blasr →
5.3+0-1+b1 →
armhf → 2017-08-01 04:28:32
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| blasr 5.3+0-1+b1 (armhf) Tue, 01 Aug 2017 04:08:26 +0000 |
+==============================================================================+
Package: blasr
Version: 5.3+0-1+b1
Source Version: 5.3+0-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-9eb1a0ba-4e81-478f-80bc-cd42996ae8bc' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [11.9 MB]
Fetched 22.0 MB in 11s (1941 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'blasr' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/blasr.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/blasr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1226 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main blasr 5.3+0-1 (dsc) [1991 B]
Get:2 http://172.17.0.1/private buster-staging/main blasr 5.3+0-1 (tar) [1211 kB]
Get:3 http://172.17.0.1/private buster-staging/main blasr 5.3+0-1 (diff) [13.1 kB]
Fetched 1226 kB in 0s (3699 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/blasr-fiUMZB/blasr-5.3+0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/blasr-fiUMZB' 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-UUEW31/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-UUEW31/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-UUEW31/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-UUEW31/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (2910 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 14 not upgraded.
Need to get 770 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 770 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14837 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), python, cmake, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev
Filtered Build-Depends: debhelper (>= 9), python, cmake, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev
dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/<<BUILDDIR>>/resolver-UUEW31/apt_archive/sbuild-build-depends-blasr-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-blasr-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ Sources [541 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ Packages [622 B]
Fetched 2496 B in 0s (3479 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install blasr build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates openssl
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-strip-nondeterminism file gettext gettext-base
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarchive13 libblasr libblasr-dev libboost-dev
libboost1.62-dev libbsd0 libcroco3 libcurl3 libcurl3-gnutls libexpat1
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgssapi-krb5-2
libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhts-dev libhts2 libicu57
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpbbam libpbbam-dev
libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev libpipeline1
libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0
librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl-dev
libssl1.0.2 libsz2 libtimedate-perl libtool libuv1 libxml2 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev
groff lrzip libboost-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user
libhdf5-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less
www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libsasl2-modules 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-strip-nondeterminism file gettext gettext-base
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarchive13 libblasr libblasr-dev libboost-dev
libboost1.62-dev libbsd0 libcroco3 libcurl3 libcurl3-gnutls libexpat1
libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libgssapi-krb5-2
libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhts-dev libhts2 libicu57
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14 libpbbam libpbbam-dev
libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev libpipeline1
libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0
librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1 libssl-dev
libssl1.0.2 libsz2 libtimedate-perl libtool libuv1 libxml2 m4 man-db
mime-support po-debconf python python-minimal python2.7 python2.7-minimal
sbuild-build-depends-blasr-dummy zlib1g-dev
0 upgraded, 88 newly installed, 0 to remove and 14 not upgraded.
Need to get 46.5 MB of archives.
After this operation, 261 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UUEW31/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [826 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-1 [95.7 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf cmake-data all 3.9.0-1 [1294 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3 [601 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libarchive13 armhf 3.2.2-2 [254 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.1-2 [58.4 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.1-2 [115 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.1-2 [265 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [132 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3 [66.9 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3 [98.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libldap-common all 2.4.45+dfsg-1 [87.0 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libldap-2.4-2 armhf 2.4.45+dfsg-1 [197 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.24.0-1 [70.4 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.17.0-5 [42.0 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2l-2 [893 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.52.1-5 [261 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libexpat1 armhf 2.2.2-2 [66.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libjsoncpp1 armhf 1.7.4-3 [66.2 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf librhash0 armhf 1.3.4-2 [94.5 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libuv1 armhf 1.9.1-3 [73.2 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf cmake armhf 3.9.0-1 [2509 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.13-2 [389 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.13-2 [1178 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.13-2 [40.5 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.13-2 [1827 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.13-2 [285 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.13-2 [20.0 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.13-2 [154 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.30-1 [105 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2+b1 [117 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2 [736 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.52.3-1 [2576 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2+b1 [1220 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.6.4 [970 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-3 [35.9 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libaec0 armhf 0.3.2-1 [19.4 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.52.1-5 [259 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.4.1-5 [247 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libpbbam armhf 0.7.4+ds-1+rpi1+b1 [395 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libpbdata armhf 0~20161219-1 [106 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libgfortran3 armhf 6.4.0-1+rpi1 [166 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libsz2 armhf 0.3.2-1 [5836 B]
Get:70 http://172.17.0.1/private buster-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-3 [1203 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-3 [118 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpbihdf armhf 0~20161219-1 [141 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libblasr armhf 0~20161219-1 [828 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libblasr-dev armhf 0~20161219-1 [1672 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b6 [3916 B]
Get:77 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 0.3.2-1 [17.6 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-3 [2093 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.4.1-5 [338 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.0f-3 [1369 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.7.4+ds-1+rpi1+b1 [90.2 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libpbdata-dev armhf 0~20161219-1 [178 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libpbihdf-dev armhf 0~20161219-1 [249 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libpbseq-dev all 0~20161219-1 [3902 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package groff-base.
