pbbam →
0.5.0-2 →
armhf → 2016-10-12 17:43:35
sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on bm-wb-03
+==============================================================================+
| pbbam 0.5.0-2 (armhf) Wed, 12 Oct 2016 17:19:21 +0000 |
+==============================================================================+
Package: pbbam
Version: 0.5.0-2
Source Version: 0.5.0-2
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-8f42a2cf-255e-4e25-957b-037bf2c5649f' 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 [9340 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.3 MB]
Fetched 20.6 MB in 23s (887 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pbbam' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/pbbam.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/pbbam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 6270 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main pbbam 0.5.0-2 (dsc) [2134 B]
Get:2 http://172.17.0.1/private stretch-staging/main pbbam 0.5.0-2 (tar) [6261 kB]
Get:3 http://172.17.0.1/private stretch-staging/main pbbam 0.5.0-2 (diff) [6668 B]
Fetched 6270 kB in 0s (7127 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbbam-Iq4WZZ/pbbam-0.5.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbbam-Iq4WZZ' 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-2J3jjD/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-2J3jjD/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-2J3jjD/gpg/trustdb.gpg: trustdb created
gpg: key 3CA43A8AAD304FAC: 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 3CA43A8AAD304FAC: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 3CA43A8AAD304FAC: 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-2J3jjD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-2J3jjD/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-2J3jjD/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-2J3jjD/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-2J3jjD/apt_archive ./ Packages [431 B]
Fetched 2079 B in 0s (3611 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 kbd libffi6 libfuse2 libgnutls30 libhogweed4
libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
libsasl2-modules-db libssl1.0.2 libtasn1-6 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 29 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-2J3jjD/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 ... 13385 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), dh-exec, cmake, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, python-cram, samtools
Filtered Build-Depends: debhelper (>= 9), dh-exec, cmake, libboost-dev (>= 1.54), zlib1g-dev, libssl-dev, libhts-dev, python-cram, samtools
dpkg-deb: building package 'sbuild-build-depends-pbbam-dummy' in '/<<BUILDDIR>>/resolver-haw43Q/apt_archive/sbuild-build-depends-pbbam-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-pbbam-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-haw43Q/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-haw43Q/gpg/trustdb.gpg: trustdb created
gpg: key 3CA43A8AAD304FAC: 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 3CA43A8AAD304FAC: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 3CA43A8AAD304FAC: 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-haw43Q/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-haw43Q/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-haw43Q/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-haw43Q/apt_archive ./ Sources [399 B]
Get:5 copy:/<<BUILDDIR>>/resolver-haw43Q/apt_archive ./ Packages [487 B]
Fetched 2185 B in 0s (3790 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pbbam 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 kbd libfuse2 libsasl2-modules manpages netbase
psmisc
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13
libboost-dev libboost1.61-dev libbsd0 libcroco3 libcurl3 libcurl3-gnutls
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
libhts-dev libhts1 libicu57 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librtmp1
libsigsegv2 libssh2-1 libssl-dev libtimedate-perl libtool libunistring0
libxml2 m4 man-db mime-support po-debconf python python-cram python-minimal
python2.7 python2.7-minimal samtools zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation codeblocks eclipse ninja-build dh-make gettext-doc libasprintf-dev
libgettextpo-dev groff lrzip libboost-doc libboost1.61-doc
libboost-atomic1.61-dev libboost-chrono1.61-dev libboost-context1.61-dev
libboost-coroutine1.61-dev libboost-date-time1.61-dev
libboost-exception1.61-dev libboost-filesystem1.61-dev
libboost-graph1.61-dev libboost-graph-parallel1.61-dev
libboost-iostreams1.61-dev libboost-locale1.61-dev libboost-log1.61-dev
libboost-math1.61-dev libboost-mpi1.61-dev libboost-mpi-python1.61-dev
libboost-program-options1.61-dev libboost-python1.61-dev
libboost-random1.61-dev libboost-regex1.61-dev
libboost-serialization1.61-dev libboost-signals1.61-dev
libboost-system1.61-dev libboost-test1.61-dev libboost-thread1.61-dev
libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev
libmpfrc++-dev libntl-dev krb5-doc krb5-user 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 ca-certificates libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libssl-doc libltdl-dev xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-exec dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13
libboost-dev libboost1.61-dev libbsd0 libcroco3 libcurl3 libcurl3-gnutls
libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2
libhts-dev libhts1 libicu57 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1
libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librtmp1
libsigsegv2 libssh2-1 libssl-dev libtimedate-perl libtool libunistring0
libxml2 m4 man-db mime-support po-debconf python python-cram python-minimal
python2.7 python2.7-minimal samtools sbuild-build-depends-pbbam-dummy
zlib1g-dev
0 upgraded, 64 newly installed, 0 to remove and 29 not upgraded.
Need to get 37.1 MB of archives.
