blasr →
5.3-1 →
armhf → 2016-10-31 23:33:34
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd.raspbian.org
+==============================================================================+
| blasr 5.3-1 (armhf) Mon, 31 Oct 2016 23:14:33 +0000 |
+==============================================================================+
Package: blasr
Version: 5.3-1
Source Version: 5.3-1
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-a5170c2b-db05-438c-b57c-1463c79bb84b' 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 [9419 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.4 MB]
Fetched 20.8 MB in 26s (777 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: 'blasr' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/blasr.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/blasr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1224 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main blasr 5.3-1 (dsc) [1956 B]
Get:2 http://172.17.0.1/private stretch-staging/main blasr 5.3-1 (tar) [1210 kB]
Get:3 http://172.17.0.1/private stretch-staging/main blasr 5.3-1 (diff) [12.2 kB]
Fetched 1224 kB in 0s (2406 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/blasr-7a8UFD/blasr-5.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/blasr-7a8UFD' 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-d36ONQ/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-d36ONQ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-d36ONQ/gpg/trustdb.gpg: trustdb created
gpg: key 5FBC947B34E39F26: 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 5FBC947B34E39F26: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 5FBC947B34E39F26: 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-d36ONQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ Packages [432 B]
Fetched 2080 B in 0s (3479 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:
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 762 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [762 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 762 B in 0s (0 B/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) ...
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), python, libhdf5-dev, zlib1g-dev, libblasr-dev, libpbdata-dev, libpbihdf-dev
Filtered Build-Depends: debhelper (>= 9), python, libhdf5-dev, zlib1g-dev, libblasr-dev, libpbdata-dev, libpbihdf-dev
dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/<<BUILDDIR>>/resolver-d36ONQ/apt_archive/sbuild-build-depends-blasr-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-blasr-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-d36ONQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ Sources [519 B]
Get:5 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ Packages [603 B]
Fetched 2427 B in 0s (3940 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install blasr 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 libgnutls30 libhogweed4 libldap-2.4-2
libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules libsasl2-modules-db
libtasn1-6 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 groff-base
hdf5-helpers intltool-debian libaec-dev libaec0 libarchive-zip-perl libblasr
libblasr-dev libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libhdf5-10 libhdf5-cpp-11 libhdf5-dev libicu57
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libmagic-mgc libmagic1
libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline6
libsigsegv2 libsz2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libhdf5-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
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 libblasr
libblasr-dev libbsd0 libcroco3 libexpat1 libfile-stripnondeterminism-perl
libgfortran3 libglib2.0-0 libhdf5-10 libhdf5-cpp-11 libhdf5-dev libicu57
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libmagic-mgc libmagic1
libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline6
libsigsegv2 libsz2 libtimedate-perl libtool libunistring0 libxml2 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
sbuild-build-depends-blasr-dummy zlib1g-dev
0 upgraded, 59 newly installed, 0 to remove and 5 not upgraded.
Need to get 33.5 MB/33.6 MB of archives.
After this operation, 125 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-d36ONQ/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [806 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 libpython2.7-minimal armhf 2.7.12-3 [388 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.12-3 [1174 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-2 [40.3 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.12-3 [1843 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.12-3 [279 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-2 [19.8 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-2 [153 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-2+rpi1 [2523 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf hdf5-helpers armhf 1.8.16+docs-8+b1 [35.7 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libpbdata armhf 0~20160705-1 [104 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.0-6+rpi1 [165 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libhdf5-10 armhf 1.8.16+docs-8+b1 [977 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libhdf5-cpp-11 armhf 1.8.16+docs-8+b1 [116 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libpbihdf armhf 0~20160705-1 [103 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libblasr armhf 0~20160705-1 [792 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libblasr-dev armhf 0~20160705-1 [1627 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libhdf5-dev armhf 1.8.16+docs-8+b1 [5530 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libpbdata-dev armhf 0~20160705-1 [175 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libpbihdf-dev armhf 0~20160705-1 [193 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../22-gettext_0.19.8.1-1_armhf.deb ...
Unpacking gettext (0.19.8.1-1) ...
Selecting previously unselected package intltool-debian.
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Unpacking intltool-debian (0.35.0+20060710.4) ...
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Unpacking po-debconf (1.0.20) ...
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Unpacking debhelper (10.2.2) ...