(Reading database ... 14837 files and directories currently installed.)
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Unpacking groff-base (1.22.3-9) ...
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Unpacking libbsd0:armhf (0.8.6-1) ...
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No schema files found: doing nothing.
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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
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Not building database; man-db/auto-update is not 'true'.
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Processing triggers for libc-bin (2.24-12) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1+rpi1 gcc-6_6.4.0-1+rpi1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.5~beta1+b3 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 cmake_3.9.0-1 cmake-data_3.9.0-1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1+rpi1 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.6.4 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-4d1 g++-6_6.4.0-1+rpi1 gcc_4:6.3.0-4d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6_6.4.0-1+rpi1 gcc-6-base_6.4.0-1+rpi1 gcc-7-base_7.1.0-9+rpi1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gpgv_2.1.18-8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-3 hostname_3.18 init-system-helpers_1.49 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libaec-dev_0.3.2-1 libaec0_0.3.2-1 libapparmor1_2.11.0-6 libapt-pkg5.0_1.5~beta1+b3 libarchive-zip-perl_1.59-1 libarchive13_3.2.2-2 libasan3_6.4.0-1+rpi1 libassuan0_2.4.3-2 libatomic1_7.1.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1 libblasr_0~20161219-1 libblasr-dev_0~20161219-1 libblkid1_2.29.2-2+rpi1 libboost-dev_1.62.0.1+b6 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-9+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libcurl3_7.52.1-5 libcurl3-gnutls_7.52.1-5 libdb5.3_5.3.28-12 libdbus-1-3_1.10.20-1 libdebconfclient0_0.229 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.81-2+rpi1 libexpat1_2.2.2-2 libfakeroot_1.21-3.1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-1+rpi1 libgcc1_1:7.1.0-9+rpi1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libgfortran3_6.4.0-1+rpi1 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-2 libgomp1_7.1.0-9+rpi1 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libhdf5-100_1.10.0-patch1+docs-3 libhdf5-cpp-100_1.10.0-patch1+docs-3 libhdf5-dev_1.10.0-patch1+docs-3 libhogweed4_3.3-1 libhts-dev_1.4.1-5 libhts2_1.4.1-5 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2 libisl15_0.18-1 libjpeg-dev_1:1.5.1-2 libjpeg62-turbo_1:1.5.1-2 libjpeg62-turbo-dev_1:1.5.1-2 libjsoncpp1_1.7.4-3 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1 libnghttp2-14_1.24.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpbbam_0.7.4+ds-1+rpi1+b1 libpbbam-dev_0.7.4+ds-1+rpi1+b1 libpbdata_0~20161219-1 libpbdata-dev_0~20161219-1 libpbihdf_0~20161219-1 libpbihdf-dev_0~20161219-1 libpbseq-dev_0~20161219-1 libpcre3_2:8.39-3 libperl5.24_5.24.1-7 libperl5.26_5.26.0-4 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-3 libpsl5_0.17.0-5 libpython-stdlib_2.7.13-2 libpython2.7-minimal_2.7.13-2 libpython2.7-stdlib_2.7.13-2 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 librhash0_1.3.4-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-2+rpi1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl-dev_1.1.0f-3 libssl1.0.2_1.0.2l-2 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 libsystemd0_233-10 libsz2_0.3.2-1 libtasn1-6_4.12-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.1.0-9+rpi1 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2+rpi1 libuv1_1.9.1-3 libxml2_2.9.4+dfsg1-3 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mime-support_3.60 mount_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-12 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-4 perl-base_5.26.0-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-4 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.13-2 python-minimal_2.7.13-2 python2.7_2.7.13-2 python2.7-minimal_2.7.13-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-blasr-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9+nmu1 systemd_233-10 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 tzdata_2017b-2 udev_233-10 util-linux_2.29.2-2+rpi1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Dec 24 01:52:57 2016 UTC
gpgv: using RSA key 59B2306F3AF9DDC1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./blasr_5.3+0-1.dsc
dpkg-source: info: extracting blasr in /<<BUILDDIR>>/blasr-5.3+0
dpkg-source: info: unpacking blasr_5.3+0.orig.tar.gz
dpkg-source: info: unpacking blasr_5.3+0-1.debian.tar.xz
dpkg-source: info: applying disable-gtest.patch
dpkg-source: info: applying cmake-utils.patch
Check disk space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 5.3+0-1+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-9eb1a0ba-4e81-478f-80bc-cd42996ae8bc
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package blasr
dpkg-buildpackage: info: source version 5.3+0-1+b1
