blasr →
5.3.2+dfsg-1.1 →
armhf → 2019-02-14 23:11:49
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| blasr 5.3.2+dfsg-1.1 (armhf) Thu, 14 Feb 2019 22:41:33 +0000 |
+==============================================================================+
Package: blasr
Version: 5.3.2+dfsg-1.1
Source Version: 5.3.2+dfsg-1.1
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-beb4b76e-6028-4bfc-8d20-ee8c49945a2d' 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 [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.4 MB in 27s (906 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://salsa.debian.org/med-team/blasr.git
Please use:
git clone https://salsa.debian.org/med-team/blasr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 137 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main blasr 5.3.2+dfsg-1.1 (dsc) [2112 B]
Get:2 http://172.17.0.1/private buster-staging/main blasr 5.3.2+dfsg-1.1 (tar) [124 kB]
Get:3 http://172.17.0.1/private buster-staging/main blasr 5.3.2+dfsg-1.1 (diff) [10.9 kB]
Fetched 137 kB in 0s (2375 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/blasr-6b3qIS/blasr-5.3.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/blasr-6b3qIS' 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-r647QI/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-r647QI/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-r647QI/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-r647QI/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2828 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 e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 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 60 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15817 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 (>= 12~), python, meson, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev (>= 0.18.0~), libpbdata-dev, libgtest-dev, libblasr-dev (>= 5.3.1+dfsg-2)
Filtered Build-Depends: debhelper (>= 12~), python, meson, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev (>= 0.18.0~), libpbdata-dev, libgtest-dev, libblasr-dev (>= 5.3.1+dfsg-2)
dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/<<BUILDDIR>>/resolver-r647QI/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-r647QI/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ Sources [579 B]
Get:5 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ Packages [663 B]
Fetched 2575 B in 1s (3732 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 e2fsprogs-l10n 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 cpp-8 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file g++-8 gcc-8 gcc-8-base
gettext gettext-base googletest groff-base hdf5-helpers intltool-debian
libaec-dev libaec0 libarchive-zip-perl libasan5 libatomic1 libblasr
libblasr-dev libboost-dev libboost1.67-dev libbsd0 libcc1-0 libcroco3
libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl libgcc-8-dev
libgcc1 libgfortran5 libglib2.0-0 libgnutls30 libgomp1 libgtest-dev
libhdf5-103 libhdf5-cpp-103 libhdf5-dev libhts-dev libhts2 libicu63
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblzma-dev liblzma5
libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpbbam-dev libpbbam0.19.0
libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev libpipeline1
libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl-dev
libstdc++-8-dev libstdc++6 libsz2 libtool libubsan1 libuchardet0 libxml2 m4
man-db meson mime-support ninja-build pkg-config po-debconf python
python-minimal python2 python2-minimal python2.7 python2.7-minimal python3
python3-minimal python3-pkg-resources python3.7 python3.7-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation 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 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
gnutls-bin 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 python3-doc python3-tk python3-venv python3-setuptools
python3.7-venv python3.7-doc
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 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libblasr libblasr-dev libboost-dev libboost1.67-dev
libbsd0 libcroco3 libcurl3-gnutls libelf1 libfile-stripnondeterminism-perl
libgfortran5 libglib2.0-0 libgtest-dev libhdf5-103 libhdf5-cpp-103
libhdf5-dev libhts-dev libhts2 libicu63 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblzma-dev libmagic-mgc libmagic1 libmpdec2
libnghttp2-14 libpbbam-dev libpbbam0.19.0 libpbdata libpbdata-dev libpbihdf
libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib
libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1
libssl-dev libsz2 libtool libuchardet0 libxml2 m4 man-db meson mime-support
ninja-build pkg-config po-debconf python python-minimal python2
python2-minimal python2.7 python2.7-minimal python3 python3-minimal
python3-pkg-resources python3.7 python3.7-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 libgnutls30 libgomp1 liblzma5 libstdc++-8-dev libstdc++6 libubsan1
15 upgraded, 89 newly installed, 0 to remove and 45 not upgraded.
Need to get 76.6 MB/77.0 MB of archives.