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Unpacking hdf5-helpers (1.8.16+docs-8+b1) ...
Selecting previously unselected package libaec0:armhf.
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Unpacking libaec0:armhf (0.3.2-1) ...
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Unpacking libpbdata:armhf (0~20160705-1) ...
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Unpacking libgfortran3:armhf (6.2.0-6+rpi1) ...
Selecting previously unselected package libsz2:armhf.
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Unpacking libsz2:armhf (0.3.2-1) ...
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Unpacking libhdf5-10:armhf (1.8.16+docs-8+b1) ...
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Unpacking libhdf5-cpp-11:armhf (1.8.16+docs-8+b1) ...
Selecting previously unselected package libpbihdf:armhf.
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Unpacking libpbihdf:armhf (0~20160705-1) ...
Selecting previously unselected package libblasr:armhf.
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Unpacking libblasr:armhf (0~20160705-1) ...
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Unpacking libblasr-dev:armhf (0~20160705-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../36-zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
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Unpacking libjpeg62-turbo:armhf (1:1.5.1-2) ...
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Unpacking libjpeg62-turbo-dev:armhf (1:1.5.1-2) ...
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Unpacking libjpeg-dev (1:1.5.1-2) ...
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Unpacking libaec-dev:armhf (0.3.2-1) ...
Selecting previously unselected package libhdf5-dev.
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Unpacking libhdf5-dev (1.8.16+docs-8+b1) ...
Selecting previously unselected package libpbdata-dev:armhf.
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Unpacking libpbihdf-dev:armhf (0~20160705-1) ...
Selecting previously unselected package sbuild-build-depends-blasr-dummy.
Preparing to unpack .../44-sbuild-build-depends-blasr-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-blasr-dummy (0.invalid.0) ...
Setting up libaec0:armhf (0.3.2-1) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.1-2) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up libgfortran3:armhf (6.2.0-6+rpi1) ...
Setting up groff-base (1.22.3-8) ...
Setting up libglib2.0-0:armhf (2.50.0-2+rpi1) ...
No schema files found: doing nothing.
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 (57.1-4) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2) ...
Setting up libmagic-mgc (1:5.29-1) ...
Setting up libmagic1:armhf (1:5.29-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libpbdata:armhf (0~20160705-1) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.1-2) ...
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 (1.8.16+docs-8+b1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up libreadline6:armhf (6.3-9) ...
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 libhdf5-10:armhf (1.8.16+docs-8+b1) ...
Setting up libhdf5-cpp-11:armhf (1.8.16+docs-8+b1) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libpbdata-dev:armhf (0~20160705-1) ...
Setting up libaec-dev:armhf (0.3.2-1) ...
Setting up libhdf5-dev (1.8.16+docs-8+b1) ...
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 autoconf (2.69-10) ...
Setting up file (1:5.29-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libjpeg-dev (1:1.5.1-2) ...
Setting up libpbihdf:armhf (0~20160705-1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython2.7-stdlib:armhf (2.7.12-3) ...
Setting up libtool (2.4.6-2) ...
Setting up libblasr:armhf (0~20160705-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libpbihdf-dev:armhf (0~20160705-1) ...
Setting up libblasr-dev:armhf (0~20160705-1) ...
Setting up python2.7 (2.7.12-3) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up python (2.7.11-2) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (10.2.2) ...
