blasr →
5.3+0-2+b1 →
armhf → 2018-12-20 02:31:47
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| blasr 5.3+0-2+b1 (armhf) Thu, 20 Dec 2018 02:13:47 +0000 |
+==============================================================================+
Package: blasr
Version: 5.3+0-2+b1
Source Version: 5.3+0-2
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-88e9d940-bdbe-478e-867c-fca4870e2efb' 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 [11.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 MB]
Fetched 24.3 MB in 27s (898 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+0-2 (dsc) [2028 B]
Get:2 http://172.17.0.1/private buster-staging/main blasr 5.3+0-2 (tar) [1211 kB]
Get:3 http://172.17.0.1/private buster-staging/main blasr 5.3+0-2 (diff) [13.4 kB]
Fetched 1226 kB in 0s (6887 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/blasr-8cPu3p/blasr-5.3+0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/blasr-8cPu3p' 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-hTCqhb/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-hTCqhb/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hTCqhb/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (3035 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 dbus dbus-user-session krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
systemd-sysv
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 21 not upgraded.
Need to get 856 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 856 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14027 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 (>= 11~), python, cmake, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev
Filtered Build-Depends: debhelper (>= 11~), 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-hTCqhb/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-hTCqhb/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ Sources [540 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ Packages [621 B]
Fetched 2494 B in 1s (3597 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 dbus dbus-user-session krb5-locales libgpg-error-l10n
libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
cpp-8 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-8 gcc-8
gcc-8-base gettext gettext-base groff-base hdf5-helpers intltool-debian
libaec-dev libaec0 libarchive-zip-perl libarchive13 libasan5 libatomic1
libblasr libblasr-dev libboost-dev libboost1.67-dev libbsd0 libcc1-0
libcroco3 libcurl3-gnutls libcurl4 libelf1 libfile-stripnondeterminism-perl
libgcc-8-dev libgcc1 libgfortran5 libglib2.0-0 libgomp1 libhdf5-103
libhdf5-cpp-103 libhdf5-dev libhts-dev libhts2 libicu63 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp1 liblzma-dev libmagic-mgc
libmagic1 libnghttp2-14 libpbbam libpbbam-dev libpbdata libpbdata-dev
libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0
librtmp1 libsigsegv2 libssh2-1 libssl-dev libstdc++-8-dev libstdc++6 libsz2
libtool libubsan1 libuv1 libxml2 m4 man-db mime-support po-debconf python
python-minimal python2 python2-minimal python2.7 python2.7-minimal
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build gcc-8-locales dh-make gcc-8-doc
libstdc++6-8-dbg libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan5-dbg liblsan0-dbg libtsan0-dbg libubsan1-dbg libmpx2-dbg
libquadmath0-dbg gettext-doc libasprintf-dev libgettextpo-dev groff lrzip
libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libhdf5-doc liblzma-doc libssl-doc libstdc++-8-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python-doc python-tk python2-doc python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs publicsuffix libltdl-dev 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 dwz file gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarchive13 libblasr libblasr-dev libboost-dev
libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libcurl4 libelf1
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libhdf5-103
libhdf5-cpp-103 libhdf5-dev libhts-dev libhts2 libicu63 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp1 liblzma-dev libmagic-mgc
libmagic1 libnghttp2-14 libpbbam libpbbam-dev libpbdata libpbdata-dev
libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib librhash0
librtmp1 libsigsegv2 libssh2-1 libssl-dev libsz2 libtool libuv1 libxml2 m4
man-db mime-support po-debconf python python-minimal python2 python2-minimal
python2.7 python2.7-minimal sbuild-build-depends-blasr-dummy zlib1g-dev
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libstdc++-8-dev libstdc++6 libubsan1
13 upgraded, 81 newly installed, 0 to remove and 8 not upgraded.
Need to get 69.0 MB/69.8 MB of archives.
After this operation, 294 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hTCqhb/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.2.0-12+rpi1 [30.1 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-12+rpi1 [188 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-12+rpi1 [36.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-12+rpi1 [63.9 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-12+rpi1 [8108 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-12+rpi1 [318 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-12+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-12+rpi1 [5942 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-12+rpi1 [1565 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-12+rpi1 [3743 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-12+rpi1 [5848 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-12+rpi1 [5475 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-12+rpi1 [326 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-3 [1160 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-5 [394 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-5 [1089 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-3 [41.3 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-3 [20.9 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-5 [1844 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-5 [299 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-3 [20.7 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-3 [20.7 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-3 [41.5 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-3 [22.7 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf cmake-data all 3.13.2-1 [1476 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libarchive13 armhf 3.3.3-1 [269 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.35.1-1 [70.8 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.62.0-1 [286 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf librhash0 armhf 1.3.6-3 [97.1 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libuv1 armhf 1.24.0-1 [96.3 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf cmake armhf 3.13.2-1 [2563 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.5.4 [1003 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.4+repack-1 [33.0 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.62.0-1 [284 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libpbbam armhf 0.7.4+ds-1+rpi1+b1 [395 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libpbdata armhf 5.3.1+dfsg-1 [107 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-12+rpi1 [205 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libhdf5-103 armhf 1.10.4+repack-1 [1258 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-103 armhf 1.10.4+repack-1 [118 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libpbihdf armhf 5.3.1+dfsg-1 [137 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libblasr armhf 5.3.1+dfsg-1 [831 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libblasr-dev armhf 5.3.1+dfsg-1 [1664 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-11 [8386 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.67.0.1+b1 [4140 B]
Get:79 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.4+repack-1 [2220 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1a-1 [1556 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.7.4+ds-1+rpi1+b1 [90.2 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libpbdata-dev armhf 5.3.1+dfsg-1 [176 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libpbihdf-dev armhf 5.3.1+dfsg-1 [243 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libpbseq-dev all 5.3.1+dfsg-1 [4436 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 69.0 MB in 7s (10.4 MB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 14027 files and directories currently installed.)