After this operation, 224 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-haw43Q/apt_archive ./ sbuild-build-depends-pbbam-dummy 0.invalid.0 [818 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 9.0.11 [177 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 cmake-data all 3.6.2-1 [1153 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libarchive13 armhf 3.2.1-2 [250 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-2 [57.5 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-2 [110 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.3+dfsg-2 [262 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.3+dfsg-2 [131 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.15.0-1 [72.6 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libcurl3 armhf 7.50.1-1 [251 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libjsoncpp1 armhf 1.7.4-3 [66.2 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf cmake armhf 3.6.2-1 [2268 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-2+rpi1 [2523 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.1 [827 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libboost1.61-dev armhf 1.61.0+dfsg-2.1+b1 [6843 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.61.0.2 [3758 B]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.50.1-1 [248 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.1-3+rpi1 [216 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3.1-3+rpi1 [270 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libssl-dev armhf 1.0.2j-1 [1149 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf python-cram all 0.7-1 [16.6 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf samtools armhf 1.3.1-2 [219 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking sbuild-build-depends-pbbam-dummy (0.invalid.0) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.15.0-1) ...
Setting up mime-support (3.60) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.10-5) ...
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 cmake-data (3.6.2-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-4) ...
Setting up libboost1.61-dev:armhf (1.61.0+dfsg-2.1+b1) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2) ...
Setting up libmagic-mgc (1:5.28-4) ...
Setting up libmagic1:armhf (1:5.28-4) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libssh2-1:armhf (1.7.0-1) ...
Processing triggers for libc-bin (2.24-3) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libboost-dev:armhf (1.61.0.2) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.11) ...
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 libpython2.7-stdlib:armhf (2.7.12-3) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up liblzo2-2:armhf (2.08-1.2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up libjsoncpp1:armhf (1.7.4-3) ...
Setting up gettext (0.19.8.1-1) ...
Setting up libarchive13:armhf (3.2.1-2) ...
Setting up libssl-dev:armhf (1.0.2j-1) ...
Setting up python2.7 (2.7.12-3) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.28-4) ...
Setting up libkrb5support0:armhf (1.14.3+dfsg-2) ...
Setting up libpython-stdlib:armhf (2.7.11-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
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 python (2.7.11-2) ...
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.14.3+dfsg-2) ...
Setting up python-cram (0.7-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libkrb5-3:armhf (1.14.3+dfsg-2) ...
Setting up libgssapi-krb5-2:armhf (1.14.3+dfsg-2) ...
Setting up libcurl3:armhf (7.50.1-1) ...
Setting up libcurl3-gnutls:armhf (7.50.1-1) ...
Setting up cmake (3.6.2-1) ...
Setting up libhts1:armhf (1.3.1-3+rpi1) ...
Setting up libhts-dev:armhf (1.3.1-3+rpi1) ...
Setting up samtools (1.3.1-2) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.1) ...
Setting up dh-autoreconf (12) ...
Setting up dh-exec (0.23) ...
Setting up sbuild-build-depends-pbbam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-3) ...
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_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.24-3 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3 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_2.26.1-1 bsdmainutils_9.0.11 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 cmake_3.6.2-1 cmake-data_3.6.2-1 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.1 debianutils_4.8 dh-autoreconf_12 dh-exec_0.23 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-3 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_1:5.28-4 findutils_4.6.0+git+20160703-2 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.1.1-11+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_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gnupg_2.1.15-3 gnupg-agent_2.1.15-3 gnupg-l10n_2.1.15-3 gpgv_2.1.15-3 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 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 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg5.0_1.3 libarchive-zip-perl_1.59-1 libarchive13_3.2.1-2 libasan3_6.1.1-11+rpi1 libassuan0_2.4.3-1 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1 libaudit1_1:2.6.6-1 libblkid1_2.28.2-1 libboost-dev_1.61.0.2 libboost1.61-dev_1.61.0+dfsg-2.1+b1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-3 libc-dev-bin_2.24-3 libc6_2.24-3 libc6-dev_2.24-3 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.0-2 libcurl3_7.50.1-1 