nanopolish →
0.5.0-1+b1 →
armhf → 2016-12-05 09:24:05
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| nanopolish 0.5.0-1+b1 (armhf) Mon, 05 Dec 2016 09:08:21 +0000 |
+==============================================================================+
Package: nanopolish
Version: 0.5.0-1+b1
Source Version: 0.5.0-1
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-e115bef3-aa82-4757-9de9-919b5147533e' 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 [9566 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.5 MB]
Fetched 21.1 MB in 26s (803 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: 'nanopolish' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/nanopolish.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/nanopolish.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1742 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main nanopolish 0.5.0-1 (dsc) [2011 B]
Get:2 http://172.17.0.1/private stretch-staging/main nanopolish 0.5.0-1 (tar) [1734 kB]
Get:3 http://172.17.0.1/private stretch-staging/main nanopolish 0.5.0-1 (diff) [6332 B]
Fetched 1742 kB in 0s (2974 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/nanopolish-TWGp2u/nanopolish-0.5.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/nanopolish-TWGp2u' 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-96obi0/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-96obi0/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-96obi0/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-96obi0/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-96obi0/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-96obi0/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-96obi0/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-96obi0/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (3465 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 kbd libfuse2 manpages netbase psmisc
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 12 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-96obi0/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 ... 13236 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev
Filtered Build-Depends: debhelper (>= 9), zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev
dpkg-deb: building package 'sbuild-build-depends-nanopolish-dummy' in '/<<BUILDDIR>>/resolver-96obi0/apt_archive/sbuild-build-depends-nanopolish-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-nanopolish-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-96obi0/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-96obi0/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-96obi0/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-96obi0/apt_archive ./ Sources [515 B]
Get:5 copy:/<<BUILDDIR>>/resolver-96obi0/apt_archive ./ Packages [597 B]
Fetched 2445 B in 0s (3944 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install nanopolish 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 kbd libfuse2 manpages netbase psmisc
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 groff-base
hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libbsd0
libcroco3 libcurl3-gnutls libeigen3-dev libfast5-dev libffi6
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgnutls30
libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhogweed4
libhts-dev libhts1 libicu57 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2
libldap-common libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0
libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1
libssl1.1 libsz2 libtasn1-6 libtimedate-perl libtool libunistring0 libxml2
m4 man-db pkg-config po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libeigen3-doc libmrpt-dev gnutls-bin krb5-doc krb5-user libhdf5-doc
libtool-doc gfortran | fortran95-compiler 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 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 groff-base
hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libbsd0
libcroco3 libcurl3-gnutls libeigen3-dev libfast5-dev libffi6
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgnutls30
libgssapi-krb5-2 libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhogweed4
libhts-dev libhts1 libicu57 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2
libldap-common libmagic-mgc libmagic1 libnettle6 libnghttp2-14 libp11-kit0
libpipeline1 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1
libssl1.1 libsz2 libtasn1-6 libtimedate-perl libtool libunistring0 libxml2
m4 man-db pkg-config po-debconf sbuild-build-depends-nanopolish-dummy
zlib1g-dev
0 upgraded, 68 newly installed, 0 to remove and 12 not upgraded.
Need to get 28.0 MB/28.6 MB of archives.
After this operation, 97.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-96obi0/apt_archive ./ sbuild-build-depends-nanopolish-dummy 0.invalid.0 [800 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 2.7.5-2 [971 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libssl1.1 armhf 1.1.0c-2 [1101 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.5.6-7 [760 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.15~beta1-1 [57.6 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.15~beta1-1 [114 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.15~beta1-1 [263 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.15~beta1-1 [131 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-1 [66.7 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-1 [97.9 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libldap-common all 2.4.44+dfsg-1+rpi1 [84.3 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-1+rpi1 [194 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-5 [7427 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.1 [804 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-5 [733 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.2-2 [2527 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-1 [35.7 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.17.0-1 [70.1 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.50.1-1 [248 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.0-13+rpi1 [166 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-1 [1201 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-1 [118 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-1 [2093 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libfast5-dev all 0.5.8-1 [23.3 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.2-1+rpi1 [215 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3.2-1+rpi1 [270 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libeigen3-dev all 3.3.0-1 [834 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking dh-strip-nondeterminism (0.028-1) ...