Preparing to unpack .../libbsd0_0.9.1-1_armhf.deb ...
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Setting up libhdf5-cpp-103:armhf (1.10.4+repack-1) ...
Setting up libhdf5-dev (1.10.4+repack-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up python2 (2.7.15-3) ...
Setting up gcc-8 (8.2.0-12+rpi1) ...
Setting up g++-8 (8.2.0-12+rpi1) ...
Setting up libpython-stdlib:armhf (2.7.15-3) ...
Setting up libboost1.67-dev:armhf (1.67.0-11) ...
Setting up libpbbam:armhf (0.7.4+ds-1+rpi1+b1) ...
Setting up libboost-dev:armhf (1.67.0.1+b1) ...
Setting up python (2.7.15-3) ...
Setting up libpbbam-dev (0.7.4+ds-1+rpi1+b1) ...
Setting up libpbdata:armhf (5.3.1+dfsg-1) ...
Setting up libpbihdf:armhf (5.3.1+dfsg-1) ...
Setting up libblasr:armhf (5.3.1+dfsg-1) ...
Setting up libpbihdf-dev:armhf (5.3.1+dfsg-1) ...
Setting up libpbdata-dev:armhf (5.3.1+dfsg-1) ...
Setting up libblasr-dev:armhf (5.3.1+dfsg-1) ...
Setting up libpbseq-dev (5.3.1+dfsg-1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (11.5.4) ...
Setting up sbuild-build-depends-blasr-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (1.0.0-1) ...
Processing triggers for libc-bin (2.28-2) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-10+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-12+rpi1 gcc-8_8.2.0-12+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-12+rpi1 libstdc++6_8.2.0-12+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-10+rpi1 binutils-arm-linux-gnueabihf_2.31.1-10+rpi1 binutils-common_2.31.1-10+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 cmake_3.13.2-1 cmake-data_3.13.2-1 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-12+rpi1 dash_0.5.10.2-2 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.69 debhelper_11.5.4 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.11-1 dmsetup_2:1.02.145-4.1+b5 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-12+rpi1 gcc_4:8.2.0-2+rpi1 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_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1 gcc-8_8.2.0-12+rpi1 gcc-8-base_8.2.0-12+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.11-1 gnupg-l10n_2.2.11-1 gnupg-utils_2.2.11-1 gpg_2.2.11-1 gpg-agent_2.2.11-1 gpg-wks-client_2.2.11-1 gpg-wks-server_2.2.11-1 gpgconf_2.2.11-1 gpgsm_2.2.11-1 gpgv_2.2.11-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hdf5-helpers_1.10.4+repack-1 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha2 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-10+rpi1 libblasr_5.3.1+dfsg-1 libblasr-dev_5.3.1+dfsg-1 libblkid1_2.33-0.2 libboost-dev_1.67.0.1+b1 libboost1.67-dev_1.67.0-11 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-12+rpi1 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.62.0-1 libcurl4_7.62.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libgcc-8-dev_8.2.0-12+rpi1 libgcc1_1:8.2.0-12+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran5_8.2.0-12+rpi1 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.5.19-1+b1 libgomp1_8.2.0-12+rpi1 libgpg-error-l10n_1.32-3 libgpg-error0_1.32-3 libgssapi-krb5-2_1.16.1-1 libhdf5-103_1.10.4+repack-1 libhdf5-cpp-103_1.10.4+repack-1 libhdf5-dev_1.10.4+repack-1 libhogweed4_3.4.1~rc1-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-2+b1 libisl19_0.20-2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1+b1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 libnpth0_1.6-1 libnss-systemd_239-15+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-15+rpi1 libpam0g_1.1.8-3.8 libpbbam_0.7.4+ds-1+rpi1+b1 libpbbam-dev_0.7.4+ds-1+rpi1+b1 libpbdata_5.3.1+dfsg-1 libpbdata-dev_5.3.1+dfsg-1 libpbihdf_5.3.1+dfsg-1 libpbihdf-dev_5.3.1+dfsg-1 libpbseq-dev_5.3.1+dfsg-1 libpcre3_2:8.39-11+rpi1 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libplymouth4_0.9.4-1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-3 libpython2-stdlib_2.7.15-3 libpython2.7-minimal_2.7.15-5 libpython2.7-stdlib_2.7.15-5 libreadline7_7.0-5 librhash0_1.3.6-3 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33-0.2 libsqlite3-0_3.26.0-3 libss2_1.44.4-2 libssh2-1_1.8.0-2 libssl-dev_1.1.1a-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-12+rpi1 libstdc++6_8.2.0-12+rpi1 libsystemd0_239-15+rpi1 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-6 libubsan1_8.2.0-12+rpi1 libudev1_239-15+rpi1 libunistring2_0.9.10-1 libuuid1_2.33-0.2 libuv1_1.24.0-1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-3 mawk_1.3.3-17 mime-support_3.61 mount_2.33-0.2 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-3 python-minimal_2.7.15-3 python2_2.7.15-3 python2-minimal_2.7.15-3 python2.7_2.7.15-5 python2.7-minimal_2.7.15-5 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-blasr-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.5-2 sensible-utils_0.0.12 systemd_239-15+rpi1 systemd-sysv_239-15+rpi1 sysvinit-utils_2.93-1 tar_1.30+dfsg-3+rpi1 tzdata_2018g-1 udev_239-15+rpi1 util-linux_2.33-0.2 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Mar 11 17:10:30 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./blasr_5.3+0-2.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+0-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying disable-gtest.patch