After this operation, 278 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-r647QI/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [952 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 8.2.0-16+rpi1 [37.9 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-16+rpi1 [189 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-16+rpi1 [36.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-16+rpi1 [63.9 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-16+rpi1 [8104 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-16+rpi1 [318 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-16+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-16+rpi1 [7467 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-16+rpi1 [1539 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-16+rpi1 [597 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-16+rpi1 [7216 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-16+rpi1 [6789 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-16+rpi1 [324 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-1 [26.6 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-1 [1231 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.15-8 [394 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.15-8 [1089 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-4 [41.4 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-4 [21.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.15-8 [1844 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.15-8 [299 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-4 [20.8 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-4 [20.8 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-4 [41.6 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-4 [22.8 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libpython3.7-minimal armhf 3.7.2-2 [582 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf python3.7-minimal armhf 3.7.2-2 [1455 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.7.2-1 [36.6 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf liblzma5 armhf 5.2.4-1 [144 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libpython3.7-stdlib armhf 3.7.2-2 [1662 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf python3.7 armhf 3.7.2-2 [323 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.7.2-1 [20.0 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.7.2-1 [61.5 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libgnutls30 armhf 3.6.6-2 [1035 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-2 [242 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-2 [109 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-2 [65.1 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.0-1 [19.5 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.0-1 [12.6 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.3-1 [1077 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf googletest armhf 1.8.1-3 [903 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.4+repack-10 [35.2 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.36.0-2 [73.6 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.64.0-1 [291 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.9-8 [254 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libpbbam0.19.0 armhf 0.19.0+dfsg-4+rpi1 [455 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libpbdata armhf 5.3.1+dfsg-2.1 [106 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-16+rpi1 [207 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libhdf5-103 armhf 1.10.4+repack-10 [1259 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-103 armhf 1.10.4+repack-10 [121 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libpbihdf armhf 5.3.1+dfsg-2.1 [138 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libblasr armhf 5.3.1+dfsg-2.1 [832 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libpbdata-dev armhf 5.3.1+dfsg-2.1 [175 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libblasr-dev armhf 5.3.1+dfsg-2.1 [1664 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.67.0.1+b1 [4140 B]
Get:87 http://172.17.0.1/private buster-staging/main armhf libgtest-dev armhf 1.8.1-3 [214 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.4+repack-10 [2221 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.9-8 [4280 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1a-1 [1556 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.19.0+dfsg-4+rpi1 [93.4 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libpbihdf-dev armhf 5.3.1+dfsg-2.1 [243 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libpbseq-dev all 5.3.1+dfsg-2.1 [4612 B]
Get:96 http://172.17.0.1/private buster-staging/main armhf ninja-build armhf 1.8.2-1 [78.8 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf python3-pkg-resources all 40.7.1-1 [152 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf meson all 0.49.2-1 [281 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
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Preparing to unpack .../61-meson_0.49.2-1_all.deb ...
Unpacking meson (0.49.2-1) ...
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Preparing to unpack .../62-pkg-config_0.29-6_armhf.deb ...
Unpacking pkg-config (0.29-6) ...
Selecting previously unselected package sbuild-build-depends-blasr-dummy.
Preparing to unpack .../63-sbuild-build-depends-blasr-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-blasr-dummy (0.invalid.0) ...
Setting up cpp-8 (8.2.0-16+rpi1) ...
Setting up libgomp1:armhf (8.2.0-16+rpi1) ...
Setting up libatomic1:armhf (8.2.0-16+rpi1) ...
Setting up libaec0:armhf (1.0.2-1) ...
Setting up libcc1-0:armhf (8.2.0-16+rpi1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libnghttp2-14:armhf (1.36.0-2) ...
Setting up mime-support (3.61) ...
Installing new version of config file /etc/mime.types ...
Setting up libicu63:armhf (63.1-6) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libelf1:armhf (0.175-2) ...
Setting up libssl-dev:armhf (1.1.1a-1) ...
Setting up libglib2.0-0:armhf (2.58.3-1) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-9) ...
Setting up libpipeline1:armhf (1.5.1-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up m4 (1.4.18-2) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libmagic-mgc (1:5.35-2) ...
Setting up libmagic1:armhf (1:5.35-2) ...
Setting up libcroco3:armhf (0.6.12-3) ...
Setting up pkg-config (0.29-6) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Setting up googletest:armhf (1.8.1-3) ...
Processing triggers for libc-bin (2.28-5+rpi1) ...
Setting up dwz (0.12-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up libgtest-dev:armhf (1.8.1-3) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up ninja-build (1.8.2-1) ...
Setting up libasan5:armhf (8.2.0-16+rpi1) ...
Setting up libgfortran5:armhf (8.2.0-16+rpi1) ...
Setting up hdf5-helpers (1.10.4+repack-10) ...
Setting up libpython2.7-stdlib:armhf (2.7.15-8) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libsz2:armhf (1.0.2-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (1.1.0-1) ...
Setting up libubsan1:armhf (8.2.0-16+rpi1) ...
Setting up libpython3.7-stdlib:armhf (3.7.2-2) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.64.0-1) ...
Setting up groff-base (1.22.4-2) ...
Setting up libaec-dev:armhf (1.0.2-1) ...
Setting up python2.7 (2.7.15-8) ...
Setting up python3.7 (3.7.2-2) ...
Setting up autoconf (2.69-11) ...
Setting up libhdf5-103:armhf (1.10.4+repack-10) ...
Setting up file (1:5.35-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up libpython2-stdlib:armhf (2.7.15-4) ...
Setting up libgcc-8-dev:armhf (8.2.0-16+rpi1) ...
Setting up libhts2:armhf (1.9-8) ...
Setting up libtool (2.4.6-9) ...
Setting up libpython3-stdlib:armhf (3.7.2-1) ...
Setting up libstdc++-8-dev:armhf (8.2.0-16+rpi1) ...
Setting up po-debconf (1.0.21) ...
Setting up python3 (3.7.2-1) ...
Setting up libhts-dev:armhf (1.9-8) ...
Setting up libhdf5-cpp-103:armhf (1.10.4+repack-10) ...
Setting up libhdf5-dev (1.10.4+repack-10) ...
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 python3-pkg-resources (40.7.1-1) ...
Setting up libpbbam0.19.0:armhf (0.19.0+dfsg-4+rpi1) ...
Setting up python2 (2.7.15-4) ...