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Unpacking sbuild-build-depends-nanopolish-dummy (0.invalid.0) ...
Setting up libnettle6:armhf (3.3-1) ...
Setting up libaec0:armhf (0.3.2-1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.1-2) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.17.0-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up libldap-common (2.4.44+dfsg-1+rpi1) ...
Setting up libgfortran3:armhf (6.2.0-13+rpi1) ...
Setting up groff-base (1.22.3-8) ...
Setting up libsasl2-modules-db:armhf (2.1.27~101-g0780600+dfsg-1) ...
Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-1) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-5) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.1) ...
Setting up libtasn1-6:armhf (4.9-4) ...
Setting up libmagic-mgc (1:5.29-1) ...
Setting up libmagic1:armhf (1:5.29-1) ...
Setting up libhogweed4:armhf (3.3-1) ...
Setting up libssh2-1:armhf (1.7.0-1) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libssl1.1:armhf (1.1.0c-2) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.1-2) ...
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
Setting up hdf5-helpers (1.10.0-patch1+docs-1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libsz2:armhf (0.3.2-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up libhdf5-100:armhf (1.10.0-patch1+docs-1) ...
Setting up libglib2.0-0:armhf (2.50.2-2) ...
No schema files found: doing nothing.
Setting up libaec-dev:armhf (0.3.2-1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.29-1) ...
Setting up libkrb5support0:armhf (1.15~beta1-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up pkg-config (0.29-4) ...
Setting up libjpeg-dev (1:1.5.1-2) ...
Setting up libp11-kit0:armhf (0.23.2-5) ...
Setting up automake (1:1.15-5) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.15~beta1-1) ...
Setting up libhdf5-cpp-100:armhf (1.10.0-patch1+docs-1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libeigen3-dev (3.3.0-1) ...
Setting up libgnutls30:armhf (3.5.6-7) ...
Setting up libhdf5-dev (1.10.0-patch1+docs-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
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-1+rpi1) ...
Setting up libkrb5-3:armhf (1.15~beta1-1) ...
Setting up libfast5-dev (0.5.8-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libgssapi-krb5-2:armhf (1.15~beta1-1) ...
Setting up libcurl3-gnutls:armhf (7.50.1-1) ...
Setting up libhts1:armhf (1.3.2-1+rpi1) ...
Setting up libhts-dev:armhf (1.3.2-1+rpi1) ...
Setting up dh-autoreconf (12) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.2) ...
Setting up sbuild-build-depends-nanopolish-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27.51.20161127-1 dpkg-dev_1.18.15 g++-6_6.2.0-13+rpi1 gcc-6_6.2.0-13+rpi1 libc6-dev_2.24-5+rpi1 libstdc++-6-dev_6.2.0-13+rpi1 libstdc++6_6.2.0-13+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_1:1.15-5 autopoint_0.19.8.1-1 autotools-dev_20161112.1 base-files_9.6+rpi1 base-passwd_3.5.41 bash_4.4-2 binutils_2.27.51.20161127-1 bsdmainutils_9.0.12 bsdutils_1:2.29-1 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_6.2.0-13+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8.1 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dmsetup_2:1.02.136-1 dpkg_1.18.15 dpkg-dev_1.18.15 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-1 findutils_4.6.0+git+20161106-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.0-13+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_6.2.0-13+rpi1 gcc-6-base_6.2.0-13+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.16-2 gnupg-agent_2.1.16-2 gnupg-l10n_2.1.16-2 gpgv_2.1.16-2 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-1 hostname_3.18 init_1.46 init-system-helpers_1.46 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_23-1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.10.95-6 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-13+rpi1 libassuan0_2.4.3-2 libatomic1_6.2.0-13+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblkid1_2.29-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-5+rpi1 libc-dev-bin_2.24-5+rpi1 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_6.2.0-13+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.3-2 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_2:1.02.136-1 libdpkg-perl_1.18.15 libdrm2_2.4.73-1 libeigen3-dev_3.3.0-1 libfakeroot_1.21-2 libfast5-dev_0.5.8-1 libfdisk1_2.29-1 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_6.2.0-13+rpi1 libgcc1_1:6.2.0-13+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran3_6.2.0-13+rpi1 libglib2.0-0_2.50.2-2 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.6-7 libgomp1_6.2.0-13+rpi1 libgpg-error0_1.25-1 libgssapi-krb5-2_1.15~beta1-1 