dpkg-source: info: applying cmake-utils.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 5.3+0-2+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=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-88e9d940-bdbe-478e-867c-fca4870e2efb
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package blasr
dpkg-buildpackage: info: source version 5.3+0-2+b1
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
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 -DHAVE_HDF5_1_10_1
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
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
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 -DHAVE_HDF5_1_10_1
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 "INSTALL=install --strip-program=true"
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 -DHAVE_HDF5_1_10_1 -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 -DHAVE_HDF5_1_10_1 -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 -DHAVE_HDF5_1_10_1 -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 -DHAVE_HDF5_1_10_1 -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 iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
iblasr/BlasrHeaders.h:24:10: fatal error: libconfig.h: No such file or directory
#include <libconfig.h>
^~~~~~~~~~~~~
compilation terminated.
make[2]: *** [<builtin>: Blasr.o] Error 1
make[2]: *** Waiting for unfinished jobs....
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 -DHAVE_HDF5_1_10_1 -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
SamToM4.cpp: In function 'int main(int, char**)':
SamToM4.cpp:34:5: error: 'string' was not declared in this scope
string program = "samtom4";
^~~~~~
SamToM4.cpp:34:5: note: suggested alternative:
In file included from /usr/include/c++/8/iosfwd:39,
from /usr/include/c++/8/ios:38,
from /usr/include/c++/8/ostream:38,
from /usr/include/c++/8/iostream:39,
from SamToM4.cpp:18:
/usr/include/c++/8/bits/stringfwd.h:74:33: note: 'std::__cxx11::string'
typedef basic_string<char> string;
^~~~~~
SamToM4.cpp:35:11: error: expected ';' before 'versionString'
string versionString = VERSION;
^~~~~~~~~~~~~~
;
SamToM4.cpp:36:55: error: 'versionString' was not declared in this scope
AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
^~~~~~~~~~~~~
SamToM4.cpp:38:11: error: expected ';' before 'samFileName'
string samFileName, refFileName, outFileName;
^~~~~~~~~~~~
;
SamToM4.cpp:44:24: error: 'program' was not declared in this scope
clp.SetProgramName(program);
^~~~~~~
SamToM4.cpp:47:48: error: 'samFileName' was not declared in this scope
clp.RegisterStringOption("in.sam", &samFileName,
^~~~~~~~~~~
SamToM4.cpp:47:48: note: suggested alternative: 'samFile'
clp.RegisterStringOption("in.sam", &samFileName,
^~~~~~~~~~~
samFile
SamToM4.cpp:49:50: error: 'refFileName' was not declared in this scope
clp.RegisterStringOption("reference.fasta", &refFileName,
^~~~~~~~~~~
SamToM4.cpp:51:50: error: 'outFileName' was not declared in this scope
clp.RegisterStringOption("out.m4", &outFileName,
^~~~~~~~~~~
SamToM4.cpp:64:5: error: 'ostream' was not declared in this scope
ostream * outFilePtr = &cout;
^~~~~~~
SamToM4.cpp:64:5: note: suggested alternative:
In file included from /usr/include/c++/8/ios:38,
from /usr/include/c++/8/ostream:38,
from /usr/include/c++/8/iostream:39,
from SamToM4.cpp:18:
/usr/include/c++/8/iosfwd:141:33: note: 'std::ostream'
typedef basic_ostream<char> ostream;
^~~~~~~
SamToM4.cpp:64:15: error: 'outFilePtr' was not declared in this scope
ostream * outFilePtr = &cout;
^~~~~~~~~~
SamToM4.cpp:64:29: error: 'cout' was not declared in this scope
ostream * outFilePtr = &cout;
^~~~
SamToM4.cpp:64:29: note: suggested alternative:
In file included from SamToM4.cpp:18:
/usr/include/c++/8/iostream:61:18: note: 'std::cout'
extern ostream cout; /// Linked to standard output
^~~~
SamToM4.cpp:65:2: error: 'ofstream' was not declared in this scope
ofstream outFileStrm;
^~~~~~~~
SamToM4.cpp:65:2: note: suggested alternative:
In file included from /usr/include/c++/8/ios:38,