libcurl3-gnutls_7.50.1-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.10-1 libdebconfclient0_0.217 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 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_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.3-1 libgdbm3_1.8.3-14 libglib2.0-0_2.50.0-2+rpi1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.4-2 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-2 libhogweed4_3.2-1 libhts-dev_1.3.1-3+rpi1 libhts1_1.3.1-3+rpi1 libicu57_57.1-4 libidn11_1.33-1 libisl15_0.17.1-1 libjsoncpp1_1.7.4-3 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.2-1 libnghttp2-14_1.15.0-1 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_2:3.3.12-2 libpython-stdlib_2.7.11-2 libpython2.7-minimal_2.7.12-3 libpython2.7-stdlib_2.7.12-3 libreadline6_6.3-8+b3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl-dev_1.0.2j-1 libssl1.0.2_1.0.2j-1 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_231-4 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.1.1-11+rpi1 libudev1_231-4 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_4.07-1 mawk_1.3.3-17 mime-support_3.60 mount_2.28.2-1 multiarch-support_2.24-3 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_0.9.7-5 po-debconf_1.0.20 procps_2:3.3.12-2 psmisc_22.21-2.1 python_2.7.11-2 python-cram_0.7-1 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_6.3-8 samtools_1.3.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbbam-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-4 systemd-sysv_231-4 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016g-1 udev_231-4 util-linux_2.28.2-1 xz-utils_5.1.1alpha+20120614-2.1 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 Jul 18 06:30:52 2016 UTC
gpgv: using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbbam_0.5.0-2.dsc
dpkg-source: info: extracting pbbam in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking pbbam_0.5.0.orig.tar.gz
dpkg-source: info: unpacking pbbam_0.5.0-2.debian.tar.xz
dpkg-source: info: applying dont-try-building-gtest.patch
dpkg-source: info: applying ssl-md5.patch
dpkg-source: info: applying remove-bam2sam.patch
dpkg-source: info: applying use-PATH-for-test-programs.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-8f42a2cf-255e-4e25-957b-037bf2c5649f
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=vt102
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbbam
dpkg-buildpackage: info: source version 0.5.0-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build pbbam-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>>'
dh_auto_clean
find -name "*.deb.t" -delete
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>>'
dh_auto_configure -- \
-DPacBioBAM_build_shared=ON \
-DPacBioBAM_build_tests=OFF \
-DCMAKE_LIBRARY_PATH=arm-linux-gnueabihf \
-DCMAKE_SKIP_RPATH=ON \
-DHTSLIB_INCLUDE_DIRS=/usr/include \
-DHTSLIB_LIBRARIES=/usr/lib \
-DCMAKE_SHARED_LINKER_FLAGS="-lssl -lhts -Wl,-z,relro"
cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DPacBioBAM_build_shared=ON -DPacBioBAM_build_tests=OFF -DCMAKE_LIBRARY_PATH=arm-linux-gnueabihf -DCMAKE_SKIP_RPATH=ON -DHTSLIB_INCLUDE_DIRS=/usr/include -DHTSLIB_LIBRARIES=/usr/lib "-DCMAKE_SHARED_LINKER_FLAGS=-lssl -lhts -Wl,-z,relro"
-- The CXX compiler identification is GNU 6.1.1
-- The C compiler identification is GNU 6.1.1
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Boost version: 1.61.0
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.8")
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD
-- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD - Success
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Configuring done
WARNING: Target "pbbam" requests linking to directory "/usr/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "pbindex" requests linking to directory "/usr/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "pbindexdump" requests linking to directory "/usr/lib". Targets may link only to libraries. CMake is dropping the item.
WARNING: Target "pbmerge" requests linking to directory "/usr/lib". Targets may link only to libraries. CMake is dropping the item.
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a -O--parallel
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -H/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/pbbam.dir/DependInfo.cmake --color=
Scanning dependencies of target pbbam
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 1%] Building CXX object src/CMakeFiles/pbbam.dir/Accuracy.cpp.o
[ 2%] Building CXX object src/CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/Accuracy.cpp.o -c /<<PKGBUILDDIR>>/src/Accuracy.cpp
[ 3%] Building CXX object src/CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o -c /<<PKGBUILDDIR>>/src/AlignmentPrinter.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o -c /<<PKGBUILDDIR>>/src/BaiIndexedBamReader.cpp
[ 5%] Building CXX object src/CMakeFiles/pbbam.dir/AssertUtils.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/AssertUtils.cpp.o -c /<<PKGBUILDDIR>>/src/AssertUtils.cpp
[ 6%] Building CXX object src/CMakeFiles/pbbam.dir/BamFile.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BamFile.cpp.o -c /<<PKGBUILDDIR>>/src/BamFile.cpp
[ 7%] Building CXX object src/CMakeFiles/pbbam.dir/BamHeader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BamHeader.cpp.o -c /<<PKGBUILDDIR>>/src/BamHeader.cpp