libhdf5-100_1.10.0-patch1+docs-1 libhdf5-cpp-100_1.10.0-patch1+docs-1 libhdf5-dev_1.10.0-patch1+docs-1 libhogweed4_3.3-1 libhts-dev_1.3.2-1+rpi1 libhts1_1.3.2-1+rpi1 libicu57_57.1-5 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libjpeg-dev_1:1.5.1-2 libjpeg62-turbo_1:1.5.1-2 libjpeg62-turbo-dev_1:1.5.1-2 libk5crypto3_1.15~beta1-1 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_23-1 libkrb5-3_1.15~beta1-1 libkrb5support0_1.15~beta1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-1+rpi1 libldap-common_2.4.44+dfsg-1+rpi1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-1 libmagic1_1:5.29-1 libmount1_2.29-1 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_1.17.0-1 libnpth0_1.2-3 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 libplymouth4_0.9.2-3 libpng12-0_1.2.54-6 libprocps6_2:3.3.12-3 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-1 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-1 libsemanage1_2.6-1 libsepol1_2.6-1 libsigsegv2_2.10-5 libsmartcols1_2.29-1 libsqlite3-0_3.15.1-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.1_1.1.0c-2 libstdc++-6-dev_6.2.0-13+rpi1 libstdc++6_6.2.0-13+rpi1 libsystemd0_232-6 libsz2_0.3.2-1 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.2.0-13+rpi1 libudev1_232-6 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_2.29-1 libxml2_2.9.4+dfsg1-2.1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20161101+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-2 manpages_4.08-1 mawk_1.3.3-17 mount_2.29-1 multiarch-support_2.24-5+rpi1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 netbase_5.3 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_0.9.7-9 pkg-config_0.29-4 po-debconf_1.0.20 procps_2:3.3.12-3 psmisc_22.21-2.1 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-nanopolish-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-6 systemd-sysv_232-6 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1.1 tzdata_2016i-1 udev_232-6 util-linux_2.29-1 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 Fri Aug 12 07:07:36 2016 UTC
gpgv: using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./nanopolish_0.5.0-1.dsc
dpkg-source: info: extracting nanopolish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking nanopolish_0.5.0.orig.tar.gz
dpkg-source: info: unpacking nanopolish_0.5.0-1.debian.tar.xz
dpkg-source: info: applying adjust-include-path.patch
dpkg-source: info: applying compiler-flags.patch
dpkg-source: info: applying external-libs.patch
dpkg-source: info: applying add-shebang-to-script.patch
dpkg-source: info: applying fix-ftbfs-with-gcc6.patch
dpkg-source: info: applying reproducible.patch
dpkg-source: info: applying fast5-0.5.6.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 0.5.0-1+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=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-e115bef3-aa82-4757-9de9-919b5147533e
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package nanopolish
dpkg-buildpackage: info: source version 0.5.0-1+b1
dpkg-buildpackage: info: source distribution stretch-staging
dpkg-source --before-build nanopolish-0.5.0
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Makefile:94: .depend: No such file or directory
rm -f ./.depend
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_common.cpp src/common/nanopolish_fast5_map.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_model_names.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_pore_model_set.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_transition_parameters.cpp src/nanopolish_call_variants.cpp src/nanopolish_consensus.cpp src/nanopolish_getmodel.cpp src/nanopolish_haplotype.cpp src/nanopolish_methyltest.cpp src/nanopolish_methyltrain.cpp src/nanopolish_poremodel.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/training_core.cpp src/thirdparty/stdaln.c > ./.depend;
rm -f nanopolish nanopolish_test src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_common.o src/common/nanopolish_fast5_map.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_model_names.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_pore_model_set.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_transition_parameters.o src/nanopolish_call_variants.o src/nanopolish_consensus.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_methyltest.o src/nanopolish_methyltrain.o src/nanopolish_poremodel.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/training_core.o src/thirdparty/stdaln.o src/main/nanopolish.o src/test/nanopolish_test.o
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f .depend
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean -O--parallel