from /usr/include/c++/8/ostream:38,
from /usr/include/c++/8/iostream:39,
from SamToM4.cpp:18:
/usr/include/c++/8/iosfwd:165:34: note: 'std::ofstream'
typedef basic_ofstream<char> ofstream;
^~~~~~~~
SamToM4.cpp:67:28: error: 'outFileStrm' was not declared in this scope
CrucialOpen(outFileName, outFileStrm, std::ios::out);
^~~~~~~~~~~
SamToM4.cpp:83:11: error: expected ';' before 'command'
string command;
^~~~~~~~
;
SamToM4.cpp:84:56: error: 'command' was not declared in this scope
CommandLineParser::CommandLineToString(argc, argv, command);
^~~~~~~
SamToM4.cpp:89:5: error: 'vector' was not declared in this scope
vector<FASTASequence> references;
^~~~~~
SamToM4.cpp:89:5: note: suggested alternative:
In file included from /usr/include/c++/8/vector:64,
from /usr/include/pbbam/Frames.h:46,
from /usr/include/pbbam/BamRecord.h:46,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from SamToM4.cpp:19:
/usr/include/c++/8/bits/stl_vector.h:339:11: note: 'std::vector'
class vector : protected _Vector_base<_Tp, _Alloc>
^~~~~~
SamToM4.cpp:89:25: error: expected primary-expression before '>' token
vector<FASTASequence> references;
^
SamToM4.cpp:89:27: error: 'references' was not declared in this scope
vector<FASTASequence> references;
^~~~~~~~~~
SamToM4.cpp:107:5: error: 'map' was not declared in this scope
map<string, string> shortRefNameToFull;
^~~
SamToM4.cpp:107:5: note: suggested alternative:
In file included from /usr/include/c++/8/map:61,
from /usr/include/boost/detail/container_fwd.hpp:94,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from /usr/include/pbbam/Tag.h:46,
from /usr/include/pbbam/TagCollection.h:46,
from /usr/include/pbbam/BamRecordImpl.h:50,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from SamToM4.cpp:19:
/usr/include/c++/8/bits/stl_map.h:100:11: note: 'std::map'
class map
^~~
SamToM4.cpp:107:25: error: 'shortRefNameToFull' was not declared in this scope
map<string, string> shortRefNameToFull;
^~~~~~~~~~~~~~~~~~
SamToM4.cpp:107:25: note: suggested alternative: 'useShortRefName'
map<string, string> shortRefNameToFull;
^~~~~~~~~~~~~~~~~~
useShortRefName
SamToM4.cpp:108:26: error: '::iterator' has not been declared
map<string, string>::iterator it;
^~~~~~~~
SamToM4.cpp:108:26: note: suggested alternatives:
In file included from /usr/include/c++/8/bits/stl_algobase.h:65,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/ostream:38,
from /usr/include/c++/8/iostream:39,
from SamToM4.cpp:18:
/usr/include/c++/8/bits/stl_iterator_base_types.h:118:12: note: 'std::iterator'
struct iterator
^~~~~~~~
/usr/include/c++/8/bits/stl_iterator_base_types.h:118:12: note: 'std::iterator'
SamToM4.cpp:112:19: error: expected ';' before 'shortRefName'
string shortRefName = alignmentSet.references[i].GetSequenceName();
^~~~~~~~~~~~~
;
SamToM4.cpp:113:19: error: expected ';' before 'fullRefName'
string fullRefName(references[i].title);
^~~~~~~~~~~~
;
SamToM4.cpp:114:41: error: 'shortRefName' was not declared in this scope
if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) {
^~~~~~~~~~~~
SamToM4.cpp:114:41: note: suggested alternative: 'useShortRefName'
if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) {
^~~~~~~~~~~~
useShortRefName
SamToM4.cpp:115:103: error: 'endl' was not declared in this scope
cout << "ERROR, Found more than one reference " << shortRefName << "in sam header" << endl;
^~~~
SamToM4.cpp:115:103: note: suggested alternative:
In file included from /usr/include/c++/8/iostream:39,
from SamToM4.cpp:18:
/usr/include/c++/8/ostream:590:5: note: 'std::endl'
endl(basic_ostream<_CharT, _Traits>& __os)
^~~~
SamToM4.cpp:118:32: error: 'shortRefName' was not declared in this scope
shortRefNameToFull[shortRefName] = fullRefName;
^~~~~~~~~~~~
SamToM4.cpp:118:32: note: suggested alternative: 'useShortRefName'
shortRefNameToFull[shortRefName] = fullRefName;
^~~~~~~~~~~~
useShortRefName
SamToM4.cpp:118:48: error: 'fullRefName' was not declared in this scope
shortRefNameToFull[shortRefName] = fullRefName;
^~~~~~~~~~~
SamToM4.cpp:124:17: error: expected primary-expression before 'int'
map<string, int> refNameToIndex;
^~~
SamToM4.cpp:126:15: error: expected ';' before 'refName'
string refName = alignmentSet.references[i].GetSequenceName();
^~~~~~~~
;
SamToM4.cpp:127:9: error: 'refNameToIndex' was not declared in this scope
refNameToIndex[refName] = i;
^~~~~~~~~~~~~~
SamToM4.cpp:127:24: error: 'refName' was not declared in this scope
refNameToIndex[refName] = i;
^~~~~~~
SamToM4.cpp:127:24: note: suggested alternative: 'rename'
refNameToIndex[refName] = i;
^~~~~~~
rename