[ 9%] Building CXX object src/CMakeFiles/pbbam.dir/BamReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BamReader.cpp.o -c /<<PKGBUILDDIR>>/src/BamReader.cpp
[ 10%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecord.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BamRecord.cpp.o -c /<<PKGBUILDDIR>>/src/BamRecord.cpp
[ 11%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o -c /<<PKGBUILDDIR>>/src/BamRecordBuilder.cpp
[ 13%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o -c /<<PKGBUILDDIR>>/src/BamRecordImpl.cpp
[ 14%] Building CXX object src/CMakeFiles/pbbam.dir/BamTagCodec.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BamTagCodec.cpp.o -c /<<PKGBUILDDIR>>/src/BamTagCodec.cpp
[ 15%] Building CXX object src/CMakeFiles/pbbam.dir/BamWriter.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BamWriter.cpp.o -c /<<PKGBUILDDIR>>/src/BamWriter.cpp
[ 17%] Building CXX object src/CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o -c /<<PKGBUILDDIR>>/src/BarcodeQuery.cpp
/<<PKGBUILDDIR>>/src/BamWriter.cpp: In member function ‘void PacBio::BAM::internal::BamWriterPrivate::Write(const std::shared_ptr<bam1_t>&, int64_t*)’:
/<<PKGBUILDDIR>>/src/BamWriter.cpp:136:21: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_flush(bgzf);
^
/<<PKGBUILDDIR>>/src/BamWriter.cpp: In destructor ‘PacBio::BAM::BamWriter::~BamWriter()’:
/<<PKGBUILDDIR>>/src/BamWriter.cpp:167:41: warning: ignoring return value of ‘int bgzf_flush(BGZF*)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_flush(d_->file_.get()->fp.bgzf);
^
[ 18%] Building CXX object src/CMakeFiles/pbbam.dir/ChemistryTable.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/ChemistryTable.cpp.o -c /<<PKGBUILDDIR>>/src/ChemistryTable.cpp
[ 19%] Building CXX object src/CMakeFiles/pbbam.dir/Cigar.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/Cigar.cpp.o -c /<<PKGBUILDDIR>>/src/Cigar.cpp
[ 21%] Building CXX object src/CMakeFiles/pbbam.dir/CigarOperation.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/CigarOperation.cpp.o -c /<<PKGBUILDDIR>>/src/CigarOperation.cpp
[ 22%] Building CXX object src/CMakeFiles/pbbam.dir/Compare.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/Compare.cpp.o -c /<<PKGBUILDDIR>>/src/Compare.cpp
[ 23%] Building CXX object src/CMakeFiles/pbbam.dir/Config.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/Config.cpp.o -c /<<PKGBUILDDIR>>/src/Config.cpp
[ 25%] Building CXX object src/CMakeFiles/pbbam.dir/DataSet.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/DataSet.cpp.o -c /<<PKGBUILDDIR>>/src/DataSet.cpp
[ 26%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o -c /<<PKGBUILDDIR>>/src/DataSetBaseTypes.cpp
[ 27%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetElement.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/DataSetElement.cpp.o -c /<<PKGBUILDDIR>>/src/DataSetElement.cpp
[ 28%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetIO.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/DataSetIO.cpp.o -c /<<PKGBUILDDIR>>/src/DataSetIO.cpp
[ 30%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetTypes.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/DataSetTypes.cpp.o -c /<<PKGBUILDDIR>>/src/DataSetTypes.cpp
[ 31%] Building CXX object src/CMakeFiles/pbbam.dir/DataSetXsd.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/DataSetXsd.cpp.o -c /<<PKGBUILDDIR>>/src/DataSetXsd.cpp
[ 32%] Building CXX object src/CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o -c /<<PKGBUILDDIR>>/src/EntireFileQuery.cpp
[ 34%] Building CXX object src/CMakeFiles/pbbam.dir/FileUtils.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/FileUtils.cpp.o -c /<<PKGBUILDDIR>>/src/FileUtils.cpp
[ 35%] Building CXX object src/CMakeFiles/pbbam.dir/FofnReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/FofnReader.cpp.o -c /<<PKGBUILDDIR>>/src/FofnReader.cpp
[ 36%] Building CXX object src/CMakeFiles/pbbam.dir/Frames.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/Frames.cpp.o -c /<<PKGBUILDDIR>>/src/Frames.cpp
[ 38%] Building CXX object src/CMakeFiles/pbbam.dir/GenomicInterval.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/GenomicInterval.cpp.o -c /<<PKGBUILDDIR>>/src/GenomicInterval.cpp
[ 39%] Building CXX object src/CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o -c /<<PKGBUILDDIR>>/src/GenomicIntervalQuery.cpp
[ 40%] Building CXX object src/CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o -c /<<PKGBUILDDIR>>/src/IndexedFastaReader.cpp
[ 42%] Building CXX object src/CMakeFiles/pbbam.dir/MemoryUtils.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/MemoryUtils.cpp.o -c /<<PKGBUILDDIR>>/src/MemoryUtils.cpp
[ 43%] Building CXX object src/CMakeFiles/pbbam.dir/PbiBuilder.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/PbiBuilder.cpp.o -c /<<PKGBUILDDIR>>/src/PbiBuilder.cpp
[ 44%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFile.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/PbiFile.cpp.o -c /<<PKGBUILDDIR>>/src/PbiFile.cpp
[ 46%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilter.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/PbiFilter.cpp.o -c /<<PKGBUILDDIR>>/src/PbiFilter.cpp
[ 47%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o -c /<<PKGBUILDDIR>>/src/PbiFilterQuery.cpp
[ 48%] Building CXX object src/CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o -c /<<PKGBUILDDIR>>/src/PbiFilterTypes.cpp