Setting up sbuild-build-depends-blasr-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
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 3.19.0-trunk-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 gnupg_2.1.15-4 gnupg-agent_2.1.15-4 gnupg-l10n_2.1.15-4 gpgv_2.1.15-4 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 hdf5-helpers_1.8.16+docs-8+b1 hostname_3.18 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.10.95-5 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-6+rpi1 libassuan0_2.4.3-1 libatomic1_6.2.0-6+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblasr_0~20160705-1 libblasr-dev_0~20160705-1 libblkid1_2.28.2-1 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_6.2.0-6+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-5 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 libexpat1_2.2.0-1 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 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 libhdf5-10_1.8.16+docs-8+b1 libhdf5-cpp-11_1.8.16+docs-8+b1 libhdf5-dev_1.8.16+docs-8+b1 libhogweed4_3.3-1 libicu57_57.1-4 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 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 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 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 libpbdata_0~20160705-1 libpbdata-dev_0~20160705-1 libpbihdf_0~20160705-1 libpbihdf-dev_0~20160705-1 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 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-3 libpython2.7-stdlib_2.7.12-3 libreadline6_6.3-9 libreadline7_7.0-1 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 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 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_6.2.0-6+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 mime-support_3.60 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 python_2.7.11-2 python-minimal_2.7.11-2 python2.7_2.7.12-3 python2.7-minimal_2.7.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-blasr-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 Mon Oct 24 02:21:27 2016 UTC
gpgv: using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./blasr_5.3-1.dsc
dpkg-source: info: extracting blasr in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking blasr_5.3.orig.tar.gz
dpkg-source: info: unpacking blasr_5.3-1.debian.tar.xz
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=111
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-a5170c2b-db05-438c-b57c-1463c79bb84b
SCHROOT_UID=106
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package blasr
dpkg-buildpackage: info: source version 5.3-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build blasr-5.3
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>>'
./configure.py --no-pbbam --shared
`uname`
Linux
writing to '/<<PKGBUILDDIR>>/defines.mk':
"""
LIBPBDATA_LIB ?= /<<PKGBUILDDIR>>/libcpp/pbdata
LIBBLASR_LIBFLAGS ?= -lblasr
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
DL_LIBFLAGS ?= -ldl
HDF5_INC ?= /usr/include/hdf5/serial
LIBPBDATA_INC ?= /usr/include/pbseq/pbdata
LIBPBIHDF_LIBFLAGS ?= -lpbihdf
LIBPBIHDF_INC ?= /usr/include/pbseq/hdf
LIBBLASR_LIB ?= /<<PKGBUILDDIR>>/libcpp/alignment
CXXFLAGS ?= -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security
SHELL ?= bash
RT_LIBFLAGS ?= -lrt
HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5
LIBPBDATA_LIBFLAGS ?= -lpbdata
ZLIB_LIBFLAGS ?= -lz
LIBBLASR_INC ?= /usr/include/pbseq/alignment
PTHREAD_LIBFLAGS ?= -lpthread
NOPBBAM ?= 1
LIBPBIHDF_LIB ?= /<<PKGBUILDDIR>>/libcpp/hdf
"""
----
/usr/bin/make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: git: Command not found
rm -f blasr Blasr.o Blasr.d blasr.d
/usr/bin/make -C utils clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/utils'
make[4]: Entering directory '/<<PKGBUILDDIR>>/utils/bam2bax'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/utils/bam2bax'
make[4]: Entering directory '/<<PKGBUILDDIR>>/utils/bax2bam'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/utils/bax2bam'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/utils'
/usr/bin/make -C extrautils clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/extrautils'
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/extrautils'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# This is created by configure.py
rm -f defines.mk
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
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
./configure.py --no-pbbam --shared
`uname`
Linux
writing to '/<<PKGBUILDDIR>>/defines.mk':
"""
LIBPBDATA_LIB ?= /<<PKGBUILDDIR>>/libcpp/pbdata
LIBBLASR_LIBFLAGS ?= -lblasr
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
DL_LIBFLAGS ?= -ldl
HDF5_INC ?= /usr/include/hdf5/serial
LIBPBDATA_INC ?= /usr/include/pbseq/pbdata
LIBPBIHDF_LIBFLAGS ?= -lpbihdf
LIBPBIHDF_INC ?= /usr/include/pbseq/hdf
LIBBLASR_LIB ?= /<<PKGBUILDDIR>>/libcpp/alignment
CXXFLAGS ?= -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security
SHELL ?= bash
RT_LIBFLAGS ?= -lrt
HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5
LIBPBDATA_LIBFLAGS ?= -lpbdata
ZLIB_LIBFLAGS ?= -lz
LIBBLASR_INC ?= /usr/include/pbseq/alignment
PTHREAD_LIBFLAGS ?= -lpthread
NOPBBAM ?= 1
LIBPBIHDF_LIB ?= /<<PKGBUILDDIR>>/libcpp/hdf
"""
----
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a -O--parallel
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make[1]: git: Command not found
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -c -o Blasr.o Blasr.cpp
make -C utils
make[2]: Entering directory '/<<PKGBUILDDIR>>/utils'
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -c -o LoadPulses.o LoadPulses.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -c -o PulseToFasta.o PulseToFasta.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -c -o SamToCmpH5.o SamToCmpH5.cpp
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:43:0,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp: In instantiation of 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]':
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:129:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (refPos + 1 < reference.length and
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:130:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
queryPos + 1 < read.length and
~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -c -o SamToM4.o SamToM4.cpp
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:5:0,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp: In instantiation of 'int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]':
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:62:41: required from 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:1068:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
index[l] + lcpLength >= targetLength or // This shouldn't
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp: In instantiation of 'long int SuffixArray<T, Sigma, Compare, Tuple>::SearchLeftBound(T*, long int, DNALength, T, long int, long int) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]':
