhf (1.3.2-2+rpi1) ...
Setting up libhts-dev:armhf (1.3.2-2+rpi1) ...
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.032-1) ...
Setting up debhelper (10.2.5) ...
Setting up sbuild-build-depends-bio-eagle-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-9) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.28-3 dpkg-dev_1.18.23 g++-6_6.3.0-11+rpi1 gcc-6_6.3.0-11+rpi1 libc6-dev_2.24-9 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-11+rpi1 libstdc++6_6.3.0-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.4 autoconf_2.69-10 automake_1:1.15-6 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.8+rpi1 base-passwd_3.5.43 bash_4.4-4 binutils_2.28-3 bsdmainutils_9.0.12 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4 cpp-6_6.3.0-11+rpi1 dash_0.5.8-2.4 debconf_1.5.60 debfoster_2.7-2.1 debhelper_10.2.5 debianutils_4.8.1 dh-autoreconf_14 dh-strip-nondeterminism_0.032-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.23 dpkg-dev_1.18.23 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.29-3 findutils_4.6.0+git+20161106-2 fuse2fs_1.43.4-2 g++_4:6.3.0-2 g++-6_6.3.0-11+rpi1 gcc_4:6.3.0-4 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.3.0-11+rpi1 gcc-6-base_6.3.0-11+rpi1 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gfortran_4:6.3.0-4 gfortran-6_6.3.0-11+rpi1 gnupg_2.1.18-6 gnupg-agent_2.1.18-6 gnupg-l10n_2.1.18-6 gpgv_2.1.18-6 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-5 init_1.47 init-system-helpers_1.47 initscripts_2.88dsf-59.9 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-2 libacl1_2.2.52-3 libapparmor1_2.11.0-3 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.4 libarchive-zip-perl_1.59-1 libasan1_4.9.3-14 libasan3_6.3.0-11+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblas-common_3.7.0-1 libblas-dev_3.7.0-1 libblas3_3.7.0-1 libblkid1_2.29.2-1 libboost-dev_1.62.0.1+b4 libboost-iostreams-dev_1.62.0.1+b4 libboost-iostreams1.62-dev_1.62.0+dfsg-4 libboost-iostreams1.62.0_1.62.0+dfsg-4 libboost-program-options-dev_1.62.0.1+b4 libboost-program-options1.62-dev_1.62.0+dfsg-4 libboost-program-options1.62.0_1.62.0+dfsg-4 libboost-regex1.62-dev_1.62.0+dfsg-4 libboost-regex1.62.0_1.62.0+dfsg-4 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-9 libc-dev-bin_2.24-9 libc6_2.24-9 libc6-dev_2.24-9 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.3.0-11+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-3 libcurl3-gnutls_7.52.1-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.16-1 libdebconfclient0_0.227 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.23 libdrm2_2.4.74-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.032-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.3.0-11+rpi1 libgcc1_1:6.3.0-11+rpi1 libgcrypt20_1.7.6-1 libgdbm3_1.8.3-14 libgfortran-6-dev_6.3.0-11+rpi1 libgfortran3_6.3.0-11+rpi1 libglib2.0-0_2.50.3-2 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.8-5 libgomp1_6.3.0-11+rpi1 libgpg-error0_1.26-2 libgssapi-krb5-2_1.15-1 libhogweed4_3.3-1 libhts-dev_1.3.2-2+rpi1 libhts1_1.3.2-2+rpi1 libicu-dev_57.1-5 libicu57_57.1-5 libidn11_1.33-1 libidn2-0_0.16-1 libip4tc0_1.6.0+snapshot20161117-5 libisl15_0.18-1 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libsigsegv2_2.10-5 libslang2_2.3.1-5 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-3 libss2_1.43.4-2 libssh2-1_1.7.0-1 libssl1.1_1.1.0e-1 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-11+rpi1 libstdc++6_6.3.0-11+rpi1 libsystemd0_232-22 libtasn1-6_4.10-1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libubsan0_6.3.0-11+rpi1 libudev1_232-22 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libxml2_2.9.4+dfsg1-2.2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.10-2 mawk_1.3.3-17 mount_2.29.2-1 multiarch-support_2.24-9 nano_2.7.4-1 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-4 patch_2.7.5-1 perl_5.24.1-2 perl-base_5.24.1-2 perl-modules-5.24_5.24.1-2 pinentry-curses_1.0.0-2 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-2 sbuild-build-depends-bio-eagle-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-22 systemd-sysv_232-22 sysv-rc_2.88dsf-59.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tzdata_2017b-1 udev_232-22 util-linux_2.29.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5