Setting up gcc-8 (8.2.0-16+rpi1) ...
Setting up g++-8 (8.2.0-16+rpi1) ...
Setting up libpython-stdlib:armhf (2.7.15-4) ...
Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up libpbdata:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbihdf:armhf (5.3.1+dfsg-2.1) ...
Setting up meson (0.49.2-1) ...
Setting up libboost-dev:armhf (1.67.0.1+b1) ...
Setting up python (2.7.15-4) ...
Setting up libblasr:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbbam-dev (0.19.0+dfsg-4+rpi1) ...
Setting up libpbihdf-dev:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbdata-dev:armhf (5.3.1+dfsg-2.1) ...
Setting up libblasr-dev:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbseq-dev (5.3.1+dfsg-2.1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12) ...
Setting up sbuild-build-depends-blasr-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (1.1.0-1) ...
Processing triggers for libc-bin (2.28-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-16+rpi1 gcc-8_8.2.0-16+rpi1 libc6-dev_2.28-5+rpi1 libstdc++-8-dev_8.2.0-16+rpi1 libstdc++6_8.2.0-16+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~beta1 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_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-16+rpi1 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-16+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-8_8.2.0-16+rpi1 gcc-8-base_8.2.0-16+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 googletest_1.8.1-3 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hdf5-helpers_1.10.4+repack-10 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.4-15+rpi1 kmod_25-2 krb5-locales_1.17-1 libacl1_2.2.52-3 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.13.2-3 libapt-pkg5.0_1.8.0~beta1 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-16+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-16+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblasr_5.3.1+dfsg-2.1 libblasr-dev_5.3.1+dfsg-2.1 libblkid1_2.33.1-0.1 libboost-dev_1.67.0.1+b1 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-5+rpi1 libc-dev-bin_2.28-5+rpi1 libc6_2.28-5+rpi1 libc6-dev_2.28-5+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-1.2 libcc1-0_8.2.0-16+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.64.0-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.155-1 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.0-1 libgcc-8-dev_8.2.0-16+rpi1 libgcc1_1:8.2.0-16+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran5_8.2.0-16+rpi1 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.2.0-16+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgssapi-krb5-2_1.17-1 libgtest-dev_1.8.1-3 libhdf5-103_1.10.4+repack-10 libhdf5-cpp-103_1.10.4+repack-10 libhdf5-dev_1.10.4+repack-10 libhogweed4_3.4.1~rc1-1 libhts-dev_1.9-8 libhts2_1.9-8 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 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 libk5crypto3_1.17-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-15+rpi1 libkmod2_25-2 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-2 libldap-common_2.4.47+dfsg-2 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2~rc1-1 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_1.36.0-2 libnpth0_1.6-1 libnss-systemd_240-4+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam-systemd_240-4+rpi1 libpam0g_1.1.8-4 libpbbam-dev_0.19.0+dfsg-4+rpi1 libpbbam0.19.0_0.19.0+dfsg-4+rpi1 libpbdata_5.3.1+dfsg-2.1 libpbdata-dev_5.3.1+dfsg-2.1 libpbihdf_5.3.1+dfsg-2.1 libpbihdf-dev_5.3.1+dfsg-2.1 libpbseq-dev_5.3.1+dfsg-2.1 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-3 libpipeline1_1.5.1-1 libplymouth4_0.9.4-1 libpng16-16_1.6.36-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7-minimal_2.7.15-8 libpython2.7-stdlib_2.7.15-8 libpython3-stdlib_3.7.2-1 libpython3.7-minimal_3.7.2-2 libpython3.7-stdlib_3.7.2-2 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl-dev_1.1.1a-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-16+rpi1 libstdc++6_8.2.0-16+rpi1 libsystemd0_240-4+rpi1 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-9 libubsan1_8.2.0-16+rpi1 libuchardet0_0.0.6-3 libudev1_240-4+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+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_2.8.5-1 mawk_1.3.3-17 meson_0.49.2-1 mime-support_3.61 mount_2.33.1-0.1 multiarch-support_2.28-5+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 ninja-build_1.8.2-1 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-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 pkg-config_0.29-6 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-4 python-minimal_2.7.15-4 python2_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.15-8 python2.7-minimal_2.7.15-8 python3_3.7.2-1 python3-minimal_3.7.2-1 python3-pkg-resources_40.7.1-1 python3.7_3.7.2-2 python3.7-minimal_3.7.2-2 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_4.7-1 sensible-utils_0.0.12 systemd_240-4+rpi1 systemd-sysv_240-4+rpi1 sysvinit-utils_2.93-5 tar_1.30+dfsg-4 tzdata_2018i-1 udev_240-4+rpi1 util-linux_2.33.1-0.1 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 Wed Feb 6 07:27:30 2019 UTC
gpgv: using RSA key 3AFA757FAC6EA11D2FF45DF088D24287A2D898B1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./blasr_5.3.2+dfsg-1.1.dsc
dpkg-source: info: extracting blasr in /<<BUILDDIR>>/blasr-5.3.2+dfsg
dpkg-source: info: unpacking blasr_5.3.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking blasr_5.3.2+dfsg-1.1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_pblibs.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=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-beb4b76e-6028-4bfc-8d20-ee8c49945a2d
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 5.3.2+dfsg-1.1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem=meson
dh_auto_clean -O--buildsystem=meson
dh_autoreconf_clean -O--buildsystem=meson
dh_clean -O--buildsystem=meson
debian/rules build-arch
dh build-arch --buildsystem=meson
dh_update_autotools_config -a -O--buildsystem=meson
dh_autoreconf -a -O--buildsystem=meson
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3.2+dfsg'
LDFLAGS="-L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lhdf5_cpp -lhdf5" CPPFLAGS="-isystem /usr/include/hdf5/serial" meson -Dtests=false -Dprefix=/usr build .