[ 50%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndex.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/PbiIndex.cpp.o -c /<<PKGBUILDDIR>>/src/PbiIndex.cpp
[ 51%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o -c /<<PKGBUILDDIR>>/src/PbiIndexedBamReader.cpp
[ 52%] Building CXX object src/CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o -c /<<PKGBUILDDIR>>/src/PbiIndexIO.cpp
[ 53%] Building CXX object src/CMakeFiles/pbbam.dir/PbiRawData.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/PbiRawData.cpp.o -c /<<PKGBUILDDIR>>/src/PbiRawData.cpp
[ 55%] Building CXX object src/CMakeFiles/pbbam.dir/ProgramInfo.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/ProgramInfo.cpp.o -c /<<PKGBUILDDIR>>/src/ProgramInfo.cpp
[ 56%] Building CXX object src/CMakeFiles/pbbam.dir/QNameQuery.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/QNameQuery.cpp.o -c /<<PKGBUILDDIR>>/src/QNameQuery.cpp
In file included from /<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:38:0:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector<T>&, uint32_t) [with T = short int]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, &data[0], numReads*sizeof(T));
^~~~~~~~~
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector<T>&, uint32_t) [with T = signed char]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadHeader(PacBio::BAM::PbiRawData&, BGZF*)’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:117:46: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, &version, sizeof(version));
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:118:47: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, §ions, sizeof(sections));
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:119:47: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, &numReads, sizeof(numReads));
^
In file included from /<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:38:0:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector<T>&, uint32_t) [with T = int]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, &data[0], numReads*sizeof(T));
^~~~~~~~~
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector<T>&, uint32_t) [with T = unsigned int]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector<T>&, uint32_t) [with T = unsigned char]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadReferenceData(PacBio::BAM::PbiRawReferenceData&, BGZF*)’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:173:31: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, &numRefs, 4);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:182:43: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, &entry.tId_, 4);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:183:43: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, &entry.beginRow_, 4);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:184:43: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, &entry.endRow_, 4);
^
In file included from /<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:38:0:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector<T>&, uint32_t) [with T = float]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_read(fp, &data[0], numReads*sizeof(T));
^~~~~~~~~
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::LoadBgzfVector(BGZF*, std::vector<T>&, uint32_t) [with T = long long int]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:121:5: warning: ignoring return value of ‘ssize_t bgzf_read(BGZF*, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector<T>&) [with T = short int]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &output[0], data.size()*sizeof(T));
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector<T>&) [with T = signed char]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteHeader(const PacBio::BAM::PbiRawData&, BGZF*)’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:260:29: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, magic, 4);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:271:34: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &version, 4);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:272:34: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &pbi_flags, 2);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:273:34: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &numReads, 4);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:278:33: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, reserved, 18);
^
In file included from /<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:38:0:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector<T>&) [with T = int]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &output[0], data.size()*sizeof(T));
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector<T>&) [with T = unsigned int]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector<T>&) [with T = unsigned char]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteReferenceData(const PacBio::BAM::PbiRawReferenceData&, BGZF*)’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:314:32: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &numRefs, 4);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:328:37: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &tId, 4);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:329:37: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &beginRow, 4);
^