SamToM4.cpp:157:13: error: 'it' was not declared in this scope
it = shortRefNameToFull.find(samAlignment.rName);
^~
SamToM4.cpp:157:13: note: suggested alternative: 'Fit'
it = shortRefNameToFull.find(samAlignment.rName);
^~
Fit
SamToM4.cpp:159:110: error: 'endl' was not declared in this scope
cout << "ERROR, Could not find " << samAlignment.rName << " in the reference repository." << endl;
^~~~
SamToM4.cpp:159:110: note: suggested alternative:
In file included from /usr/include/c++/8/iostream:39,
from SamToM4.cpp:18:
/usr/include/c++/8/ostream:590:5: note: 'std::endl'
endl(basic_ostream<_CharT, _Traits>& __os)
^~~~
SamToM4.cpp:166:45: error: 'string' is not a class, namespace, or enumeration
if (samAlignment.cigar.find('P') != string::npos) {
^~~~~~
SamToM4.cpp:168:21: error: 'endl' was not declared in this scope
<< endl;
^~~~
SamToM4.cpp:168:21: note: suggested alternative:
In file included from /usr/include/c++/8/iostream:39,
from SamToM4.cpp:18:
/usr/include/c++/8/ostream:590:5: note: 'std::endl'
endl(basic_ostream<_CharT, _Traits>& __os)
^~~~
SamToM4.cpp:172:37: error: expected primary-expression before '>' token
vector<AlignmentCandidate<> > convertedAlignments;
^
SamToM4.cpp:172:39: error: 'convertedAlignments' was not declared in this scope
vector<AlignmentCandidate<> > convertedAlignments;
^~~~~~~~~~~~~~~~~~~
SamToM4.cpp:181:61: error: 'refNameToIndex' was not declared in this scope
SAMAlignmentsToCandidates(samAlignment, references, refNameToIndex,
^~~~~~~~~~~~~~
SamToM4.cpp:186:84: error: 'endl' was not declared in this scope
cout << "WARNING. Ignore an alignment which has multiple segments." << endl;
^~~~
SamToM4.cpp:186:84: note: suggested alternative:
In file included from /usr/include/c++/8/iostream:39,
from SamToM4.cpp:18:
/usr/include/c++/8/ostream:590:5: note: 'std::endl'
endl(basic_ostream<_CharT, _Traits>& __os)
^~~~
SamToM4.cpp:219:3: error: 'outFileStrm' was not declared in this scope
outFileStrm.close();
^~~~~~~~~~~
In file included from PulseToFasta.cpp:5:
/usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function 'int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)':
/usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (DataSetIException e) {
^
SamToCmpH5.cpp: In function 'int main(int, char**)':
SamToCmpH5.cpp:19:3: error: 'string' was not declared in this scope
string program = "samtoh5";
^~~~~~
SamToCmpH5.cpp:19:3: note: suggested alternative:
In file included from /usr/include/c++/8/iosfwd:39,
from /usr/include/c++/8/ios:38,
from /usr/include/c++/8/ostream:38,
from /usr/include/c++/8/iostream:39,
from SamToCmpH5.cpp:1:
/usr/include/c++/8/bits/stringfwd.h:74:33: note: 'std::__cxx11::string'
typedef basic_string<char> string;
^~~~~~
SamToCmpH5.cpp:20:9: error: expected ';' before 'versionString'
string versionString = VERSION;
^~~~~~~~~~~~~~
;
SamToCmpH5.cpp:21:53: error: 'versionString' was not declared in this scope
AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
^~~~~~~~~~~~~
SamToCmpH5.cpp:22:9: error: expected ';' before 'samFileName'
string samFileName, cmpFileName, refFileName;
^~~~~~~~~~~~
;
SamToCmpH5.cpp:27:9: error: expected ';' before 'readType'
string readType = "standard";
^~~~~~~~~
;
SamToCmpH5.cpp:30:22: error: 'program' was not declared in this scope
clp.SetProgramName(program);
^~~~~~~
SamToCmpH5.cpp:34:39: error: 'samFileName' was not declared in this scope
clp.RegisterStringOption("in.sam", &samFileName,
^~~~~~~~~~~
SamToCmpH5.cpp:34:39: note: suggested alternative: 'samFile'
clp.RegisterStringOption("in.sam", &samFileName,
^~~~~~~~~~~
samFile
SamToCmpH5.cpp:36:48: error: 'refFileName' was not declared in this scope
clp.RegisterStringOption("reference.fasta", &refFileName,
^~~~~~~~~~~
SamToCmpH5.cpp:38:43: error: 'cmpFileName' was not declared in this scope
clp.RegisterStringOption("out.cmp.h5", &cmpFileName,
^~~~~~~~~~~
SamToCmpH5.cpp:38:43: note: suggested alternative: 'CmpFile'
clp.RegisterStringOption("out.cmp.h5", &cmpFileName,
^~~~~~~~~~~
CmpFile
SamToCmpH5.cpp:50:41: error: 'readType' was not declared in this scope
clp.RegisterStringOption("readType", &readType,
^~~~~~~~
In file included from LoadPulses.cpp:5:
/usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function 'int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)':
/usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (DataSetIException e) {
^
SamToCmpH5.cpp:50:41: note: suggested alternative: 'ReadType'
clp.RegisterStringOption("readType", &readType,
^~~~~~~~
ReadType
SamToCmpH5.cpp:64:9: error: expected ';' before 'description'
string description = ("Because SAM has optional tags that have different "