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build blasr-5.3+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 '/<<BUILDDIR>>/blasr-5.3+0'
./configure.py --shared
`uname`
Linux
writing to '/<<BUILDDIR>>/blasr-5.3+0/defines.mk':
"""
HTSLIB_INC ?= /usr/include/htslib
HDF5_INC ?= /usr/include/hdf5/serial
PBBAM_INC ?= /usr/include
CXXFLAGS ?= -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security
LIBPBDATA_LIBFLAGS ?= -lpbdata
LIBPBIHDF_LIB ?= /usr/lib/arm-linux-gnueabihf
SHELL ?= bash
LIBPBDATA_INC ?= /usr/include/pbseq/pbdata
PBBAM_LIBFLAGS ?= -lpbbam
LIBPBIHDF_INC ?= /usr/include/pbseq/hdf
RT_LIBFLAGS ?= -lrt
ZLIB_LIBFLAGS ?= -lz
HTSLIB_LIB ?= /usr/lib/arm-linux-gnueabihf
PTHREAD_LIBFLAGS ?= -lpthread
LIBBLASR_LIBFLAGS ?= -lblasr
LIBPBDATA_LIB ?= /usr/lib/arm-linux-gnueabihf
HTSLIB_LIBFLAGS ?= -lhts
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5
DL_LIBFLAGS ?= -ldl
LIBPBIHDF_LIBFLAGS ?= -lpbihdf
LIBBLASR_INC ?= /usr/include/pbseq/alignment
LIBBLASR_LIB ?= /usr/lib/arm-linux-gnueabihf
PBBAM_LIB ?= /usr/lib/arm-linux-gnueabihf
BOOST_INC ?= /usr/include/boost
"""
----
/usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
make[2]: git: Command not found
rm -f blasr Blasr.o Blasr.d blasr.d
/usr/bin/make -C utils clean
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[4]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
make[4]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
make[4]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
make[4]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
/usr/bin/make -C extrautils clean
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/extrautils'
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/extrautils'
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
/usr/bin/make -C utils/bam2bax clean
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
/usr/bin/make -C utils/bax2bam clean
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
# This is created by configure.py
rm -f defines.mk
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
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 '/<<BUILDDIR>>/blasr-5.3+0'
./configure.py --shared
`uname`
Linux
writing to '/<<BUILDDIR>>/blasr-5.3+0/defines.mk':
"""
HTSLIB_INC ?= /usr/include/htslib
HDF5_INC ?= /usr/include/hdf5/serial
PBBAM_INC ?= /usr/include
CXXFLAGS ?= -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security
LIBPBDATA_LIBFLAGS ?= -lpbdata
LIBPBIHDF_LIB ?= /usr/lib/arm-linux-gnueabihf
SHELL ?= bash
LIBPBDATA_INC ?= /usr/include/pbseq/pbdata
PBBAM_LIBFLAGS ?= -lpbbam
LIBPBIHDF_INC ?= /usr/include/pbseq/hdf
RT_LIBFLAGS ?= -lrt
ZLIB_LIBFLAGS ?= -lz
HTSLIB_LIB ?= /usr/lib/arm-linux-gnueabihf
PTHREAD_LIBFLAGS ?= -lpthread
LIBBLASR_LIBFLAGS ?= -lblasr
LIBPBDATA_LIB ?= /usr/lib/arm-linux-gnueabihf
HTSLIB_LIBFLAGS ?= -lhts
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5
DL_LIBFLAGS ?= -ldl
LIBPBIHDF_LIBFLAGS ?= -lpbihdf
LIBBLASR_INC ?= /usr/include/pbseq/alignment
LIBBLASR_LIB ?= /usr/lib/arm-linux-gnueabihf
PBBAM_LIB ?= /usr/lib/arm-linux-gnueabihf
BOOST_INC ?= /usr/include/boost
"""
----
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
dh_auto_build
make -j4
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
make[2]: git: Command not found
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o Blasr.o Blasr.cpp
make -C utils
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o LoadPulses.o LoadPulses.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o PulseToFasta.o PulseToFasta.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SamToCmpH5.o SamToCmpH5.cpp
In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29:0,
from iblasr/BlasrHeaders.h:100,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In instantiation of 'void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]':
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:164:25: required from 'void BAMOutput::PrintAlignment(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::IRecordWriter&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]'
iblasr/BlasrUtilsImpl.hpp:974:182: required from here
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:24:44: warning: the compiler can assume that the address of 'read' will never be NULL [-Waddress]
if (dynamic_cast<SMRTSequence*>(&read) == NULL) {
^
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:43:0,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp: In instantiation of 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]':
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:129:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (refPos + 1 < reference.length and
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:130:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
queryPos + 1 < read.length and
~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:5:0,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp: In instantiation of 'int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]':
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:62:41: required from 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:1068:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
index[l] + lcpLength >= targetLength or // This shouldn't
