pbseqlib →
5.3.1+dfsg-2.1 →
armhf → 2019-02-14 18:33:46
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| pbseqlib 5.3.1+dfsg-2.1 (armhf) Thu, 14 Feb 2019 18:15:40 +0000 |
+==============================================================================+
Package: pbseqlib
Version: 5.3.1+dfsg-2.1
Source Version: 5.3.1+dfsg-2.1
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-3b44f8d2-a0d2-4653-99cc-8b417ab5da58' 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 9s (2634 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: 'pbseqlib' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/pbseqlib.git
Please use:
git clone https://salsa.debian.org/med-team/pbseqlib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 980 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main pbseqlib 5.3.1+dfsg-2.1 (dsc) [2478 B]
Get:2 http://172.17.0.1/private buster-staging/main pbseqlib 5.3.1+dfsg-2.1 (tar) [968 kB]
Get:3 http://172.17.0.1/private buster-staging/main pbseqlib 5.3.1+dfsg-2.1 (diff) [8576 B]
Fetched 980 kB in 0s (2873 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbseqlib-b2xdgv/pbseqlib-5.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbseqlib-b2xdgv' 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-8qBIgu/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-8qBIgu/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-8qBIgu/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ Packages [429 B]
Fetched 2105 B in 0s (11.0 kB/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-8qBIgu/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 all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12~), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libhts-dev, libgtest-dev
Filtered Build-Depends: debhelper (>= 12~), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libhts-dev, libgtest-dev
dpkg-deb: building package 'sbuild-build-depends-pbseqlib-dummy' in '/<<BUILDDIR>>/resolver-8qBIgu/apt_archive/sbuild-build-depends-pbseqlib-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pbseqlib-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-8qBIgu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ Sources [562 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ Packages [632 B]
Fetched 2527 B in 0s (13.1 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pbseqlib 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-exec 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
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
libnghttp2-14 libpbbam-dev libpbbam0.19.0 libpipeline1 libpsl5
libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib
librtmp1 libsigsegv2 libssh2-1 libssl-dev libstdc++-8-dev libstdc++6 libsz2
libtool libubsan1 libuchardet0 libxml2 m4 man-db mime-support po-debconf
python python-minimal python2 python2-minimal python2.7 python2.7-minimal
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation 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
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-exec dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl 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 libnghttp2-14 libpbbam-dev libpbbam0.19.0
libpipeline1 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl-dev libsz2 libtool
libuchardet0 libxml2 m4 man-db mime-support po-debconf python python-minimal
python2 python2-minimal python2.7 python2.7-minimal
sbuild-build-depends-pbseqlib-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, 71 newly installed, 0 to remove and 45 not upgraded.
Need to get 68.7 MB/69.0 MB of archives.
After this operation, 240 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8qBIgu/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [920 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 libgnutls30 armhf 3.6.6-2 [1035 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf liblzma5 armhf 5.2.4-1 [144 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-2 [242 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-2 [109 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-2 [65.1 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.0-1 [19.5 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.0-1 [12.6 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.3-1 [1077 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf googletest armhf 1.8.1-3 [903 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.4+repack-10 [35.2 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.67.0.1+b1 [4140 B]
Get:64 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.36.0-2 [73.6 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.64.0-1 [291 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-16+rpi1 [207 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libgtest-dev armhf 1.8.1-3 [214 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libhdf5-103 armhf 1.10.4+repack-10 [1259 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-103 armhf 1.10.4+repack-10 [121 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.4+repack-10 [2221 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 liblzma-dev armhf 5.2.4-1 [203 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.9-8 [4280 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libpbbam0.19.0 armhf 0.19.0+dfsg-4+rpi1 [455 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1a-1 [1556 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.19.0+dfsg-4+rpi1 [93.4 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23.1 [25.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
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-exec_0.23.1 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 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 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 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 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 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 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 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 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbseqlib-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 07:10:41 2019 UTC
gpgv: using RSA key 3AFA757FAC6EA11D2FF45DF088D24287A2D898B1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbseqlib_5.3.1+dfsg-2.1.dsc
dpkg-source: info: extracting pbseqlib in /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg
dpkg-source: info: unpacking pbseqlib_5.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking pbseqlib_5.3.1+dfsg-2.1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hdf5-1.10.1-support.patch
dpkg-source: info: applying hdf5-1.10.0-support.patch
Check disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-3b44f8d2-a0d2-4653-99cc-8b417ab5da58
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbseqlib
dpkg-buildpackage: info: source version 5.3.1+dfsg-2.1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//pbdata clean
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
rm -f libpbdata.a libpbdata.so *.o *.d
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//hdf clean
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/hdf'
rm -f libpbihdf.a libpbihdf.so *.o *.d
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/hdf'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//alignment clean
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/alignment'
rm -f libblasr.a libblasr.so *.o *.d
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/alignment'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//unittest clean
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest'
rm -f -r *.o libblasr-test-runner
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest'
make[2]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
find -name defines.mk -delete
rm -f pbdata/libconfig.h
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
./configure.py PREFIX=/usr/
uname -s
uname='Linux'
writing to '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata/LibBlasrConfig.h'
"""
#define USE_PBBAM
"""
writing to 'defines.mk'
"""
