Raspbian Package Auto-Building

Build log for bio-eagle (2.3-2) on armhf

bio-eagle2.3-2armhf → 2016-11-02 08:11:14

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01

+==============================================================================+
| bio-eagle 2.3-2 (armhf)                      Wed, 02 Nov 2016 07:56:16 +0000 |
+==============================================================================+

Package: bio-eagle
Version: 2.3-2
Source Version: 2.3-2
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-c7177a7b-5569-42b1-a451-686fa8ddb61c' 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 [9427 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.4 MB]
Fetched 20.8 MB in 23s (878 kB/s)
Reading package lists...

+------------------------------------------------------------------------------+
| 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 2.3-2 (dsc) [2126 B]
Get:2 http://172.17.0.1/private stretch-staging/main bio-eagle 2.3-2 (tar) [1626 kB]
Get:3 http://172.17.0.1/private stretch-staging/main bio-eagle 2.3-2 (diff) [6592 B]
Fetched 1635 kB in 0s (7362 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bio-eagle-eh6QWi/bio-eagle-2.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bio-eagle-eh6QWi' 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-oTrrhj/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-oTrrhj/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-oTrrhj/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-oTrrhj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Release.gpg [342 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Packages [434 B]
Fetched 2082 B in 0s (3404 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-oTrrhj/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user 'root' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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:
  dirmngr fuse2fs gnupg-l10n libffi6 libfuse2 libgnutls30 libhogweed4
  libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
  libsasl2-modules-db libssl1.0.2 libtasn1-6 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 5 not upgraded.
Need to get 764 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 764 B in 0s (20.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13152 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) ...

+------------------------------------------------------------------------------+
| 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-oTrrhj/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-oTrrhj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Release.gpg [342 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Sources [534 B]
Get:5 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Packages [615 B]
Fetched 2454 B in 0s (3575 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-oTrrhj/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user 'root' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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:
  dirmngr fuse2fs gnupg-l10n libfuse2 libsasl2-modules manpages
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-iostreams1.61-dev libboost-iostreams1.61.0
  libboost-program-options-dev libboost-program-options1.61-dev
  libboost-program-options1.61.0 libboost-regex1.61-dev libboost-regex1.61.0
  libboost1.61-dev libbsd0 libcroco3 libcurl3-gnutls
  libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
  libgssapi-krb5-2 libhts-dev libhts1 libicu-dev libicu57 libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libnghttp2-14
  libopenblas-base libopenblas-dev libpipeline1 librtmp1 libsigsegv2 libssh2-1
  libtimedate-perl libtool libunistring0 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-man
  liblapack-doc libboost-doc libboost1.61-doc libboost-atomic1.61-dev
  libboost-chrono1.61-dev libboost-context1.61-dev libboost-coroutine1.61-dev
  libboost-date-time1.61-dev libboost-exception1.61-dev
  libboost-filesystem1.61-dev libboost-graph1.61-dev
  libboost-graph-parallel1.61-dev libboost-locale1.61-dev libboost-log1.61-dev
  libboost-math1.61-dev libboost-mpi1.61-dev libboost-mpi-python1.61-dev
  libboost-python1.61-dev libboost-random1.61-dev
  libboost-serialization1.61-dev libboost-signals1.61-dev
  libboost-system1.61-dev libboost-test1.61-dev libboost-thread1.61-dev
  libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev
  libmpfrc++-dev libntl-dev krb5-doc krb5-user icu-doc libtool-doc gcj-jdk
  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 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-iostreams1.61-dev libboost-iostreams1.61.0
  libboost-program-options-dev libboost-program-options1.61-dev
  libboost-program-options1.61.0 libboost-regex1.61-dev libboost-regex1.61.0
  libboost1.61-dev libbsd0 libcroco3 libcurl3-gnutls
  libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
  libgssapi-krb5-2 libhts-dev libhts1 libicu-dev libicu57 libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 libmagic-mgc libmagic1 libnghttp2-14
  libopenblas-base libopenblas-dev libpipeline1 librtmp1 libsigsegv2 libssh2-1
  libtimedate-perl libtool libunistring0 libxml2 m4 man-db po-debconf
  sbuild-build-depends-bio-eagle-dummy zlib1g-dev
0 upgraded, 64 newly installed, 0 to remove and 5 not upgraded.
Need to get 54.0 MB of archives.
After this operation, 305 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-oTrrhj/apt_archive ./ sbuild-build-depends-bio-eagle-dummy 0.invalid.0 [812 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 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 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-2 [57.5 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-2 [110 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.3+dfsg-2 [262 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.3+dfsg-2 [131 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-2+rpi1 [2523 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.0-6+rpi1 [165 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.2.0-6+rpi1 [199 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.2.0-6+rpi1 [5405 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.1.1-1 [1370 B]
Get:41 http://172.17.0.1/private stretch-staging/main armhf icu-devtools armhf 57.1-4 [156 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.1-2 [13.9 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-2 [112 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.1-2 [18.9 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libboost1.61-dev armhf 1.61.0+dfsg-3 [6843 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.61.0.2 [3758 B]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libboost-regex1.61.0 armhf 1.61.0+dfsg-3 [233 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libicu-dev armhf 57.1-4 [15.7 MB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libboost-regex1.61-dev armhf 1.61.0+dfsg-3 [324 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams1.61.0 armhf 1.61.0+dfsg-3 [48.5 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams1.61-dev armhf 1.61.0+dfsg-3 [57.7 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libboost-iostreams-dev armhf 1.61.0.2 [3392 B]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.61.0 armhf 1.61.0+dfsg-3 [136 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options1.61-dev armhf 1.61.0+dfsg-3 [178 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libboost-program-options-dev armhf 1.61.0.2 [3416 B]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.16.0-1 [72.5 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.50.1-1 [248 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.1-3+rpi1 [216 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3.1-3+rpi1 [270 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libopenblas-base armhf 0.2.19-1+rpi1 [1847 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libopenblas-dev armhf 0.2.19-1+rpi1 [1732 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.24-5+rpi1) ...