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp: In instantiation of 'long int SuffixArray<T, Sigma, Compare, Tuple>::SearchLeftBound(T*, long int, DNALength, T, long int, long int) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]':
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:1056:32: required from 'int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:62:41: required from 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:763:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen == targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:773:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen < targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/cassert:44:0,
from /usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/../tuples/../../pbdata/CompressedSequence.hpp:3,
from /usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/../tuples/CompressedDNATuple.hpp:5,
from /usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:20,
from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:5,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:781:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
assert(index[m]+targetOffset < targetLength);
^
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:5:0,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp: In instantiation of 'long int SuffixArray<T, Sigma, Compare, Tuple>::SearchRightBound(T*, long int, DNALength, T, long int, long int) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]':
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:1057:33: required from 'int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:62:41: required from 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:813:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen == targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:817:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen < targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SamToM4.o SamToM4.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SamFilter.o SamFilter.cpp
In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29:0,
from iblasr/BlasrHeaders.h:100,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In function 'void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence]':
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:24:5: warning: nonnull argument 'read' compared to NULL [-Wnonnull-compare]
if (dynamic_cast<SMRTSequence*>(&read) == NULL) {
^~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o ToAfg.o ToAfg.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SAWriter.o SAWriter.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SDPMatcher.o SDPMatcher.cpp
g++ -o loadPulses LoadPulses.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"loadPulses.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
g++ -o pls2fasta PulseToFasta.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"pls2fasta.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
g++ -o samtoh5 SamToCmpH5.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"samtoh5.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
g++ -o samtom4 SamToM4.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"samtom4.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
g++ -o samFilter SamFilter.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"samFilter.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
g++ -o sawriter SAWriter.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"sawriter.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbbam/BamWriter.h:46,
from iblasr/BlasrHeaders.h:26,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
g++ -o toAfg ToAfg.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"toAfg.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbbam/BamWriter.h:46,
from iblasr/BlasrHeaders.h:26,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Distance = int; _Tp = PositionDNATuple; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbbam/BamWriter.h:46,
from iblasr/BlasrHeaders.h:26,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
^~~
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1960:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__sort(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~
/usr/include/c++/6/bits/stl_algo.h:1960:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In function 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>]':
/usr/include/c++/6/bits/stl_algo.h:4707:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
^~~
/usr/include/c++/6/bits/stl_algo.h:4707:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
^~~
/usr/include/c++/6/bits/stl_algo.h:4707:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
^~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:5,
from SDPMatcher.cpp:7:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h: In function 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>]':
/usr/include/c++/6/bits/stl_algo.h:4707:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
^~~
/usr/include/c++/6/bits/stl_algo.h:4707:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
^~~