The Meson build system
Version: 0.49.2
Source dir: /<<BUILDDIR>>/blasr-5.3.2+dfsg
Build dir: /<<BUILDDIR>>/blasr-5.3.2+dfsg/build
Build type: native build
Project name: blasr
Project version: 5.3.2
Appending CXXFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1'
Appending LDFLAGS from environment: '-L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lhdf5_cpp -lhdf5'
Appending CPPFLAGS from environment: '-isystem /usr/include/hdf5/serial'
Native C++ compiler: c++ (gcc 8.2.0 "c++ (Raspbian 8.2.0-16+rpi1) 8.2.0")
Build machine cpu family: arm
Build machine cpu: armv7l
Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor -Wdelete-non-virtual-dtor: YES
Compiler for C++ supports arguments -Wno-non-virtual-dtor -Wnon-virtual-dtor: YES
Compiler for C++ supports arguments -Wno-unused-but-set-variable -Wunused-but-set-variable: YES
Compiler for C++ supports arguments -Wno-unused-variable -Wunused-variable: YES
Dependency threads found: YES
Dependency Boost found: YES 1.67
Found pkg-config: /usr/bin/pkg-config (0.29)
Dependency pbbam found: YES 0.19.0
Dependency libblasr found: YES 5.3.1
Dependency zlib found: YES 1.2.11
Library pbdata found: YES
Library pbihdf found: YES
Configuring BlasrVersion.h using configuration
Build targets in project: 5
Found ninja-1.8.2 at /usr/bin/ninja
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3.2+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3.2+dfsg'
ln -s build obj-arm-linux-gnueabihf
dh_auto_build
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v
[1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h '' /<<BUILDDIR>>/blasr-5.3.2+dfsg @BLASR_GIT_SHA1@ '(.*)' /<<BUILDDIR>>/blasr-5.3.2+dfsg/git describe --always '--dirty=*'
[2/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -MF 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o.d' -o 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -c ../extrautils/SuffixArrayToBWT.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/bwt/Occ.hpp:8,
from /usr/include/pbseq/alignment/bwt/BWT.hpp:7,
from ../extrautils/SuffixArrayToBWT.cpp:4:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
In file included from ../extrautils/SuffixArrayToBWT.cpp:4:
/usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt<T_BWT_Sequence, T_DNASequence>::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’:
/usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
charCount[0]++;
^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here
case 0: //A
^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
charCount[1]++;
^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here
case 1: //C
^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
charCount[2]++;
^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here
case 2: //G
^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
charCount[3]++;
^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here
case 3: //T
^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
charCount[4]++;
^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here
case 4: //N
^~~~
[3/25] c++ -Isawriter@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'sawriter@exe/utils_SAWriter.cpp.o' -MF 'sawriter@exe/utils_SAWriter.cpp.o.d' -o 'sawriter@exe/utils_SAWriter.cpp.o' -c ../utils/SAWriter.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/algorithms/sorting/Karkkainen.hpp:4,
from ../utils/SAWriter.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[4/25] c++ -ItoAfg@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'toAfg@exe/utils_ToAfg.cpp.o' -MF 'toAfg@exe/utils_ToAfg.cpp.o.d' -o 'toAfg@exe/utils_ToAfg.cpp.o' -c ../utils/ToAfg.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19,
from /usr/include/pbseq/hdf/HDFArray.hpp:9,
from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
from ../utils/ToAfg.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
In file included from ../utils/ToAfg.cpp:9:
/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) {
^
[5/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -MF 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o.d' -o 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -c ../extrautils/BwtToSuffixArray.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/bwt/Occ.hpp:8,
from /usr/include/pbseq/alignment/bwt/BWT.hpp:7,
from ../extrautils/BwtToSuffixArray.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[6/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -MF 'blasr_impl@sta/extrautils_SWMatcher.cpp.o.d' -o 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -c ../extrautils/SWMatcher.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../extrautils/SWMatcher.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[7/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SAModify.cpp.o' -MF 'blasr_impl@sta/extrautils_SAModify.cpp.o.d' -o 'blasr_impl@sta/extrautils_SAModify.cpp.o' -c ../extrautils/SAModify.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21,
from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8,
from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13,
from ../extrautils/SAModify.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[8/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -MF 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o.d' -o 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -c ../extrautils/SimpleShredder.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:7,
from ../extrautils/SimpleShredder.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[9/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_Evolve.cpp.o' -MF 'blasr_impl@sta/extrautils_Evolve.cpp.o.d' -o 'blasr_impl@sta/extrautils_Evolve.cpp.o' -c ../extrautils/Evolve.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:7,
from ../extrautils/Evolve.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[10/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -MF 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o.d' -o 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -c ../extrautils/ExciseRepeats.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:7,
from ../extrautils/ExciseRepeats.cpp:3:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[11/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SALS.cpp.o' -MF 'blasr_impl@sta/extrautils_SALS.cpp.o.d' -o 'blasr_impl@sta/extrautils_SALS.cpp.o' -c ../extrautils/SALS.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21,
from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8,