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
dh_auto_configure -a -O--parallel
dh_auto_build -a -O--parallel
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Makefile:94: .depend: No such file or directory
rm -f ./.depend
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_common.cpp src/common/nanopolish_fast5_map.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_model_names.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_pore_model_set.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_transition_parameters.cpp src/nanopolish_call_variants.cpp src/nanopolish_consensus.cpp src/nanopolish_getmodel.cpp src/nanopolish_haplotype.cpp src/nanopolish_methyltest.cpp src/nanopolish_methyltrain.cpp src/nanopolish_poremodel.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/training_core.cpp src/thirdparty/stdaln.c > ./.depend;
g++ -o src/main/nanopolish.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/main/nanopolish.cpp
g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/alignment/nanopolish_alignment_db.cpp
g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/alignment/nanopolish_anchor.cpp
g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/alignment/nanopolish_eventalign.cpp
src/alignment/nanopolish_eventalign.cpp: In function 'void emit_sam_header(samFile*, const bam_hdr_t*)':
src/alignment/nanopolish_eventalign.cpp:225:27: warning: ignoring return value of 'int sam_hdr_write(samFile*, const bam_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_hdr_write(fp, hdr);
^
src/alignment/nanopolish_eventalign.cpp: In function 'void emit_event_alignment_sam(htsFile*, const SquiggleRead&, const bam_hdr_t*, const bam1_t*, const std::vector<EventAlignment>&)':
src/alignment/nanopolish_eventalign.cpp:364:43: warning: ignoring return value of 'int sam_write1(samFile*, const bam_hdr_t*, const bam1_t*)', declared with attribute warn_unused_result [-Wunused-result]
sam_write1(fp, base_hdr, event_record);
^
g++ -o src/common/logsum.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/common/logsum.cpp
g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/common/nanopolish_alphabet.cpp
In file included from src/common/nanopolish_alphabet.cpp:10:0:
src/common/nanopolish_alphabet.h:237:29: warning: inline function 'virtual bool Alphabet::contains_all(const char*) const' used but never defined
virtual inline bool contains_all(const char *bases) const = 0;
^~~~~~~~~~~~
g++ -o src/common/nanopolish_common.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/common/nanopolish_common.cpp
g++ -o src/common/nanopolish_fast5_map.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/common/nanopolish_fast5_map.cpp
g++ -o src/common/nanopolish_iupac.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/common/nanopolish_iupac.cpp
g++ -o src/common/nanopolish_klcs.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/common/nanopolish_klcs.cpp
g++ -o src/common/nanopolish_model_names.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/common/nanopolish_model_names.cpp
g++ -o src/common/nanopolish_variant.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/common/nanopolish_variant.cpp
g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/hmm/nanopolish_duration_model.cpp
g++ -o src/hmm/nanopolish_pore_model_set.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/hmm/nanopolish_pore_model_set.cpp
g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/hmm/nanopolish_profile_hmm.cpp
g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/hmm/nanopolish_transition_parameters.cpp
g++ -o src/nanopolish_call_variants.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_call_variants.cpp
g++ -o src/nanopolish_consensus.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_consensus.cpp
g++ -o src/nanopolish_getmodel.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_getmodel.cpp
g++ -o src/nanopolish_haplotype.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_haplotype.cpp
g++ -o src/nanopolish_methyltest.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_methyltest.cpp
g++ -o src/nanopolish_methyltrain.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_methyltrain.cpp
g++ -o src/nanopolish_poremodel.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_poremodel.cpp
g++ -o src/nanopolish_scorereads.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_scorereads.cpp
g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_squiggle_read.cpp
g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp
g++ -o src/training_core.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/training_core.cpp
gcc -o src/thirdparty/stdaln.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fPIC src/thirdparty/stdaln.c