/usr/include/c++/6/bits/stl_algo.h:4707:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
^~~
In file included from /usr/include/c++/6/bits/char_traits.h:39:0,
from /usr/include/c++/6/string:40,
from SDPMatcher.cpp:1:
/usr/include/c++/6/bits/stl_algobase.h: In function 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _ForwardIterator2 = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >]':
/usr/include/c++/6/bits/stl_algobase.h:120:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
iter_swap(_ForwardIterator1 __a, _ForwardIterator2 __b)
^~~~~~~~~
/usr/include/c++/6/bits/stl_algobase.h:120:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algobase.h:120:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:5,
from SDPMatcher.cpp:7:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:84:6: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::iter_swap(__result, __b);
^~~
/usr/include/c++/6/bits/stl_algo.h:91:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::iter_swap(__result, __a);
^~~
/usr/include/c++/6/bits/stl_algo.h:93:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::iter_swap(__result, __c);
^~~
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:5,
from SDPMatcher.cpp:7:
/usr/include/c++/6/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Distance = int; _Tp = PositionDNATuple; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:5,
from SDPMatcher.cpp:7:
/usr/include/c++/6/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
^~~
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1918:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In function 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTASequence; T_TargetSequence = FASTASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, DNASequence>; T_TupleList = TupleList<PositionDNATuple>]':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -o sdpMatcher SDPMatcher.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"sdpMatcher.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
/usr/include/c++/6/bits/stl_algo.h: In function 'void AlignSubreadToAlignmentTarget(ReadAlignments&, SMRTSequence&, SMRTSequence&, T_AlignmentCandidate*, int, ReadInterval&, int, MappingParameters&, MappingBuffers&, std::ostream&)':
/usr/include/c++/6/bits/stl_algo.h:4707:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
^~~
/usr/include/c++/6/bits/stl_algo.h:4707:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
^~~
/usr/include/c++/6/bits/stl_algo.h:4707:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' will change in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
^~~
g++ -o blasr -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"blasr.d" Blasr.o -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
LD_LIBRARY_PATH=/usr/lib/arm-linux-gnueabihf:/usr/lib/arm-linux-gnueabihf:/usr/lib/arm-linux-gnueabihf:/usr/lib/arm-linux-gnueabihf/hdf5/serial:/usr/lib/arm-linux-gnueabihf:/usr/lib/arm-linux-gnueabihf::
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
/usr/bin/make -C utils/bax2bam
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Re-run cmake no build system arguments
-- The C compiler identification is GNU 6.4.0
-- The CXX compiler identification is GNU 6.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
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-- Detecting C compile features
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-- 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
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-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.8")
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-- Looking for pthread_create in pthreads - not found
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-- Found Threads: TRUE
-- Performing Test HAS_NO_OVERLOADED_VIRTUAL
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-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNINITIALIZED
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-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEF - Success
-- Configuring done
-- Generating done
-- Build files have been written to: /<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build
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/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wno-overloaded-virtual -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-declarations -Wno-unused-local-typedef -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -Wl,--no-as-needed -ldl -pthread -lrt -rdynamic CMakeFiles/bax2bam.dir/main.cpp.o CMakeFiles/bax2bam.dir/Bax2Bam.cpp.o CMakeFiles/bax2bam.dir/CcsConverter.cpp.o CMakeFiles/bax2bam.dir/HqRegionConverter.cpp.o CMakeFiles/bax2bam.dir/IConverter.cpp.o CMakeFiles/bax2bam.dir/OptionParser.cpp.o CMakeFiles/bax2bam.dir/PolymeraseReadConverter.cpp.o CMakeFiles/bax2bam.dir/Settings.cpp.o CMakeFiles/bax2bam.dir/SubreadConverter.cpp.o -o ../../bin/bax2bam -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lpbbam -lhts -lz -lpthread -lrt -ldl
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-- The CXX compiler identification is GNU 6.4.0
-- The C compiler identification is GNU 6.4.0