from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13,
from ../extrautils/SALS.cpp:4:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[12/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -MF 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o.d' -o 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -c ../extrautils/BuildSequenceDB.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:7,
from ../extrautils/BuildSequenceDB.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[13/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -MF 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o.d' -o 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -c ../extrautils/PrintTupleCountTable.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/tuples/DNATuple.hpp:15,
from /usr/include/pbseq/alignment/tuples/CompressedDNATuple.hpp:4,
from ../extrautils/PrintTupleCountTable.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
[14/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -MF 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d' -o 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -c ../extrautils/StoreQualityByContextFromCmpH5.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19,
from /usr/include/pbseq/hdf/HDFArray.hpp:9,
from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217,
from /usr/include/pbseq/hdf/HDFArray.hpp:9,
from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2:
/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=]
[15/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToM4.cpp.o' -MF 'blasr_impl@sta/utils_SamToM4.cpp.o.d' -o 'blasr_impl@sta/utils_SamToM4.cpp.o' -c ../utils/SamToM4.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SamToM4.cpp:21:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
In file included from /usr/include/c++/8/vector:69,
from /usr/include/pbbam/BamRecord.h:15,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SamToM4.cpp:21:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[16/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_PulseToFasta.cpp.o' -MF 'blasr_impl@sta/utils_PulseToFasta.cpp.o.d' -o 'blasr_impl@sta/utils_PulseToFasta.cpp.o' -c ../utils/PulseToFasta.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19,
from /usr/include/pbseq/hdf/HDFArray.hpp:9,
from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
from ../utils/PulseToFasta.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
In file included from ../utils/PulseToFasta.cpp:8:
/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) {
^
In file included from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
from ../utils/PulseToFasta.cpp:5:
/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’:
../utils/PulseToFasta.cpp:157:41: 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) {
^~~~~
/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]’
../utils/PulseToFasta.cpp:157:41: 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) {
^~~~~
[17/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamFilter.cpp.o' -MF 'blasr_impl@sta/utils_SamFilter.cpp.o.d' -o 'blasr_impl@sta/utils_SamFilter.cpp.o' -c ../utils/SamFilter.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SamFilter.cpp:32:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
In file included from /usr/include/c++/8/vector:69,
from /usr/include/pbbam/BamRecord.h:15,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SamFilter.cpp:32:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[18/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -MF 'blasr_impl@sta/utils_SamToCmpH5.cpp.o.d' -o 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -c ../utils/SamToCmpH5.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:9,
from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
from ../utils/SamToCmpH5.cpp:3:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
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 /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:7,
from ../utils/SamToCmpH5.cpp:5:
/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/c++/8/vector:69,
from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:5,
from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
from ../utils/SamToCmpH5.cpp:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[19/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -MF 'blasr_impl@sta/utils_SDPMatcher.cpp.o.d' -o 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -c ../utils/SDPMatcher.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SDPMatcher.cpp:8:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
In file included from /usr/include/c++/8/vector:69,
from /usr/include/pbbam/BamRecord.h:15,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PositionDNATuple&}; _Tp = PositionDNATuple; _Alloc = std::allocator<PositionDNATuple>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /usr/include/pbbam/BamRecord.h:15,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/bits/stl_vector.h: In function ‘int SequenceToTupleList(Sequence&, TupleMetrics&, TupleList<PositionDNATuple>&) [with Sequence = DNASequence]’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:8,
from /usr/include/pbbam/QualityValues.h:132,
from /usr/include/pbbam/BamRecordImpl.h:20,
from /usr/include/pbbam/BamRecord.h:19,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/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++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:8,
from /usr/include/pbbam/QualityValues.h:132,
from /usr/include/pbbam/BamRecordImpl.h:20,
from /usr/include/pbbam/BamRecord.h:19,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:8,
from /usr/include/pbbam/QualityValues.h:132,
from /usr/include/pbbam/BamRecordImpl.h:20,
from /usr/include/pbbam/BamRecord.h:19,
from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _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++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[20/25] c++ -Iblasr@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'blasr@exe/Blasr.cpp.o' -MF 'blasr@exe/Blasr.cpp.o.d' -o 'blasr@exe/Blasr.cpp.o' -c ../Blasr.cpp
In file included from ../iblasr/BlasrHeaders.h:22,
from ../iblasr/BlasrAlign.hpp:4,
from ../Blasr.cpp:3:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
In file included from ../iblasr/BlasrUtils.hpp:138,
from ../iblasr/BlasrAlignImpl.hpp:4,
from ../iblasr/BlasrAlign.hpp:67,
from ../Blasr.cpp:3:
../iblasr/BlasrUtilsImpl.hpp: In function ‘void PrintAlignment(T_AlignmentCandidate&, SMRTSequence&, MappingParameters&, AlignmentContext&, std::ostream&, SMRTSequence&, PacBio::BAM::IRecordWriter*)’:
../iblasr/BlasrUtilsImpl.hpp:976:36: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=]
} catch (std::ostream::failure f) {
^
../Blasr.cpp: In function ‘int main(int, char**)’:
../Blasr.cpp:1411:51: warning: cast between incompatible function types from ‘void (*)(MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>*)’ to ‘void* (*)(void*)’ [-Wcast-function-type]
(void *(*)(void *))MapReads, &mapdb[procIndex]);
^~~~~~~~
../Blasr.cpp:1466:37: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
} catch (std::exception e) {
^
In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29,
from ../iblasr/BlasrHeaders.h:60,
from ../iblasr/BlasrAlign.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:167:25: 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:953:65: required from here
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:45: 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:38,
from ../iblasr/BlasrHeaders.h:49,
from ../iblasr/BlasrAlign.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:210:36: 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:34:45: 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:371:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:126:35: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
while (refPos + 1 < reference.length and queryPos + 1 < read.length and
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:126:71: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
while (refPos + 1 < reference.length and queryPos + 1 < read.length and
~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/pbseq/alignment/bwt/BWT.hpp:9,
from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:6,
from ../iblasr/BlasrHeaders.h:42,
from ../iblasr/BlasrAlign.hpp:4,
from ../Blasr.cpp:3:
/usr/include/pbseq/alignment/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:54:19: 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:210:36: 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:34:45: 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:371:27: required from here
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:1110:38: warning: comparison of integer expressions of different signedness: ‘SAIndex’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare]
index[l] + lcpLength >= targetLength or // This shouldn't
/usr/include/pbseq/alignment/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/suffixarray/SuffixArray.hpp:1099:17: 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:54:19: 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:210:36: 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:34:45: 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:371:27: required from here
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:807:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
if (targetSufLen == targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:817:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
if (targetSufLen < targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
from /usr/include/pbseq/pbdata/CompressedSequence.hpp:4,
from /usr/include/pbseq/alignment/tuples/CompressedDNATuple.hpp:5,
from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:16,
from /usr/include/pbseq/alignment/bwt/BWT.hpp:9,
from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:6,
from ../iblasr/BlasrHeaders.h:42,
from ../iblasr/BlasrAlign.hpp:4,
from ../Blasr.cpp:3:
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:824:48: warning: comparison of integer expressions of different signedness: ‘SAIndex’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare]
assert(index[m] + targetOffset < targetLength);
In file included from /usr/include/pbseq/alignment/bwt/BWT.hpp:9,
from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:6,
from ../iblasr/BlasrHeaders.h:42,
from ../iblasr/BlasrAlign.hpp:4,
from ../Blasr.cpp:3:
/usr/include/pbseq/alignment/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/suffixarray/SuffixArray.hpp:1100:17: 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:54:19: 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:210:36: 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:34:45: 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:371:27: required from here
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:855:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
if (targetSufLen == targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:859:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
if (targetSufLen < targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29,
from ../iblasr/BlasrHeaders.h:60,
from ../iblasr/BlasrAlign.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:27:5: warning: nonnull argument ‘read’ compared to NULL [-Wnonnull-compare]
if (dynamic_cast<SMRTSequence *>(&read) == NULL) {
^~
In file included from /usr/include/c++/8/vector:69,
from ../iblasr/BlasrHeaders.h:14,
from ../iblasr/BlasrAlign.hpp:4,
from ../Blasr.cpp:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PositionDNATuple&}; _Tp = PositionDNATuple; _Alloc = std::allocator<PositionDNATuple>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../iblasr/BlasrHeaders.h:14,
from ../iblasr/BlasrAlign.hpp:4,
from ../Blasr.cpp:3:
/usr/include/c++/8/bits/stl_vector.h: In function ‘int SequenceToTupleList(Sequence&, TupleMetrics&, TupleList<PositionDNATuple>&) [with Sequence = DNASequence]’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:8,
from /usr/include/pbbam/QualityValues.h:132,
from /usr/include/pbbam/BamRecordImpl.h:20,
from /usr/include/pbbam/BamRecord.h:19,
from /usr/include/pbbam/BamWriter.h:15,
from ../iblasr/BlasrHeaders.h:24,
from ../iblasr/BlasrAlign.hpp:4,
from ../Blasr.cpp:3:
/usr/include/c++/8/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++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:8,
from /usr/include/pbbam/QualityValues.h:132,
from /usr/include/pbbam/BamRecordImpl.h:20,
from /usr/include/pbbam/BamRecord.h:19,
from /usr/include/pbbam/BamWriter.h:15,
from ../iblasr/BlasrHeaders.h:24,
from ../iblasr/BlasrAlign.hpp:4,
from ../Blasr.cpp:3:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:8,
from /usr/include/pbbam/QualityValues.h:132,
from /usr/include/pbbam/BamRecordImpl.h:20,
from /usr/include/pbbam/BamRecord.h:19,
from /usr/include/pbbam/BamWriter.h:15,