g++ -o src/test/nanopolish_test.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/test/nanopolish_test.cpp
g++ -o nanopolish -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_common.o src/common/nanopolish_fast5_map.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_model_names.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_pore_model_set.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_transition_parameters.o src/nanopolish_call_variants.o src/nanopolish_consensus.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_methyltest.o src/nanopolish_methyltrain.o src/nanopolish_poremodel.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/training_core.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
g++ -o nanopolish_test -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -O3 -std=c++11 -fopenmp -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I./fast5 -I./src -I./src/hmm -I./src/thirdparty -I./src/common -I./src/alignment -fPIC src/test/nanopolish_test.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_common.o src/common/nanopolish_fast5_map.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_model_names.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_pore_model_set.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_transition_parameters.o src/nanopolish_call_variants.o src/nanopolish_consensus.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_methyltest.o src/nanopolish_methyltrain.o src/nanopolish_poremodel.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/training_core.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a -O--parallel
make -j4 test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
./nanopolish_test
===============================================================================
All tests passed (421 assertions in 4 test cases)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
dh_auto_install -a -O--parallel
dh_install -a -O--parallel
dh_installdocs -a -O--parallel
dh_installchangelogs -a -O--parallel
dh_installexamples -a -O--parallel
dh_installman -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
dh_fixperms -a -O--parallel
dh_strip -a -O--parallel
dh_makeshlibs -a -O--parallel
dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: debian/nanopolish/usr/lib/nanopolish/nanopolish_test contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/nanopolish/usr/bin/nanopolish contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/nanopolish/usr/lib/nanopolish/nanopolish_test debian/nanopolish/usr/bin/nanopolish were not linked against librt.so.1 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package nanopolish: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package nanopolish: unused substitution variable ${perl:Depends}
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package 'nanopolish-dbgsym' in '../nanopolish-dbgsym_0.5.0-1+b1_armhf.deb'.
dpkg-deb: building package 'nanopolish' in '../nanopolish_0.5.0-1+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../nanopolish_0.5.0-1+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build nanopolish-0.5.0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-12-05T09:23:55Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
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+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
nanopolish_0.5.0-1+b1_armhf.changes:
------------------------------------
Format: 1.8
Date: Fri, 12 Aug 2016 00:05:16 -0700
Source: nanopolish (0.5.0-1)
Binary: nanopolish
Binary-Only: yes
Architecture: armhf
Version: 0.5.0-1+b1
Distribution: stretch-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
nanopolish - consensus caller for nanopore sequencing data
Changes:
nanopolish (0.5.0-1+b1) stretch-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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eb9312fe9f3f2eeb5e043d25bb6d558af4ff4af8 1842044 nanopolish_0.5.0-1+b1_armhf.deb
077ac511e2be621a54885ae8507cef621a1848ca 5911 nanopolish_0.5.0-1_armhf.buildinfo
Checksums-Sha256:
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1d4c9b9598cb8d62464318083648faf454fd9747a812a46b0cf1cddf118717ce 1842044 nanopolish_0.5.0-1+b1_armhf.deb
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Files:
4bcc9a746a17110a7d7289758067751c 9528954 debug extra nanopolish-dbgsym_0.5.0-1+b1_armhf.deb
e58dc13bcf85f0170b3bd12aaed1e1fb 1842044 science optional nanopolish_0.5.0-1+b1_armhf.deb
7e7590e4beacbee25bc24f2d90ce0e3a 5911 science optional nanopolish_0.5.0-1_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
nanopolish-dbgsym_0.5.0-1+b1_armhf.deb
--------------------------------------
new debian package, version 2.0.
size 9528954 bytes: control archive=553 bytes.