/<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:330:37: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &endRow, 4);
^
In file included from /<<PKGBUILDDIR>>/src/PbiIndexIO.cpp:38:0:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector<T>&) [with T = float]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
bgzf_write(fp, &output[0], data.size()*sizeof(T));
^~~~~~~~~~
/<<PKGBUILDDIR>>/src/PbiIndexIO.h: In static member function ‘static void PacBio::BAM::internal::PbiIndexIO::WriteBgzfVector(BGZF*, const std::vector<T>&) [with T = long long int]’:
/<<PKGBUILDDIR>>/src/PbiIndexIO.h:158:5: warning: ignoring return value of ‘ssize_t bgzf_write(BGZF*, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
[ 57%] Building CXX object src/CMakeFiles/pbbam.dir/QualityValue.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/QualityValue.cpp.o -c /<<PKGBUILDDIR>>/src/QualityValue.cpp
[ 59%] Building CXX object src/CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o -c /<<PKGBUILDDIR>>/src/ReadAccuracyQuery.cpp
[ 60%] Building CXX object src/CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o -c /<<PKGBUILDDIR>>/src/ReadGroupInfo.cpp
[ 61%] Building CXX object src/CMakeFiles/pbbam.dir/SamTagCodec.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/SamTagCodec.cpp.o -c /<<PKGBUILDDIR>>/src/SamTagCodec.cpp
[ 63%] Building CXX object src/CMakeFiles/pbbam.dir/SequenceInfo.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/SequenceInfo.cpp.o -c /<<PKGBUILDDIR>>/src/SequenceInfo.cpp
[ 64%] Building CXX object src/CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o -c /<<PKGBUILDDIR>>/src/SubreadLengthQuery.cpp
[ 65%] Building CXX object src/CMakeFiles/pbbam.dir/Tag.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/Tag.cpp.o -c /<<PKGBUILDDIR>>/src/Tag.cpp
[ 67%] Building CXX object src/CMakeFiles/pbbam.dir/TagCollection.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/TagCollection.cpp.o -c /<<PKGBUILDDIR>>/src/TagCollection.cpp
[ 68%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualPolymeraseBamRecord.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/VirtualPolymeraseBamRecord.cpp.o -c /<<PKGBUILDDIR>>/src/VirtualPolymeraseBamRecord.cpp
[ 69%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualPolymeraseCompositeReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/VirtualPolymeraseCompositeReader.cpp.o -c /<<PKGBUILDDIR>>/src/VirtualPolymeraseCompositeReader.cpp
[ 71%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualPolymeraseReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/VirtualPolymeraseReader.cpp.o -c /<<PKGBUILDDIR>>/src/VirtualPolymeraseReader.cpp
[ 72%] Building CXX object src/CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o -c /<<PKGBUILDDIR>>/src/VirtualRegionTypeMap.cpp
[ 73%] Building CXX object src/CMakeFiles/pbbam.dir/XmlReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/XmlReader.cpp.o -c /<<PKGBUILDDIR>>/src/XmlReader.cpp
[ 75%] Building CXX object src/CMakeFiles/pbbam.dir/XmlWriter.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/XmlWriter.cpp.o -c /<<PKGBUILDDIR>>/src/XmlWriter.cpp
[ 76%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o -c /<<PKGBUILDDIR>>/src/ZmwGroupQuery.cpp
[ 77%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwQuery.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/ZmwQuery.cpp.o -c /<<PKGBUILDDIR>>/src/ZmwQuery.cpp
[ 78%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o -c /<<PKGBUILDDIR>>/src/ZmwTypeMap.cpp
[ 80%] Building CXX object src/CMakeFiles/pbbam.dir/ZmwWhitelistVirtualReader.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/ZmwWhitelistVirtualReader.cpp.o -c /<<PKGBUILDDIR>>/src/ZmwWhitelistVirtualReader.cpp
[ 81%] Building CXX object src/CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DPBBAM_LIBRARY -Dpbbam_EXPORTS -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -fPIC -o CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o -c /<<PKGBUILDDIR>>/src/pugixml/pugixml.cpp
[ 82%] Linking CXX shared library ../../lib/libpbbam.so
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/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -lssl -lhts -Wl,-z,relro -shared -Wl,-soname,libpbbam.so -o ../../lib/libpbbam.so CMakeFiles/pbbam.dir/Accuracy.cpp.o CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o CMakeFiles/pbbam.dir/AssertUtils.cpp.o CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o CMakeFiles/pbbam.dir/BamFile.cpp.o CMakeFiles/pbbam.dir/BamHeader.cpp.o CMakeFiles/pbbam.dir/BamReader.cpp.o CMakeFiles/pbbam.dir/BamRecord.cpp.o CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o CMakeFiles/pbbam.dir/BamTagCodec.cpp.o CMakeFiles/pbbam.dir/BamWriter.cpp.o CMakeFiles/pbbam.dir/BarcodeQuery.cpp.o CMakeFiles/pbbam.dir/ChemistryTable.cpp.o CMakeFiles/pbbam.dir/Cigar.cpp.o CMakeFiles/pbbam.dir/CigarOperation.cpp.o CMakeFiles/pbbam.dir/Compare.cpp.o CMakeFiles/pbbam.dir/Config.cpp.o CMakeFiles/pbbam.dir/DataSet.cpp.o CMakeFiles/pbbam.dir/DataSetBaseTypes.cpp.o CMakeFiles/pbbam.dir/DataSetElement.cpp.o CMakeFiles/pbbam.dir/DataSetIO.cpp.o CMakeFiles/pbbam.dir/DataSetTypes.cpp.o CMakeFiles/pbbam.dir/DataSetXsd.cpp.o CMakeFiles/pbbam.dir/EntireFileQuery.cpp.o CMakeFiles/pbbam.dir/FileUtils.cpp.o CMakeFiles/pbbam.dir/FofnReader.cpp.o CMakeFiles/pbbam.dir/Frames.cpp.o CMakeFiles/pbbam.dir/GenomicInterval.cpp.o CMakeFiles/pbbam.dir/GenomicIntervalQuery.cpp.o