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:1056:32: required from 'int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:62:41: required from 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:763:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen == targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:773:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen < targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/cassert:44:0,
from /usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/../tuples/../../pbdata/CompressedSequence.hpp:3,
from /usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/../tuples/CompressedDNATuple.hpp:5,
from /usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:20,
from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:5,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:781:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
assert(index[m]+targetOffset < targetLength);
^
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:5:0,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp: In instantiation of 'long int SuffixArray<T, Sigma, Compare, Tuple>::SearchRightBound(T*, long int, DNALength, T, long int, long int) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]':
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:1057:33: required from 'int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:62:41: required from 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:813:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen == targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:817:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen < targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -c -o SamFilter.o SamFilter.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -c -o ToAfg.o ToAfg.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -c -o SAWriter.o SAWriter.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -c -o SDPMatcher.o SDPMatcher.cpp
g++ -o pls2fasta PulseToFasta.o -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -MF"pls2fasta.d" -Wl,-z,relro -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lpbihdf -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lz -lrt -lpthread -ldl
g++ -o samtoh5 SamToCmpH5.o -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -MF"samtoh5.d" -Wl,-z,relro -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lpbihdf -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lz -lrt -lpthread -ldl
g++ -o samtom4 SamToM4.o -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -MF"samtom4.d" -Wl,-z,relro -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lpbihdf -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lz -lrt -lpthread -ldl
g++ -o samFilter SamFilter.o -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -MF"samFilter.d" -Wl,-z,relro -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lpbihdf -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lz -lrt -lpthread -ldl
g++ -o toAfg ToAfg.o -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -MF"toAfg.d" -Wl,-z,relro -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lpbihdf -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lz -lrt -lpthread -ldl
g++ -o sawriter SAWriter.o -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -MF"sawriter.d" -Wl,-z,relro -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lpbihdf -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lz -lrt -lpthread -ldl
g++ -o loadPulses LoadPulses.o -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -MF"loadPulses.d" -Wl,-z,relro -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lpbihdf -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lz -lrt -lpthread -ldl
g++ -o sdpMatcher SDPMatcher.o -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -MF"sdpMatcher.d" -Wl,-z,relro -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lpbihdf -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lz -lrt -lpthread -ldl
make[2]: Leaving directory '/<<PKGBUILDDIR>>/utils'
g++ -o blasr -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include/hdf5/serial -MF"blasr.d" Blasr.o -Wl,-z,relro -L/<<PKGBUILDDIR>>/libcpp/alignment -L/<<PKGBUILDDIR>>/libcpp/hdf -L/<<PKGBUILDDIR>>/libcpp/pbdata -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lpbihdf -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lz -lrt -lpthread -ldl
LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/libcpp/alignment:/<<PKGBUILDDIR>>/libcpp/hdf:/<<PKGBUILDDIR>>/libcpp/pbdata:/usr/lib/arm-linux-gnueabihf/hdf5/serial::::
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make[1]: 'override_dh_auto_test' is up to date.
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_installman -a -O--parallel
dh_lintian -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: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/loadPulses contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/toAfg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/blasr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/sdpMatcher contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/pls2fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/sawriter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samtom4 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samtoh5 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samFilter 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/blasr/usr/bin/loadPulses debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/blasr debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/samFilter were not linked against libdl.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/blasr debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/samFilter were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/blasr debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/samFilter were not linked against librt.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/blasr debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/samFilter were not linked against libz.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: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3-1_armhf.deb'.
dpkg-deb: building package 'blasr' in '../blasr_5.3-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian nitrogen6x test autobuilder <root@raspbian.org> >../blasr_5.3-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build blasr-5.3
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-10-31T23:28:43Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
blasr_5.3-1_armhf.changes:
--------------------------
Format: 1.8
Date: Sun, 23 Oct 2016 18:21:55 -0700
Source: blasr
Binary: blasr
Architecture: armhf
Version: 5.3-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian nitrogen6x test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@debian.org>
Description:
blasr - mapping single-molecule sequencing reads
Changes:
blasr (5.3-1) unstable; urgency=medium
.