481 bytes, 13 lines control
212 bytes, 2 lines md5sums
Package: nanopolish-dbgsym
Source: nanopolish (0.5.0-1)
Version: 0.5.0-1+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9713
Depends: nanopolish (= 0.5.0-1+b1)
Section: debug
Priority: extra
Homepage: https://github.com/jts/nanopolish
Description: Debug symbols for nanopolish
Auto-Built-Package: debug-symbols
Build-Ids: 785c36ee64e4af78a0dcc3362faf30f561cea64c d15333f8d922f71cb678152e8c5d8fe959b009d3
drwxr-xr-x root/root 0 2016-08-12 07:05 ./
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/lib/debug/.build-id/78/
-rw-r--r-- root/root 5578384 2016-08-12 07:05 ./usr/lib/debug/.build-id/78/5c36ee64e4af78a0dcc3362faf30f561cea64c.debug
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/lib/debug/.build-id/d1/
-rw-r--r-- root/root 4355304 2016-08-12 07:05 ./usr/lib/debug/.build-id/d1/5333f8d922f71cb678152e8c5d8fe959b009d3.debug
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/share/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-08-12 07:05 ./usr/share/doc/nanopolish-dbgsym -> nanopolish
nanopolish_0.5.0-1+b1_armhf.deb
-------------------------------
new debian package, version 2.0.
size 1842044 bytes: control archive=1044 bytes.
611 bytes, 14 lines control
1062 bytes, 14 lines md5sums
Package: nanopolish
Source: nanopolish (0.5.0-1)
Version: 0.5.0-1+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3185
Depends: libc6 (>= 2.23), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libhdf5-100, libhts1 (>= 1.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Suggests: python, perl, make
Section: science
Priority: optional
Homepage: https://github.com/jts/nanopolish
Description: consensus caller for nanopore sequencing data
Nanopolish uses a signal-level hidden Markov model for consensus
calling of nanopore genome sequencing data.
drwxr-xr-x root/root 0 2016-08-12 07:05 ./
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/bin/
-rwxr-xr-x root/root 738092 2016-08-12 07:05 ./usr/bin/nanopolish
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/lib/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/lib/nanopolish/
-rwxr-xr-x root/root 603 2016-08-11 16:14 ./usr/lib/nanopolish/consensus-preprocess.pl
-rwxr-xr-x root/root 1044 2016-08-12 07:05 ./usr/lib/nanopolish/consensus.make
-rw-r--r-- root/root 2022 2016-08-11 16:14 ./usr/lib/nanopolish/dropmodel.py
-rw-r--r-- root/root 476 2016-08-11 16:14 ./usr/lib/nanopolish/nanopolish_makerange.py
-rw-r--r-- root/root 2827 2016-08-11 16:14 ./usr/lib/nanopolish/nanopolish_merge.py
-rwxr-xr-x root/root 1074020 2016-08-12 07:05 ./usr/lib/nanopolish/nanopolish_test
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/share/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/share/doc/nanopolish/
-rw-r--r-- root/root 190 2016-01-19 07:41 ./usr/share/doc/nanopolish/README.Debian
-rw-r--r-- root/root 3574 2016-08-11 16:14 ./usr/share/doc/nanopolish/README.md
-rw-r--r-- root/root 222 2016-08-12 07:05 ./usr/share/doc/nanopolish/changelog.Debian.armhf.gz
-rw-r--r-- root/root 499 2016-08-12 07:05 ./usr/share/doc/nanopolish/changelog.Debian.gz
-rw-r--r-- root/root 4067 2016-08-12 03:33 ./usr/share/doc/nanopolish/copyright
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/share/doc/nanopolish/examples/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/share/doc/nanopolish/examples/data/
-rw-r--r-- root/root 1413462 2016-08-11 16:14 ./usr/share/doc/nanopolish/examples/data/LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fast5.gz
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/share/man/
drwxr-xr-x root/root 0 2016-08-12 07:05 ./usr/share/man/man1/
-rw-r--r-- root/root 329 2016-08-12 07:05 ./usr/share/man/man1/nanopolish.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 93340
Build-Time: 612
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 271
Job: nanopolish_0.5.0-1
Machine Architecture: armhf
Package: nanopolish
Package-Time: 934
Source-Version: 0.5.0-1
Space: 93340
Status: successful
Version: 0.5.0-1+b1
--------------------------------------------------------------------------------
Finished at 2016-12-05T09:23:55Z
Build needed 00:15:34, 93340k disc space