CMakeFiles/pbbam.dir/IndexedFastaReader.cpp.o CMakeFiles/pbbam.dir/MemoryUtils.cpp.o CMakeFiles/pbbam.dir/PbiBuilder.cpp.o CMakeFiles/pbbam.dir/PbiFile.cpp.o CMakeFiles/pbbam.dir/PbiFilter.cpp.o CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o CMakeFiles/pbbam.dir/PbiIndex.cpp.o CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o CMakeFiles/pbbam.dir/PbiRawData.cpp.o CMakeFiles/pbbam.dir/ProgramInfo.cpp.o CMakeFiles/pbbam.dir/QNameQuery.cpp.o CMakeFiles/pbbam.dir/QualityValue.cpp.o CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o CMakeFiles/pbbam.dir/SamTagCodec.cpp.o CMakeFiles/pbbam.dir/SequenceInfo.cpp.o CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o CMakeFiles/pbbam.dir/Tag.cpp.o CMakeFiles/pbbam.dir/TagCollection.cpp.o CMakeFiles/pbbam.dir/VirtualPolymeraseBamRecord.cpp.o CMakeFiles/pbbam.dir/VirtualPolymeraseCompositeReader.cpp.o CMakeFiles/pbbam.dir/VirtualPolymeraseReader.cpp.o CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o CMakeFiles/pbbam.dir/XmlReader.cpp.o CMakeFiles/pbbam.dir/XmlWriter.cpp.o CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o CMakeFiles/pbbam.dir/ZmwQuery.cpp.o CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o CMakeFiles/pbbam.dir/ZmwWhitelistVirtualReader.cpp.o CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o -lz -lpthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 82%] Built target pbbam
make -f tools/pbindex/CMakeFiles/pbindex.dir/build.make tools/pbindex/CMakeFiles/pbindex.dir/depend
make -f tools/pbindexdump/CMakeFiles/pbindexdump.dir/build.make tools/pbindexdump/CMakeFiles/pbindexdump.dir/depend
make -f tools/pbmerge/CMakeFiles/pbmerge.dir/build.make tools/pbmerge/CMakeFiles/pbmerge.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/tools/pbindex /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindex /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindex/CMakeFiles/pbindex.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/tools/pbmerge /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbmerge /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbmerge/CMakeFiles/pbmerge.dir/DependInfo.cmake --color=
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/tools/pbindexdump /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump/CMakeFiles/pbindexdump.dir/DependInfo.cmake --color=
Scanning dependencies of target pbindex
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make -f tools/pbindexdump/CMakeFiles/pbindexdump.dir/build.make tools/pbindexdump/CMakeFiles/pbindexdump.dir/build
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[ 84%] Building CXX object tools/pbindex/CMakeFiles/pbindex.dir/src/main.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindex && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindex -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbindex.dir/src/main.cpp.o -c /<<PKGBUILDDIR>>/tools/pbindex/src/main.cpp
[ 85%] Building CXX object tools/pbindex/CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindex && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindex -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o -c /<<PKGBUILDDIR>>/tools/common/OptionParser.cpp
[ 86%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o -c /<<PKGBUILDDIR>>/tools/common/OptionParser.cpp
[ 88%] Building CXX object tools/pbmerge/CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbmerge && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbmerge -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o -c /<<PKGBUILDDIR>>/tools/common/OptionParser.cpp
[ 89%] Building CXX object tools/pbindex/CMakeFiles/pbindex.dir/src/PbIndex.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindex && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindex -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbindex.dir/src/PbIndex.cpp.o -c /<<PKGBUILDDIR>>/tools/pbindex/src/PbIndex.cpp
[ 90%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o -c /<<PKGBUILDDIR>>/tools/pbindexdump/src/CppFormatter.cpp
[ 92%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o -c /<<PKGBUILDDIR>>/tools/pbindexdump/src/JsonFormatter.cpp
[ 93%] Building CXX object tools/pbmerge/CMakeFiles/pbmerge.dir/src/main.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbmerge && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbmerge -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbmerge.dir/src/main.cpp.o -c /<<PKGBUILDDIR>>/tools/pbmerge/src/main.cpp
[ 94%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o -c /<<PKGBUILDDIR>>/tools/pbindexdump/src/PbIndexDump.cpp
[ 96%] Linking CXX executable ../../../bin/pbindex
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindex && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbindex.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -Wl,-z,relro CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o CMakeFiles/pbindex.dir/src/main.cpp.o CMakeFiles/pbindex.dir/src/PbIndex.cpp.o -o ../../../bin/pbindex -rdynamic ../../../lib/libpbbam.so -lz -lpthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 96%] Built target pbindex
[ 97%] Building CXX object tools/pbindexdump/CMakeFiles/pbindexdump.dir/src/main.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump && /usr/bin/c++ -I/<<PKGBUILDDIR>>/tools/common -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump -I/<<PKGBUILDDIR>>/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -o CMakeFiles/pbindexdump.dir/src/main.cpp.o -c /<<PKGBUILDDIR>>/tools/pbindexdump/src/main.cpp