^~~~~~~~~~~~
;
SamToCmpH5.cpp:72:19: error: 'description' was not declared in this scope
clp.SetExamples(description);
^~~~~~~~~~~
SamToCmpH5.cpp:72:19: note: suggested alternatives:
In file included from /usr/include/pbseq/pbdata/reads/RegionTable.hpp:15,
from /usr/include/pbseq/pbdata/SMRTSequence.hpp:14,
from /usr/include/pbseq/hdf/HDFCmpFile.hpp:25,
from SamToCmpH5.cpp:6:
/usr/include/pbseq/pbdata/PacBioDefs.h:72:26: note: 'PacBio::AttributeNames::Common::description'
static const std::string description = "Description";
^~~~~~~~~~~
/usr/include/pbseq/pbdata/PacBioDefs.h:107:26: note: 'PacBio::AttributeValues::ZMW::HoleNumber::description'
static const std::string description = "Hole number on chip array";
^~~~~~~~~~~
/usr/include/pbseq/pbdata/PacBioDefs.h:111:26: note: 'PacBio::AttributeValues::ZMW::HoleStatus::description'
static const std::string description = "Type of data coming from ZMW";
^~~~~~~~~~~
/usr/include/pbseq/pbdata/PacBioDefs.h:121:26: note: 'PacBio::AttributeValues::ZMW::HoleXY::description'
static const std::string description = "Coordinates of ZMW on Chip";
^~~~~~~~~~~
/usr/include/pbseq/pbdata/PacBioDefs.h:125:26: note: 'PacBio::AttributeValues::ZMW::BaseLineSigma::description'
static const std::string description = "Estimated baseline sigma (std dev) over trace";
^~~~~~~~~~~
/usr/include/pbseq/pbdata/PacBioDefs.h:145:26: note: 'PacBio::AttributeValues::ZMWMetrics::HQRegionSNR::description'
static const std::string description = "HQRegion average signal to noise ratio";
^~~~~~~~~~~
/usr/include/pbseq/pbdata/PacBioDefs.h:148:26: note: 'PacBio::AttributeValues::ZMWMetrics::ReadScore::description'
static const std::string description = "Read raw accuracy prediction";
^~~~~~~~~~~
/usr/include/pbseq/pbdata/PacBioDefs.h:151:26: note: 'PacBio::AttributeValues::ZMWMetrics::Productivity::description'
static const std::string description = "ZMW productivity classification";
^~~~~~~~~~~
SamToCmpH5.cpp:78:5: error: 'cout' was not declared in this scope
cout << "ERROR. Read type '" << readType
^~~~
SamToCmpH5.cpp:78:5: note: suggested alternative:
In file included from SamToCmpH5.cpp:1:
/usr/include/c++/8/iostream:61:18: note: 'std::cout'
extern ostream cout; /// Linked to standard output
^~~~
SamToCmpH5.cpp:80:13: error: 'endl' was not declared in this scope
<< endl;
^~~~
SamToCmpH5.cpp:80:13: note: suggested alternative:
In file included from /usr/include/c++/8/iostream:39,
from SamToCmpH5.cpp:1:
/usr/include/c++/8/ostream:590:5: note: 'std::endl'
endl(basic_ostream<_CharT, _Traits>& __os)
^~~~
SamToCmpH5.cpp:84:3: error: 'cerr' was not declared in this scope
cerr << "[INFO] " << GetTimestamp() << " [" << program << "] started." << endl;
^~~~
SamToCmpH5.cpp:84:3: note: suggested alternative:
In file included from SamToCmpH5.cpp:1:
/usr/include/c++/8/iostream:62:18: note: 'std::cerr'
extern ostream cerr; /// Linked to standard error (unbuffered)
^~~~
SamToCmpH5.cpp:84:77: error: 'endl' was not declared in this scope
cerr << "[INFO] " << GetTimestamp() << " [" << program << "] started." << endl;
^~~~
SamToCmpH5.cpp:84:77: note: suggested alternative:
In file included from /usr/include/c++/8/iostream:39,
from SamToCmpH5.cpp:1:
/usr/include/c++/8/ostream:590:5: note: 'std::endl'
endl(basic_ostream<_CharT, _Traits>& __os)
^~~~
SamToCmpH5.cpp:100:9: error: expected ';' before 'command'
string command;
^~~~~~~~
;
SamToCmpH5.cpp:101:54: error: 'command' was not declared in this scope
CommandLineParser::CommandLineToString(argc, argv, command);
^~~~~~~
SamToCmpH5.cpp:102:9: error: expected ';' before 'log'
string log = "Convert sam to cmp.h5";
^~~~
;
SamToCmpH5.cpp:114:3: error: 'vector' was not declared in this scope
vector<FASTASequence> references;
^~~~~~
SamToCmpH5.cpp:114:3: note: suggested alternative:
In file included from /usr/include/c++/8/vector:64,
from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:5,
from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
from SamToCmpH5.cpp:3:
/usr/include/c++/8/bits/stl_vector.h:339:11: note: 'std::vector'
class vector : protected _Vector_base<_Tp, _Alloc>
^~~~~~
SamToCmpH5.cpp:114:23: error: expected primary-expression before '>' token
vector<FASTASequence> references;
^
SamToCmpH5.cpp:114:25: error: 'references' was not declared in this scope
vector<FASTASequence> references;
^~~~~~~~~~
SamToCmpH5.cpp:114:25: note: suggested alternative: 'H5Rdereference1'
vector<FASTASequence> references;
^~~~~~~~~~
H5Rdereference1
SamToCmpH5.cpp:146:3: error: 'map' was not declared in this scope
map<string, string> shortRefNameToFull;