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-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.8")
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-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEF - Success
-- Configuring done
-- Generating done
-- Build files have been written to: /<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
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/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wno-overloaded-virtual -Wno-unused-variable -Wno-uninitialized -Wunused-but-set-variable -Wno-deprecated-declarations -Wno-unused-local-typedef -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -Wl,--no-as-needed -ldl -pthread -lrt -rdynamic CMakeFiles/bam2bax.dir/Bam2BaxMain.cpp.o CMakeFiles/bam2bax.dir/Settings.cpp.o CMakeFiles/bam2bax.dir/Converter.cpp.o CMakeFiles/bam2bax.dir/Bam2Bax.cpp.o CMakeFiles/bam2bax.dir/OptionParser.cpp.o CMakeFiles/bam2bax.dir/MetadataWriter.cpp.o -o ../../bin/bam2bax -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lpbbam -lhts -lz -lrt
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/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wno-overloaded-virtual -Wno-unused-variable -Wno-uninitialized -Wunused-but-set-variable -Wno-deprecated-declarations -Wno-unused-local-typedef -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -Wl,--no-as-needed -ldl -pthread -lrt -rdynamic CMakeFiles/bam2plx.dir/Bam2PlxMain.cpp.o CMakeFiles/bam2plx.dir/Settings.cpp.o CMakeFiles/bam2plx.dir/Converter.cpp.o CMakeFiles/bam2plx.dir/Bam2Bax.cpp.o CMakeFiles/bam2plx.dir/OptionParser.cpp.o CMakeFiles/bam2plx.dir/MetadataWriter.cpp.o -o ../../bin/bam2plx -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lpbbam -lhts -lz -lrt
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dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samtoh5 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/sawriter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/bam2plx contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/bax2bam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/blasr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samtom4 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/sdpMatcher contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/bam2bax contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
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dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
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dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/loadPulses contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/pls2fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
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dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samFilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/toAfg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/blasr debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/toAfg were not linked against librt.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/blasr debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/toAfg were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/blasr debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/toAfg were not linked against libhts.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/blasr debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/toAfg were not linked against libdl.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/blasr debian/blasr/usr/bin/samtom4 debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/toAfg were not linked against libz.so.1 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
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dh_builddeb -a -O--parallel
dpkg-deb: building package 'blasr' in '../blasr_5.3+0-1+b1_armhf.deb'.
dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3+0-1+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../blasr_5.3+0-1+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build blasr-5.3+0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-08-01T04:28:27Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
blasr_5.3+0-1+b1_armhf.changes:
-------------------------------
Format: 1.8
Date: Fri, 23 Dec 2016 17:50:11 -0800
Source: blasr (5.3+0-1)
Binary: blasr
Binary-Only: yes
Architecture: armhf
Version: 5.3+0-1+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
blasr - mapping single-molecule sequencing reads
Changes:
blasr (5.3+0-1+b1) buster-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
c95399dae963f0c2afe79f8b8281faf22da0106b 10245422 blasr-dbgsym_5.3+0-1+b1_armhf.deb
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Checksums-Sha256:
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Files:
9ce9e4fd275d2fa4ca51a6b404af1f0a 10245422 debug extra blasr-dbgsym_5.3+0-1+b1_armhf.deb
f6194dd43c52a3703500bc6bbe2fd013 557198 science optional blasr_5.3+0-1+b1_armhf.deb
4509ea6a5b533c3b637b4070d5f2342a 6758 science optional blasr_5.3+0-1_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
blasr-dbgsym_5.3+0-1+b1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 10245422 bytes: control archive=1058 bytes.