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

Kernel: Linux 4.6.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27-9 dpkg-dev_1.18.10 g++-6_6.2.0-6+rpi1 gcc-6_6.2.0-6+rpi1 libc6-dev_2.24-5+rpi1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3.1 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.27-9 bsdmainutils_9.0.12 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.2.0-6+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-4 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-1 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.0-6+rpi1 gcc_4:6.1.1-1 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_6.2.0-6+rpi1 gcc-6-base_6.2.0-6+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.1.1-1 gfortran-6_6.2.0-6+rpi1 gnupg_2.1.15-4 gnupg-agent_2.1.15-4 gnupg-l10n_2.1.15-4 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libc6_2.24-5+rpi1 libc6-dev_2.24-5+rpi1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.0-6+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-5 libcurl3-gnutls_7.50.1-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.12-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.71-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-6+rpi1 libgcc1_1:6.2.0-6+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran-6-dev_6.2.0-6+rpi1 libgfortran3_6.2.0-6+rpi1 libglib2.0-0_2.50.0-2+rpi1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.5-2 libgomp1_6.2.0-6+rpi1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-2 libhogweed4_3.3-1 libhts-dev_1.3.1-3+rpi1 libhts1_1.3.1-3+rpi1 libicu-dev_57.1-4 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b3 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-1 libmagic1_1:5.29-1 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnghttp2-14_1.16.0-1 libnpth0_1.2-3 libopenblas-base_0.2.19-1+rpi1 libopenblas-dev_0.2.19-1+rpi1 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-2 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2j-1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 libsystemd0_231-9 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.0-6+rpi1 libudev1_231-9 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libxml2_2.9.4+dfsg1-2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.08-1 mawk_1.3.3-17 mount_2.28.2-1 multiarch-support_2.24-5+rpi1 nano_2.7.0-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-6 po-debconf_1.0.20 procps_2:3.3.12-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-bio-eagle-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-9 systemd-sysv_231-9 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016h-1 udev_231-9 util-linux_2.28.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1

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


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

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Oct 27 20:04:48 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_2.3-2.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_2.3-2.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-c7177a7b-5569-42b1-a451-686fa8ddb61c
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 2.3-2
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>>=. -fPIE -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
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12:0,
                 from /usr/include/boost/iostreams/detail/resolve.hpp:26,
                 from /usr/include/boost/iostreams/detail/push.hpp:24,
                 from /usr/include/boost/iostreams/filtering_stream.hpp:19,
                 from FileUtils.hpp:28,
                 from GenoData.hpp:28,
                 from Eagle.hpp:30,
                 from EagleMain.cpp:30:
/usr/include/boost/type_traits/detail/bool_trait_def.hpp:18:79: note: #pragma message: NOTE: Use of this header (bool_trait_def.hpp) is deprecated
 # pragma message("NOTE: Use of this header (bool_trait_def.hpp) is deprecated")
                                                                               ^
In file included from /usr/include/boost/type_traits/detail/bool_trait_def.hpp:21:0,
                 from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:12,
                 from /usr/include/boost/iostreams/detail/resolve.hpp:26,
                 from /usr/include/boost/iostreams/detail/push.hpp:24,
                 from /usr/include/boost/iostreams/filtering_stream.hpp:19,
                 from FileUtils.hpp:28,
                 from GenoData.hpp:28,
                 from Eagle.hpp:30,
                 from EagleMain.cpp:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
In file included from /usr/include/boost/iostreams/detail/is_dereferenceable.hpp:13:0,
                 from /usr/include/boost/iostreams/detail/resolve.hpp:26,
                 from /usr/include/boost/iostreams/detail/push.hpp:24,
                 from /usr/include/boost/iostreams/filtering_stream.hpp:19,
                 from FileUtils.hpp:28,
                 from GenoData.hpp:28,
                 from Eagle.hpp:30,
                 from EagleMain.cpp:30:
/usr/include/boost/type_traits/detail/template_arity_spec.hpp:13:84: note: #pragma message: NOTE: Use of this header (template_arity_spec.hpp) is deprecated
 # pragma message("NOTE: Use of this header (template_arity_spec.hpp) is deprecated")
                                                                                    ^
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>>=. -fPIE -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>>=. -fPIE -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 2016-11-02T08:06:56Z

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: 79
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 508
Job: bio-eagle_2.3-2
Machine Architecture: armhf
Package: bio-eagle
Package-Time: 640
Source-Version: 2.3-2
Space: 0
Status: failed
Version: 2.3-2
--------------------------------------------------------------------------------
Finished at 2016-11-02T08:06:56Z
Build needed 00:00:00, 0k disc space