Raspbian Package Auto-Building

Build log for bio-eagle (2.3.4-1) on armhf

bio-eagle2.3.4-1armhf → 2017-07-31 19:49:20

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03

+==============================================================================+
| bio-eagle 2.3.4-1 (armhf)                    Mon, 31 Jul 2017 19:35:16 +0000 |
+==============================================================================+

Package: bio-eagle
Version: 2.3.4-1
Source Version: 2.3.4-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-81a472ea-b032-47df-ad6f-461bce399a4a' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [11.9 MB]
Fetched 22.0 MB in 24s (887 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 1636 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main bio-eagle 2.3.4-1 (dsc) [2150 B]
Get:2 http://172.17.0.1/private buster-staging/main bio-eagle 2.3.4-1 (tar) [1627 kB]
Get:3 http://172.17.0.1/private buster-staging/main bio-eagle 2.3.4-1 (diff) [6696 B]
Fetched 1636 kB in 0s (4433 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bio-eagle-hVAamG/bio-eagle-2.3.4' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bio-eagle-hVAamG' 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-gFYown/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-gFYown/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-gFYown/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-gFYown/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-gFYown/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-gFYown/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-gFYown/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-gFYown/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (2890 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:
  ca-certificates libssl1.1 openssl
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 13 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-gFYown/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 ... 14837 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 (>= 10), libopenblas-dev, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev (>= 1.4), zlib1g-dev
Filtered Build-Depends: debhelper (>= 10), libopenblas-dev, libboost-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev (>= 1.4), zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-bio-eagle-dummy' in '/<<BUILDDIR>>/resolver-gFYown/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-gFYown/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-gFYown/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-gFYown/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-gFYown/apt_archive ./ Sources [538 B]
Get:5 copy:/<<BUILDDIR>>/resolver-gFYown/apt_archive ./ Packages [621 B]
Fetched 2492 B in 0s (3372 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:
  ca-certificates openssl
Use 'apt autoremove' to remove them.
The following additional 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
  libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
  libgssapi-krb5-2 libhts-dev libhts2 libicu-dev libicu57 libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
  libmagic-mgc libmagic1 libnghttp2-14 libopenblas-base libopenblas-dev
  libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
  libssh2-1 libtimedate-perl libtool libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc
  gfortran-6-doc libgfortran3-dbg libcoarrays-dev groff 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 krb5-doc krb5-user icu-doc
  libtool-doc gcj-jdk m4-doc less www-browser libmail-box-perl
Recommended packages:
  curl | wget | lynx-cur libarchive-cpio-perl 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
  libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
  libgssapi-krb5-2 libhts-dev libhts2 libicu-dev libicu57 libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
  libmagic-mgc libmagic1 libnghttp2-14 libopenblas-base libopenblas-dev
  libpipeline1 libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2
  libssh2-1 libtimedate-perl libtool libxml2 m4 man-db po-debconf
  sbuild-build-depends-bio-eagle-dummy zlib1g-dev
0 upgraded, 68 newly installed, 0 to remove and 13 not upgraded.
Need to get 54.7 MB of archives.
After this operation, 310 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-gFYown/apt_archive ./ sbuild-build-depends-bio-eagle-dummy 0.invalid.0 [830 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-1 [95.7 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.30-1 [105 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2+b1 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.1-2 [58.4 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.1-2 [115 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.1-2 [265 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [132 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3 [66.9 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3 [98.1 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libldap-common all 2.4.45+dfsg-1 [87.0 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libldap-2.4-2 armhf 2.4.45+dfsg-1 [197 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3 [601 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2 [736 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.52.3-1 [2576 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2+b1 [1220 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.6.4 [970 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libgfortran3 armhf 6.4.0-1+rpi1 [166 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libgfortran-6-dev armhf 6.4.0-1+rpi1 [199 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf gfortran-6 armhf 6.4.0-1+rpi1 [5420 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:6.3.0-4d1 [1358 B]
Get:44 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 57.1-6 [156 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libblas-common armhf 3.7.1-1 [14.6 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.7.1-1 [108 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-1 [118 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b6 [3916 B]
Get:50 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-4 [232 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 57.1-6 [15.8 MB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-4 [325 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-4 [48.7 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-4 [57.7 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b6 [3694 B]
Get:56 http://172.17.0.1/private buster-staging/main armhf libboost-program-options1.62.0 armhf 1.62.0+dfsg-4 [136 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libboost-program-options1.62-dev armhf 1.62.0+dfsg-4 [178 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libboost-program-options-dev armhf 1.62.0.1+b6 [3712 B]
Get:59 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.24.0-1 [70.4 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.17.0-5 [42.0 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.52.1-5 [259 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.4.1-5 [247 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.4.1-5 [338 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libopenblas-base armhf 0.2.19-3+rpi1 [1978 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libopenblas-dev armhf 0.2.19-3+rpi1 [1847 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
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Setting up libopenblas-base (0.2.19-3+rpi1) ...
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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 (6.4.0-1+rpi1) ...
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Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libk5crypto3:armhf (1.15.1-2) ...