828 bytes, 12 lines control
1272 bytes, 12 lines md5sums
Package: blasr-dbgsym
Source: blasr (5.3+0-1)
Version: 5.3+0-1+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10623
Depends: blasr (= 5.3+0-1+b1)
Section: debug
Priority: extra
Description: Debug symbols for blasr
Build-Ids: 17758d17fc7392fd1150f717544e037f4e30f680 227d03b146ce592ffda14f006faeddb5bae58967 25e21ab337c15d1667eaef11bb03b6b2716d1dc5 3ddbc2367745a9c4bc1797918fa493a81b3ec53a 72330ba59245b3f985cb6d7520944dfbbc13a710 8a008796a899b11c23674a73f7c37d2a1c9007e2 8b0aa3a985d73694d1791f95315609c6a03ef80a 990ff724b48980ab259648c3a8baa8ac6982e79e 99111459ccff07b05a21c73a4a349653990dcd5f a0d04b4130b9d66c512f54a93894804be6a1022e cb2893e0665f79452d1f69e7718811227bbace45 e989f0126cafc7046aef3612fa44b02019735e29
drwxr-xr-x root/root 0 2016-12-24 01:50 ./
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/
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-rw-r--r-- root/root 497648 2016-12-24 01:50 ./usr/lib/debug/.build-id/22/7d03b146ce592ffda14f006faeddb5bae58967.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/25/
-rw-r--r-- root/root 2487344 2016-12-24 01:50 ./usr/lib/debug/.build-id/25/e21ab337c15d1667eaef11bb03b6b2716d1dc5.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/3d/
-rw-r--r-- root/root 139664 2016-12-24 01:50 ./usr/lib/debug/.build-id/3d/dbc2367745a9c4bc1797918fa493a81b3ec53a.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/72/
-rw-r--r-- root/root 388416 2016-12-24 01:50 ./usr/lib/debug/.build-id/72/330ba59245b3f985cb6d7520944dfbbc13a710.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/8a/
-rw-r--r-- root/root 940016 2016-12-24 01:50 ./usr/lib/debug/.build-id/8a/008796a899b11c23674a73f7c37d2a1c9007e2.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/8b/
-rw-r--r-- root/root 274120 2016-12-24 01:50 ./usr/lib/debug/.build-id/8b/0aa3a985d73694d1791f95315609c6a03ef80a.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/99/
-rw-r--r-- root/root 834520 2016-12-24 01:50 ./usr/lib/debug/.build-id/99/0ff724b48980ab259648c3a8baa8ac6982e79e.debug
-rw-r--r-- root/root 3219068 2016-12-24 01:50 ./usr/lib/debug/.build-id/99/111459ccff07b05a21c73a4a349653990dcd5f.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/a0/
-rw-r--r-- root/root 563976 2016-12-24 01:50 ./usr/lib/debug/.build-id/a0/d04b4130b9d66c512f54a93894804be6a1022e.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/cb/
-rw-r--r-- root/root 274136 2016-12-24 01:50 ./usr/lib/debug/.build-id/cb/2893e0665f79452d1f69e7718811227bbace45.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/lib/debug/.build-id/e9/
-rw-r--r-- root/root 398048 2016-12-24 01:50 ./usr/lib/debug/.build-id/e9/89f0126cafc7046aef3612fa44b02019735e29.debug
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/share/
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-12-24 01:50 ./usr/share/doc/blasr-dbgsym -> blasr
blasr_5.3+0-1+b1_armhf.deb
--------------------------
new debian package, version 2.0.
size 557198 bytes: control archive=1490 bytes.
781 bytes, 15 lines control
1764 bytes, 29 lines md5sums
Package: blasr
Source: blasr (5.3+0-1)
Version: 5.3+0-1+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2158
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libhdf5-100, libhdf5-cpp-100 (>= 1.10.0), libhts2, libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), libpbseq (>= 0~20160912), libpbbam
Section: science
Priority: optional
Homepage: https://github.com/PacificBiosciences/blasr
Description: mapping single-molecule sequencing reads
Basic local alignment with successive refinement (BLASR) is a method
for mapping single-molecule sequencing reads against a reference genome.