from ../iblasr/BlasrHeaders.h:24,
from ../iblasr/BlasrAlign.hpp:4,
from ../Blasr.cpp:3:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _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++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__heap_select(_RandomAccessIterator __first,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__heap_select(__first, __middle, __last, __comp);
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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 = SMRTSequence; T_TargetSequence = DNASequence; T_ScoreFn = IDSScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>]’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[21/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_LoadPulses.cpp.o' -MF 'blasr_impl@sta/utils_LoadPulses.cpp.o.d' -o 'blasr_impl@sta/utils_LoadPulses.cpp.o' -c ../utils/LoadPulses.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6,
from ../utils/LoadPulses.cpp:11:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
#define USE_PBBAM
<command-line>: note: this is the location of the previous definition
In file included from ../utils/LoadPulses.cpp:19:
/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) {
^
In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217,
from /usr/include/pbseq/hdf/HDFArray.hpp:9,
from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
from ../utils/LoadPulses.cpp:16:
/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 ../utils/LoadPulses.cpp:16:
/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]’
../utils/LoadPulses.cpp:680:59: 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/HDFBasReader.hpp:13,
from ../utils/LoadPulses.cpp:16:
/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]’
../utils/LoadPulses.cpp:1525:62: 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]’
../utils/LoadPulses.cpp:1537:64: 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]’
../utils/LoadPulses.cpp:1547:76: 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 ../utils/LoadPulses.cpp:16:
/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]’
../utils/LoadPulses.cpp:680:59: 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) {
^~~~~
[22/25] rm -f libblasr_impl.a && gcc-ar csrD libblasr_impl.a 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' 'blasr_impl@sta/extrautils_SAModify.cpp.o' 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' 'blasr_impl@sta/extrautils_SALS.cpp.o' 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' 'blasr_impl@sta/extrautils_Evolve.cpp.o' 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' 'blasr_impl@sta/utils_SamToM4.cpp.o' 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' 'blasr_impl@sta/utils_SDPMatcher.cpp.o' 'blasr_impl@sta/utils_LoadPulses.cpp.o' 'blasr_impl@sta/utils_PulseToFasta.cpp.o' 'blasr_impl@sta/utils_SamFilter.cpp.o'
[23/25] c++ -o sawriter 'sawriter@exe/utils_SAWriter.cpp.o' -I/usr/include/pbseq -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/arm-linux-gnueabihf/libpbbam.so /usr/lib/arm-linux-gnueabihf/libhts.so -lblasr /usr/lib/arm-linux-gnueabihf/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<<BUILDDIR>>/blasr-5.3.2+dfsg/build/
[24/25] c++ -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/arm-linux-gnueabihf/libpbbam.so /usr/lib/arm-linux-gnueabihf/libhts.so -lblasr /usr/lib/arm-linux-gnueabihf/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<<BUILDDIR>>/blasr-5.3.2+dfsg/build/
[25/25] c++ -o blasr 'blasr@exe/Blasr.cpp.o' -I/usr/include/pbseq -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a /usr/lib/arm-linux-gnueabihf/libpbbam.so /usr/lib/arm-linux-gnueabihf/libhts.so -lblasr /usr/lib/arm-linux-gnueabihf/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group -pthread '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<<BUILDDIR>>/blasr-5.3.2+dfsg/build/
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3.2+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3.2+dfsg'
echo Tests require data not available in the source distribution
Tests require data not available in the source distribution
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3.2+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem=meson
dh_testroot -a -O--buildsystem=meson
dh_prep -a -O--buildsystem=meson
dh_auto_install -a -O--buildsystem=meson
cd obj-arm-linux-gnueabihf && DESTDIR=/<<BUILDDIR>>/blasr-5.3.2\+dfsg/debian/blasr LC_ALL=C.UTF-8 ninja install
[1/4] Generating BlasrGitHash.h with a custom command.
[1/2] Installing files.
Installing blasr to /<<BUILDDIR>>/blasr-5.3.2+dfsg/debian/blasr/usr/bin
Installing sawriter to /<<BUILDDIR>>/blasr-5.3.2+dfsg/debian/blasr/usr/bin
dh_install -a -O--buildsystem=meson
dh_installdocs -a -O--buildsystem=meson
dh_installchangelogs -a -O--buildsystem=meson
dh_installman -a -O--buildsystem=meson
dh_installinit -a -O--buildsystem=meson
dh_installsystemduser -a -O--buildsystem=meson
dh_lintian -a -O--buildsystem=meson
dh_perl -a -O--buildsystem=meson
dh_link -a -O--buildsystem=meson
dh_strip_nondeterminism -a -O--buildsystem=meson
dh_compress -a -O--buildsystem=meson
dh_fixperms -a -O--buildsystem=meson
dh_missing -a -O--buildsystem=meson
dh_dwz -a -O--buildsystem=meson
dh_strip -a -O--buildsystem=meson
dh_makeshlibs -a -O--buildsystem=meson
dh_shlibdeps -a -O--buildsystem=meson
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: debian/blasr/usr/bin/sawriter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/blasr 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/sawriter debian/blasr/usr/bin/blasr were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--buildsystem=meson
dh_gencontrol -a -O--buildsystem=meson
dh_md5sums -a -O--buildsystem=meson
dh_builddeb -a -O--buildsystem=meson
dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3.2+dfsg-1.1_armhf.deb'.
dpkg-deb: building package 'blasr' in '../blasr_5.3.2+dfsg-1.1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../blasr_5.3.2+dfsg-1.1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-02-14T23:11:34Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
blasr_5.3.2+dfsg-1.1_armhf.changes:
-----------------------------------
Format: 1.8
Date: Wed, 06 Feb 2019 09:24:24 +0200
Source: blasr
Binary: blasr
Architecture: armhf
Version: 5.3.2+dfsg-1.1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Adrian Bunk <bunk@debian.org>
Description:
blasr - mapping single-molecule sequencing reads
Changes:
blasr (5.3.2+dfsg-1.1) unstable; urgency=medium
.