^~~
SamToCmpH5.cpp:146:3: note: suggested alternative:
In file included from /usr/include/c++/8/map:61,
from /usr/include/boost/detail/container_fwd.hpp:94,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from /usr/include/pbbam/Tag.h:46,
from /usr/include/pbbam/TagCollection.h:46,
from /usr/include/pbbam/BamRecordImpl.h:50,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:9,
from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
from SamToCmpH5.cpp:3:
/usr/include/c++/8/bits/stl_map.h:100:11: note: 'std::map'
class map
^~~
SamToCmpH5.cpp:146:23: error: 'shortRefNameToFull' was not declared in this scope
map<string, string> shortRefNameToFull;
^~~~~~~~~~~~~~~~~~
SamToCmpH5.cpp:146:23: note: suggested alternative: 'useShortRefName'
map<string, string> shortRefNameToFull;
^~~~~~~~~~~~~~~~~~
useShortRefName
SamToCmpH5.cpp:147:24: error: '::iterator' has not been declared
map<string, string>::iterator it;
^~~~~~~~
SamToCmpH5.cpp:147:24: note: suggested alternatives:
In file included from /usr/include/c++/8/bits/stl_algobase.h:65,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/ios:40,
from /usr/include/c++/8/ostream:38,
from /usr/include/c++/8/iostream:39,
from SamToCmpH5.cpp:1:
/usr/include/c++/8/bits/stl_iterator_base_types.h:118:12: note: 'std::iterator'
struct iterator
^~~~~~~~
/usr/include/c++/8/bits/stl_iterator_base_types.h:118:12: note: 'std::iterator'
SamToCmpH5.cpp:151:17: error: expected ';' before 'shortRefName'
string shortRefName = alignmentSet.references[i].GetSequenceName();
^~~~~~~~~~~~~
;
SamToCmpH5.cpp:152:17: error: expected ';' before 'fullRefName'
string fullRefName(references[i].title);
^~~~~~~~~~~~
;
SamToCmpH5.cpp:153:39: error: 'shortRefName' was not declared in this scope
if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) {
^~~~~~~~~~~~
SamToCmpH5.cpp:153:39: note: suggested alternative: 'useShortRefName'
if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) {
^~~~~~~~~~~~
useShortRefName
SamToCmpH5.cpp:154:15: error: 'cout' was not declared in this scope
cout << "ERROR, Found more than one reference " << shortRefName << "in sam header" << endl;
^~~~
SamToCmpH5.cpp:154:15: note: suggested alternative:
In file included from SamToCmpH5.cpp:1:
/usr/include/c++/8/iostream:61:18: note: 'std::cout'
extern ostream cout; /// Linked to standard output
^~~~
SamToCmpH5.cpp:157:30: error: 'shortRefName' was not declared in this scope
shortRefNameToFull[shortRefName] = fullRefName;
^~~~~~~~~~~~
SamToCmpH5.cpp:157:30: note: suggested alternative: 'useShortRefName'
shortRefNameToFull[shortRefName] = fullRefName;
^~~~~~~~~~~~
useShortRefName
SamToCmpH5.cpp:157:46: error: 'fullRefName' was not declared in this scope
shortRefNameToFull[shortRefName] = fullRefName;
^~~~~~~~~~~
SamToCmpH5.cpp:179:9: error: 'it' was not declared in this scope
it = shortRefNameToFull.find(samAlignment.rName);
^~
SamToCmpH5.cpp:179:9: note: suggested alternative: 'Fit'
it = shortRefNameToFull.find(samAlignment.rName);
^~
Fit
SamToCmpH5.cpp:181:13: error: 'cout' was not declared in this scope
cout << "ERROR, Could not find " << samAlignment.rName << " in the reference repository." << endl;
^~~~
SamToCmpH5.cpp:181:13: note: suggested alternative:
In file included from SamToCmpH5.cpp:1:
/usr/include/c++/8/iostream:61:18: note: 'std::cout'
extern ostream cout; /// Linked to standard output
^~~~
SamToCmpH5.cpp:186:33: error: expected primary-expression before '>' token
vector<AlignmentCandidate<> > convertedAlignments;
^
SamToCmpH5.cpp:186:35: error: 'convertedAlignments' was not declared in this scope
vector<AlignmentCandidate<> > convertedAlignments;
^~~~~~~~~~~~~~~~~~~
SamToCmpH5.cpp:186:35: note: suggested alternative: 'ByteAlignment'
vector<AlignmentCandidate<> > convertedAlignments;
^~~~~~~~~~~~~~~~~~~
ByteAlignment
SamToCmpH5.cpp:188:7: error: 'cout' was not declared in this scope
cout << "Storing alignment for " << samAlignment.qName << endl;
^~~~
SamToCmpH5.cpp:188:7: note: suggested alternative:
In file included from SamToCmpH5.cpp:1:
/usr/include/c++/8/iostream:61:18: note: 'std::cout'
extern ostream cout; /// Linked to standard output
^~~~
In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217,
from /usr/include/pbseq/hdf/HDFArray.hpp:9,
from /usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp:6,
from /usr/include/pbseq/hdf/HDFCmpFile.hpp:12,
from SamToCmpH5.cpp:6:
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = std::__cxx11::basic_string<char>; DSLength = long long unsigned int]':
/usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]'
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
/usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned int]'
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]':
/usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from 'void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]'
/usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from /usr/include/pbseq/hdf/HDFPlsReader.hpp:12,
from PulseToFasta.cpp:5:
/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]':
PulseToFasta.cpp:145:41: required from here
/usr/include/pbseq/hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217,
from /usr/include/pbseq/hdf/HDFArray.hpp:9,
from /usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp:6,
from /usr/include/pbseq/hdf/HDFCmpFile.hpp:12,
from LoadPulses.cpp:3:
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = std::__cxx11::basic_string<char>; DSLength = long long unsigned int]':
/usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]'
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43: required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
/usr/include/pbseq/hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned int]'
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29: required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]':
/usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from 'void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]'
/usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60: required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from LoadPulses.cpp:4:
/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]':
/usr/include/pbseq/hdf/HDFBasReader.hpp:135:28: required from 'DNALength T_HDFBasReader<T_Sequence>::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]'
LoadPulses.cpp:701:59: required from here
/usr/include/pbseq/hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217,
from /usr/include/pbseq/hdf/HDFArray.hpp:9,
from /usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp:6,
from /usr/include/pbseq/hdf/HDFCmpFile.hpp:12,
from LoadPulses.cpp:3:
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
/usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from 'void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = unsigned char; UInt = unsigned int]'
LoadPulses.cpp:1565:62: required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = char; DSLength = long long unsigned int]':
/usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from 'void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = char; UInt = unsigned int]'
LoadPulses.cpp:1577:64: required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long long unsigned int]':
/usr/include/pbseq/hdf/HDFArray.hpp:51:9: required from 'void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = short unsigned int; UInt = unsigned int]'
LoadPulses.cpp:1588:76: required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
make[3]: *** [<builtin>: SamToM4.o] Error 1
make[3]: *** Waiting for unfinished jobs....
In file included from LoadPulses.cpp:4:
/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]':
/usr/include/pbseq/hdf/HDFBasReader.hpp:726:25: required from 'int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]'
/usr/include/pbseq/hdf/HDFBasReader.hpp:135:28: required from 'DNALength T_HDFBasReader<T_Sequence>::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]'
LoadPulses.cpp:701:59: required from here
/usr/include/pbseq/hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]':
/usr/include/pbseq/hdf/HDFBasReader.hpp:726:25: required from 'int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]'
PulseToFasta.cpp:145:41: required from here
/usr/include/pbseq/hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
make[3]: *** [<builtin>: SamToCmpH5.o] Error 1
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[2]: *** [makefile:67: makeutils] Error 2
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
dh_auto_build: make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make[1]: *** [debian/rules:42: main] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
make: *** [debian/rules:33: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2018-12-20T02:31:42Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 262
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 763
Job: blasr_5.3+0-2
Machine Architecture: armhf
Package: blasr
Package-Time: 1075
Source-Version: 5.3+0-2
Space: 0
Status: failed
Version: 5.3+0-2+b1
--------------------------------------------------------------------------------
Finished at 2018-12-20T02:31:42Z
Build needed 00:00:00, 0k disc space