Such reads are thousands of bases long, with divergence between them
and the genome being dominated by insertion and deletion error.
drwxr-xr-x root/root 0 2016-12-24 01:50 ./
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/bin/
-rwxr-xr-x root/root 149808 2016-12-24 01:50 ./usr/bin/bam2bax
-rwxr-xr-x root/root 145716 2016-12-24 01:50 ./usr/bin/bam2plx
-rwxr-xr-x root/root 506668 2016-12-24 01:50 ./usr/bin/bax2bam
-rwxr-xr-x root/root 474300 2016-12-24 01:50 ./usr/bin/blasr
-rwxr-xr-x root/root 289412 2016-12-24 01:50 ./usr/bin/loadPulses
-rwxr-xr-x root/root 108848 2016-12-24 01:50 ./usr/bin/pls2fasta
-rwxr-xr-x root/root 96412 2016-12-24 01:50 ./usr/bin/samFilter
-rwxr-xr-x root/root 133516 2016-12-24 01:50 ./usr/bin/samtoh5
-rwxr-xr-x root/root 55240 2016-12-24 01:50 ./usr/bin/samtom4
-rwxr-xr-x root/root 46952 2016-12-24 01:50 ./usr/bin/sawriter
-rwxr-xr-x root/root 79732 2016-12-24 01:50 ./usr/bin/sdpMatcher
-rwxr-xr-x root/root 79964 2016-12-24 01:50 ./usr/bin/toAfg
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/share/
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/share/doc/blasr/
-rw-r--r-- root/root 193 2016-10-24 02:19 ./usr/share/doc/blasr/NEWS.Debian.gz
-rw-r--r-- root/root 1173 2016-12-16 01:59 ./usr/share/doc/blasr/README.MANUAL.md
-rw-r--r-- root/root 92 2016-12-16 01:59 ./usr/share/doc/blasr/README.md
-rw-r--r-- root/root 95 2016-12-20 10:01 ./usr/share/doc/blasr/TODO.Debian
-rw-r--r-- root/root 218 2016-12-24 01:50 ./usr/share/doc/blasr/changelog.Debian.armhf.gz
-rw-r--r-- root/root 829 2016-12-24 01:50 ./usr/share/doc/blasr/changelog.Debian.gz
-rw-r--r-- root/root 2007 2016-07-24 23:35 ./usr/share/doc/blasr/copyright
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/share/lintian/
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 84 2016-10-24 00:26 ./usr/share/lintian/overrides/blasr
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/share/man/
drwxr-xr-x root/root 0 2016-12-24 01:50 ./usr/share/man/man1/
-rw-r--r-- root/root 5732 2016-12-24 01:50 ./usr/share/man/man1/blasr.1.gz
-rw-r--r-- root/root 936 2016-12-24 01:50 ./usr/share/man/man1/loadPulses.1.gz
-rw-r--r-- root/root 925 2016-12-24 01:50 ./usr/share/man/man1/pls2fasta.1.gz
-rw-r--r-- root/root 1397 2016-12-24 01:50 ./usr/share/man/man1/samFilter.1.gz
-rw-r--r-- root/root 925 2016-12-24 01:50 ./usr/share/man/man1/samtoh5.1.gz
-rw-r--r-- root/root 401 2016-12-24 01:50 ./usr/share/man/man1/samtom4.1.gz
-rw-r--r-- root/root 841 2016-12-24 01:50 ./usr/share/man/man1/sawriter.1.gz
-rw-r--r-- root/root 440 2016-12-24 01:50 ./usr/share/man/man1/sdpMatcher.1.gz
-rw-r--r-- root/root 311 2016-12-24 01:50 ./usr/share/man/man1/toAfg.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 119044
Build-Time: 754
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 426
Job: blasr_5.3+0-1
Machine Architecture: armhf
Package: blasr
Package-Time: 1201
Source-Version: 5.3+0-1
Space: 119044
Status: successful
Version: 5.3+0-1+b1
--------------------------------------------------------------------------------
Finished at 2017-08-01T04:28:27Z
Build needed 00:20:01, 119044k disk space