* Non-maintainer upload.
* Remove manual dependency on libpbbam, a proper one is already
being generated.
Checksums-Sha1:
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2cd672ad2073e470b26f0740e234ca450b1ad1c5 6823 blasr_5.3.2+dfsg-1.1_armhf.buildinfo
2a11684456ba5823e927215a20b709e67352e1e2 175828 blasr_5.3.2+dfsg-1.1_armhf.deb
Checksums-Sha256:
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b62e7a2207f45f65820fb84eb97b815f3767631f3de72c8b629c9a0fc0e5d127 6823 blasr_5.3.2+dfsg-1.1_armhf.buildinfo
c0f46e0321c8a792ef0653b2b4da92c8d4cc20dfad94738cc6c81c6ef3dbc0c5 175828 blasr_5.3.2+dfsg-1.1_armhf.deb
Files:
bca19e1f1bbcb2fd343797f4e1d1c08e 3081940 debug optional blasr-dbgsym_5.3.2+dfsg-1.1_armhf.deb
f9bc14e299a1da3cc14f2734685c981d 6823 science optional blasr_5.3.2+dfsg-1.1_armhf.buildinfo
25769992901354d7c8876f7af4eb7b57 175828 science optional blasr_5.3.2+dfsg-1.1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
blasr-dbgsym_5.3.2+dfsg-1.1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 3081940 bytes: control archive=644 bytes.
418 bytes, 12 lines control
297 bytes, 3 lines md5sums
Package: blasr-dbgsym
Source: blasr
Version: 5.3.2+dfsg-1.1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3173
Depends: blasr (= 5.3.2+dfsg-1.1)
Section: debug
Priority: optional
Description: debug symbols for blasr
Build-Ids: 1d94023c9a1a44de376f2530bcc3648b9731b7e2 7ad8e7b93e2ff2eb73ffba5f4ef18cedd2100676
drwxr-xr-x root/root 0 2019-02-06 07:24 ./
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/lib/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/lib/debug/.build-id/1d/
-rw-r--r-- root/root 130032 2019-02-06 07:24 ./usr/lib/debug/.build-id/1d/94023c9a1a44de376f2530bcc3648b9731b7e2.debug
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/lib/debug/.build-id/7a/
-rw-r--r-- root/root 3068888 2019-02-06 07:24 ./usr/lib/debug/.build-id/7a/d8e7b93e2ff2eb73ffba5f4ef18cedd2100676.debug
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 36136 2019-02-06 07:24 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/blasr.debug
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-02-06 07:24 ./usr/share/doc/blasr-dbgsym -> blasr
blasr_5.3.2+dfsg-1.1_armhf.deb
------------------------------
new Debian package, version 2.0.
size 175828 bytes: control archive=1028 bytes.
740 bytes, 14 lines control
635 bytes, 10 lines md5sums
Package: blasr
Version: 5.3.2+dfsg-1.1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 522
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libhdf5-cpp-103 (>= 1.10.1), libpbbam0.19.0 (>= 0.19.0+dfsg), libstdc++6 (>= 5.2), libpbseq (>= 0~20160912)
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 2019-02-06 07:24 ./
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/bin/
-rwxr-xr-x root/root 462100 2019-02-06 07:24 ./usr/bin/blasr
-rwxr-xr-x root/root 47040 2019-02-06 07:24 ./usr/bin/sawriter
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/doc/blasr/
-rw-r--r-- root/root 373 2019-01-28 15:10 ./usr/share/doc/blasr/NEWS.Debian.gz
-rw-r--r-- root/root 1587 2018-06-08 20:17 ./usr/share/doc/blasr/README.md
-rw-r--r-- root/root 41 2019-01-28 15:10 ./usr/share/doc/blasr/TODO.Debian
-rw-r--r-- root/root 1387 2019-02-06 07:24 ./usr/share/doc/blasr/changelog.Debian.gz
-rw-r--r-- root/root 2081 2019-01-28 15:10 ./usr/share/doc/blasr/copyright
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/lintian/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 84 2019-01-28 15:10 ./usr/share/lintian/overrides/blasr
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/man/
drwxr-xr-x root/root 0 2019-02-06 07:24 ./usr/share/man/man1/
-rw-r--r-- root/root 1369 2019-02-06 07:24 ./usr/share/man/man1/blasr.1.gz
-rw-r--r-- root/root 872 2019-02-06 07:24 ./usr/share/man/man1/sawriter.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 97324
Build-Time: 828
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 925
Job: blasr_5.3.2+dfsg-1.1
Machine Architecture: armhf
Package: blasr
Package-Time: 1801
Source-Version: 5.3.2+dfsg-1.1
Space: 97324
Status: successful
Version: 5.3.2+dfsg-1.1
--------------------------------------------------------------------------------
Finished at 2019-02-14T23:11:34Z
Build needed 00:30:01, 97324k disc space