[ 98%] Linking CXX executable ../../../bin/pbindexdump
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbindexdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbindexdump.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -Wl,-z,relro CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o CMakeFiles/pbindexdump.dir/src/main.cpp.o -o ../../../bin/pbindexdump -rdynamic ../../../lib/libpbbam.so -lz -lpthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 98%] Built target pbindexdump
[100%] Linking CXX executable ../../../bin/pbmerge
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/tools/pbmerge && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbmerge.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wno-sign-compare -Wno-unused-local-typedefs -Wno-unused-private-field -Wl,-z,relro CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o CMakeFiles/pbmerge.dir/src/main.cpp.o -o ../../../bin/pbmerge -rdynamic ../../../lib/libpbbam.so -lz -lpthread
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target pbmerge
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
tests/src/cram/pbmerge_pacbio_ordering.t > tests/src/cram/pbmerge_pacbio_ordering.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
tests/src/cram/pbmerge_mixed_ordering.t > tests/src/cram/pbmerge_mixed_ordering.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
tests/src/cram/pbmerge_aligned_ordering.t > tests/src/cram/pbmerge_aligned_ordering.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
tests/src/cram/pbindexdump_json.t > tests/src/cram/pbindexdump_json.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
tests/src/cram/pbindexdump_cpp.t > tests/src/cram/pbindexdump_cpp.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
tests/src/cram/pbmerge_fofn.t > tests/src/cram/pbmerge_fofn.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
tests/src/cram/pbmerge_dataset.t > tests/src/cram/pbmerge_dataset.deb.t
TESTDIR=tests/src/cram cram -v tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbmerge_dataset.deb.t
tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed
tests/src/cram/pbmerge_mixed_ordering.deb.t: passed
tests/src/cram/pbmerge_aligned_ordering.deb.t: failed
--- tests/src/cram/pbmerge_aligned_ordering.deb.t
+++ tests/src/cram/pbmerge_aligned_ordering.deb.t.err
@@ -122,35 +122,13 @@
Explicit Output Filename (also enables PBI):
$ $PBMERGE -o $MERGED_BAM $INPUT_1 $INPUT_2
+ pbmerge: /<<PKGBUILDDIR>>/src/PbiBuilder.cpp:322: bool PacBio::BAM::internal::PbiBuilderPrivate::HasBarcodeData() const: Assertion `bcForward.size() == rawData_.NumReads()' failed.
+ Aborted
+ [134]
$ samtools view -H $MERGED_BAM
- @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
- @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
- @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
- @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
- @PG\tID:pbmerge-0.5.0\tPN:pbmerge\tVN:0.5.0 (esc)
$ samtools view $MERGED_BAM | cut -f 1,3,4 | head -n 20
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/7247/7338_7831\tlambda_NEB3011\t4904 (esc)
$ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
Found
tests/src/cram/pbindexdump_json.deb.t: passed
tests/src/cram/pbindexdump_cpp.deb.t: passed
tests/src/cram/pbmerge_fofn.deb.t: failed
--- tests/src/cram/pbmerge_fofn.deb.t
+++ tests/src/cram/pbmerge_fofn.deb.t.err
@@ -53,6 +53,9 @@
Normal Merge from FOFN:
$ $PBMERGE -o $MERGED_BAM $INPUT_FOFN
+ pbmerge: /<<PKGBUILDDIR>>/src/PbiBuilder.cpp:322: bool PacBio::BAM::internal::PbiBuilderPrivate::HasBarcodeData() const: Assertion `bcForward.size() == rawData_.NumReads()' failed.
+ Aborted
+ [134]
$ [ -f $MERGED_BAM ] && echo "Found" || echo "Not found"
Found
@@ -61,33 +64,8 @@
Found
$ samtools view -H $MERGED_BAM
- @HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
- @SQ\tSN:lambda_NEB3011\tLN:48502\tM5:a1319ff90e994c8190a4fe6569d0822a (esc)
- @RG\tID:a9a22406c5\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;SubstitutionTag=st;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0\tSM:c100564852550000001823085912221377\tPM:SEQUEL (esc)
- @PG\tID:BLASR\tVN:1.3.1.141565\tCL:/home/UNIXHOME/yli/for_the_people/blasr_bam_out/blasr m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5 lambdaNEB.fa -out tmp.bam -bam -bestn 10 -minMatch 12 -nproc 8 -minSubreadLength 50 -minReadLength 50 -randomSeed 1 -clipping subread (esc)
- @PG\tID:pbmerge-0.5.0\tPN:pbmerge\tVN:0.5.0 (esc)
$ samtools view $MERGED_BAM | cut -f 1,3,4 | head -n 20
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/7247/7338_7831\tlambda_NEB3011\t4904 (esc)
$ rm $MERGED_BAM
$ rm $MERGED_BAM_PBI
tests/src/cram/pbmerge_dataset.deb.t: passed
# Ran 7 tests, 0 skipped, 2 failed.
debian/rules:25: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:10: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2016-10-12T17:41:30Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 870
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 412
Job: pbbam_0.5.0-2
Machine Architecture: armhf
Package: pbbam
Package-Time: 1329
Source-Version: 0.5.0-2
Space: 0
Status: failed
Version: 0.5.0-2
--------------------------------------------------------------------------------
Finished at 2016-10-12T17:41:30Z
Build needed 00:00:00, 0k disc space