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


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

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Nov  2 21:02:15 2016 UTC
gpgv:                using RSA key 612EF1613E050F54
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bio-eagle_2.3-3.dsc
dpkg-source: info: extracting bio-eagle in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking bio-eagle_2.3.orig.tar.gz
dpkg-source: info: unpacking bio-eagle_2.3-3.debian.tar.xz
dpkg-source: info: applying Makefile_config.patch
dpkg-source: info: applying Fix_FTBFS.patch
dpkg-source: info: applying Clarify_license.patch

Check disc 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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-b9bc92df-79a4-40ce-9783-8bb68ad3c793
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

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

dpkg-buildpackage: info: source package bio-eagle
dpkg-buildpackage: info: source version 2.3-3
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build bio-eagle-2.3
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean --sourcedirectory=src
   dh_testdir -O--sourcedirectory=src
   dh_auto_clean -O--sourcedirectory=src
	make -j1 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -f *.o
rm -f eagle
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
   dh_clean -O--sourcedirectory=src
 debian/rules build-arch
dh build-arch --sourcedirectory=src
   dh_testdir -a -O--sourcedirectory=src
   dh_update_autotools_config -a -O--sourcedirectory=src
   dh_auto_configure -a -O--sourcedirectory=src
   dh_auto_build -a -O--sourcedirectory=src
	make -j1
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2  -o EagleMain.o -c EagleMain.cpp
EagleMain.cpp: In function 'void phaseWithRef(EAGLE::EagleParams&, Timer&, double, int, char**)':
EagleMain.cpp:108:17: warning: unused variable 'hapBitsTptr' [-Wunused-variable]
       HapBitsT *hapBitsTptr = NULL;
                 ^~~~~~~~~~~
EagleMain.cpp:109:17: warning: unused variable 'hapHedgePtr' [-Wunused-variable]
       HapHedge *hapHedgePtr = NULL;
                 ^~~~~~~~~~~
EagleMain.cpp:103:25: warning: unused variable 'timeImpMissing' [-Wunused-variable]
     double timeMN2 = 0, timeImpMissing = 0;
                         ^~~~~~~~~~~~~~
EagleMain.cpp: In function 'int main(int, char**)':
EagleMain.cpp:442:61: warning: unused variable 'timeImpMissing' [-Wunused-variable]
  double t23 = timer.get_time(); timer.update_time(); double timeImpMissing = 0;
                                                             ^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2  -o DipTreePBWT.o -c DipTreePBWT.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O2 -std=c++0x -fopenmp -Wall -Wdate-time -D_FORTIFY_SOURCE=2  -o Eagle.o -c Eagle.cpp
In file included from Eagle.cpp:43:0:
MemoryUtils.hpp:34:23: fatal error: xmmintrin.h: No such file or directory
 #include <xmmintrin.h>
                       ^
compilation terminated.
Makefile:99: recipe for target 'Eagle.o' failed
make[1]: *** [Eagle.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: make -j1 returned exit code 2
debian/rules:6: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2017-04-17T19:04:04Z

Finished
--------


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

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

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

Build Architecture: armhf
Build-Space: 0
Build-Time: 77
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 385
Job: bio-eagle_2.3-3
Machine Architecture: armhf
Package: bio-eagle
Package-Time: 511
Source-Version: 2.3-3
Space: 0
Status: failed
Version: 2.3-3
--------------------------------------------------------------------------------
Finished at 2017-04-17T19:04:04Z
Build needed 00:00:00, 0k disc space