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update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
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Setting up libboost-iostreams-dev:armhf (1.62.0.1+b6) ...
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Setting up libopenblas-dev (0.2.19-3+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 libgssapi-krb5-2:armhf (1.15.1-2) ...
Setting up libcurl3-gnutls:armhf (7.52.1-5) ...
Setting up libhts2:armhf (1.4.1-5) ...
Setting up libhts-dev:armhf (1.4.1-5) ...
Setting up dh-autoreconf (14) ...
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Setting up debhelper (10.6.4) ...
Setting up sbuild-build-depends-bio-eagle-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-12) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1+rpi1 gcc-6_6.4.0-1+rpi1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.5~beta1+b3 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1+rpi1 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.6.4 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-4d1 g++-6_6.4.0-1+rpi1 gcc_4:6.3.0-4d1 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-5-base_5.4.1-4 gcc-6_6.4.0-1+rpi1 gcc-6-base_6.4.0-1+rpi1 gcc-7-base_7.1.0-9+rpi1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gfortran_4:6.3.0-4d1 gfortran-6_6.4.0-1+rpi1 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gpgv_2.1.18-8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-6 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-6 libapt-pkg5.0_1.5~beta1+b3 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1+rpi1 libassuan0_2.4.3-2 libatomic1_7.1.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1 libblas-common_3.7.1-1 libblas-dev_3.7.1-1 libblas3_3.7.1-1 libblkid1_2.29.2-2+rpi1 libboost-dev_1.62.0.1+b6 libboost-iostreams-dev_1.62.0.1+b6 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+b6 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_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-9+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libcurl3-gnutls_7.52.1-5 libdb5.3_5.3.28-12 libdbus-1-3_1.10.20-1 libdebconfclient0_0.229 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.81-2+rpi1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-1+rpi1 libgcc1_1:7.1.0-9+rpi1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libgfortran-6-dev_6.4.0-1+rpi1 libgfortran3_6.4.0-1+rpi1 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-2 libgomp1_7.1.0-9+rpi1 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libhogweed4_3.3-1 libhts-dev_1.4.1-5 libhts2_1.4.1-5 libicu-dev_57.1-6 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2 libisl15_0.18-1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1 libnghttp2-14_1.24.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libopenblas-base_0.2.19-3+rpi1 libopenblas-dev_0.2.19-3+rpi1 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-7 libperl5.26_5.26.0-4 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-3 libpsl5_0.17.0-5 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-2+rpi1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 libsystemd0_233-10 libtasn1-6_4.12-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.1.0-9+rpi1 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2+rpi1 libxml2_2.9.4+dfsg1-3 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 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 mawk_1.3.3-17 mount_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-12 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-4 perl-base_5.26.0-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-4 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 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+nmu1 systemd_233-10 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 tzdata_2017b-2 udev_233-10 util-linux_2.29.2-2+rpi1 xz-utils_5.2.2-1.3 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 Mon Jul 24 19:38:33 2017 UTC
gpgv:                using RSA key 612EF1613E050F54
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bio-eagle_2.3.4-1.dsc
dpkg-source: info: extracting bio-eagle in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking bio-eagle_2.3.4.orig.tar.gz
dpkg-source: info: unpacking bio-eagle_2.3.4-1.debian.tar.xz
dpkg-source: info: applying Makefile_config.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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-81a472ea-b032-47df-ad6f-461bce399a4a
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 2.3.4-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build bio-eagle-2.3.4
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 -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
rm -f *.o
rm -f eagle
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
   dh_autoreconf_clean -O--sourcedirectory=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_autoreconf -a -O--sourcedirectory=src
   dh_auto_configure -a -O--sourcedirectory=src
   dh_auto_build -a -O--sourcedirectory=src
	make -j4
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
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
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 EagleImpMiss.o -c EagleImpMiss.cpp
In file included from EagleImpMiss.cpp:24:0:
MemoryUtils.hpp:34:23: fatal error: xmmintrin.h: No such file or directory
 #include <xmmintrin.h>
                       ^
compilation terminated.
Makefile:99: recipe for target 'EagleImpMiss.o' failed
make[1]: *** [EagleImpMiss.o] Error 1
make[1]: *** Waiting for unfinished jobs....
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
EagleMain.cpp: In function 'void phaseWithRef(EAGLE::EagleParams&, Timer&, double, int, char**)':
EagleMain.cpp:109:17: warning: unused variable 'hapBitsTptr' [-Wunused-variable]
       HapBitsT *hapBitsTptr = NULL;
                 ^~~~~~~~~~~
EagleMain.cpp:110:17: warning: unused variable 'hapHedgePtr' [-Wunused-variable]
       HapHedge *hapHedgePtr = NULL;
                 ^~~~~~~~~~~
EagleMain.cpp:104:25: warning: unused variable 'timeImpMissing' [-Wunused-variable]
     double timeMN2 = 0, timeImpMissing = 0;
                         ^~~~~~~~~~~~~~
EagleMain.cpp: In function 'int main(int, char**)':
EagleMain.cpp:445:61: warning: unused variable 'timeImpMissing' [-Wunused-variable]
  double t23 = timer.get_time(); timer.update_time(); double timeImpMissing = 0;
                                                             ^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
                 from DipTreePBWT.cpp:23:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
                 from /usr/include/c++/6/algorithm:62,
                 from DipTreePBWT.cpp:23:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >; _Distance = int; _Tp = EAGLE::DipTreeNode; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
                 from DipTreePBWT.cpp:23:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'void EAGLE::DipTree::advance()':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
    std::__introsort_loop(__first, __last,
    ^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<EAGLE::DipTreeNode*, std::vector<EAGLE::DipTreeNode> >' will change in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ^~~
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
dh_auto_build: make -j4 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 2017-07-31T19:45:12Z

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: 50
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 500
Job: bio-eagle_2.3.4-1
Machine Architecture: armhf
Package: bio-eagle
Package-Time: 596
Source-Version: 2.3.4-1
Space: 0
Status: failed
Version: 2.3.4-1
--------------------------------------------------------------------------------
Finished at 2017-07-31T19:45:12Z
Build needed 00:00:00, 0k disc space