* Imported Upstream version 5.3
(upstream git revision 1baabc8 from 2016-09-12)
* Find PB libraries in the default LD path
* Bump Standards-Version to 3.9.8
* Use encrypted protocols for VCS
* Update email address and copyright year
* Update paths to pbseqlib headers
* Remove unused lintian overrides
* Update debian/TODO
* Add d/NEWS to explain interface change
* d/rules: Minor clean-ups
Checksums-Sha1:
19c59a7ed851d2e1281535942d2d929c43512d59 5128594 blasr-dbgsym_5.3-1_armhf.deb
243b73f56d2961de54aedc6e14dd3d878480456a 384066 blasr_5.3-1_armhf.deb
Checksums-Sha256:
5777b61824c446c57e524addf5a22890285170501540ac2a77079836679537ed 5128594 blasr-dbgsym_5.3-1_armhf.deb
4f2bc22f28dc752837b7c3a9488cdf01ca5861fb464ada141233f6699027f72f 384066 blasr_5.3-1_armhf.deb
Files:
528b4c4acad4ba901814c174a727c9c5 5128594 debug extra blasr-dbgsym_5.3-1_armhf.deb
9c747bdf6409199257d49512f2c8c43d 384066 science optional blasr_5.3-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
blasr-dbgsym_5.3-1_armhf.deb
----------------------------
new debian package, version 2.0.
size 5128594 bytes: control archive=929 bytes.
738 bytes, 13 lines control
954 bytes, 9 lines md5sums
Package: blasr-dbgsym
Source: blasr
Version: 5.3-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5379
Depends: blasr (= 5.3-1)
Section: debug
Priority: extra
Homepage: https://github.com/PacificBiosciences/blasr
Description: Debug symbols for blasr
Auto-Built-Package: debug-symbols
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blasr_5.3-1_armhf.deb
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new debian package, version 2.0.
size 384066 bytes: control archive=1354 bytes.
737 bytes, 14 lines control
1534 bytes, 25 lines md5sums
Package: blasr
Version: 5.3-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1356
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libhdf5-10, libhdf5-cpp-11 (>= 1.8.16), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), libblasr, libpbdata, libpbihdf
Section: science
Priority: optional
Homepage: https://github.com/PacificBiosciences/blasr
Description: mapping single-molecule sequencing reads
Basic local alignment with successive refinement (BLASR) is a method
for mapping single-molecule sequencing reads against a reference genome.
Such reads are thousands of bases long, with divergence between them
and the genome being dominated by insertion and deletion error.
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-rwxr-xr-x root/root 108788 2016-10-24 01:21 ./usr/bin/pls2fasta
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-rwxr-xr-x root/root 75812 2016-10-24 01:21 ./usr/bin/toAfg
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drwxr-xr-x root/root 0 2016-10-24 01:21 ./usr/share/doc/blasr/
-rw-r--r-- root/root 193 2016-10-24 01:21 ./usr/share/doc/blasr/NEWS.Debian.gz
-rw-r--r-- root/root 1173 2016-09-12 08:56 ./usr/share/doc/blasr/README.MANUAL.md
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-rw-r--r-- root/root 670 2016-10-24 01:21 ./usr/share/doc/blasr/changelog.Debian.gz
-rw-r--r-- root/root 2007 2016-07-24 23:35 ./usr/share/doc/blasr/copyright
drwxr-xr-x root/root 0 2016-10-24 01:21 ./usr/share/lintian/
drwxr-xr-x root/root 0 2016-10-24 01:21 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 84 2016-10-24 00:26 ./usr/share/lintian/overrides/blasr
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-rw-r--r-- root/root 1397 2016-10-24 01:21 ./usr/share/man/man1/samFilter.1.gz
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 56316
Build-Time: 417
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 383
Job: blasr_5.3-1
Machine Architecture: armhf
Package: blasr
Package-Time: 850
Source-Version: 5.3-1
Space: 56316
Status: successful
Version: 5.3-1
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Finished at 2016-10-31T23:28:43Z
Build needed 00:14:10, 56316k disc space