CXXFLAGS := -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3
PREFIX_INC := /usr/include
PREFIX_LIB := /usr/lib
SH_LIB_EXT := .so
GTEST_INC ?= /usr/include
GTEST_SRCDIR ?= /usr/src/gtest
HDF5_INC ?= /usr/include/hdf5/serial
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
LIBBLASR_INC ?= ../alignment
LIBBLASR_LIB ?= ../alignment/
LIBPBDATA_INC ?= ../pbdata
LIBPBDATA_LIB ?= ../pbdata/
LIBPBIHDF_INC ?= ../hdf
LIBPBIHDF_LIB ?= ../hdf/
SHELL ?= bash
# Use PREFIX dir, if available.
INCLUDES += ${PREFIX_INC} ../pbdata
LIBS += ${PREFIX_LIB}
"""
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
dh_auto_build -- PREFIX_INC=..
make -j4 "INSTALL=install --strip-program=true" PREFIX_INC=..
make[2]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make libpbdata
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//pbdata LibBlasrConfig.h
make[4]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
make[4]: 'LibBlasrConfig.h' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//pbdata all
make[4]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c ChangeListID.cpp -o ChangeListID.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/BitUtils.cpp -o BitUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/SMRTTitle.cpp -o SMRTTitle.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c utils/TimeUtils.cpp -o TimeUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c StringUtils.cpp -o StringUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c SMRTSequence.cpp -o SMRTSequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c BlasrFASTQReader.cpp -o BlasrFASTQReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c BlasrFASTAReader.cpp -o BlasrFASTAReader.o
In file included from SMRTSequence.cpp:3:
SMRTSequence.cpp: In member function 'float SMRTSequence::HQRegionSnr(char) const':
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \
^~~
SMRTSequence.cpp:329:9: note: in expansion of macro 'BLASR_THROW'
BLASR_THROW("Base must be in A, C, G, T");
^~~~~~~~~~~
SMRTSequence.cpp:328:5: note: some parts of macro expansion are not guarded by this 'else' clause
else
^~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c FASTASequence.cpp -o FASTASequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c loadpulses/MetricField.cpp -o MetricField.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c NucConversion.cpp -o NucConversion.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c qvs/QualityTransform.cpp -o QualityTransform.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c qvs/BlasrQualityValue.cpp -o BlasrQualityValue.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c MD5Utils.cpp -o MD5Utils.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c alignment/CmpAlignment.cpp -o CmpAlignment.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c metagenome/TitleTable.cpp -o TitleTable.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c CommandLineParser.cpp -o CommandLineParser.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c CCSSequence.cpp -o CCSSequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c amos/AfgBasWriter.cpp -o AfgBasWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionAnnotations.cpp -o RegionAnnotations.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/HoleXY.cpp -o HoleXY.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/PulseFile.cpp -o PulseFile.o
In file included from reads/RegionAnnotations.cpp:3:
reads/RegionAnnotations.cpp: In member function 'RegionAnnotation RegionAnnotations::TheHQRegion() const':
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \
^~~
reads/RegionAnnotations.cpp:67:9: note: in expansion of macro 'BLASR_THROW'
BLASR_THROW("Zmw has more than one HQRegion");
^~~~~~~~~~~
reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this 'else' clause
else
^~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionTypeMap.cpp -o RegionTypeMap.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/ReadType.cpp -o ReadType.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/AcqParams.cpp -o AcqParams.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/ScanData.cpp -o ScanData.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/BaseFile.cpp -o BaseFile.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionTable.cpp -o RegionTable.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c reads/RegionAnnotation.cpp -o RegionAnnotation.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c FASTQSequence.cpp -o FASTQSequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c GFFFile.cpp -o GFFFile.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c ReverseCompressIndex.cpp -o ReverseCompressIndex.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/RefInfo.cpp -o RefInfo.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/MovieInfo.cpp -o MovieInfo.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/AlnGroup.cpp -o AlnGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c saf/RefGroup.cpp -o RefGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c DNASequence.cpp -o DNASequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c PackedDNASequence.cpp -o PackedDNASequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/ReadGroup.cpp -o ReadGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/ReferenceSequence.cpp -o ReferenceSequence.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/SAMHeader.cpp -o SAMHeader.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -c sam/SAMAlignment.cpp -o SAMAlignment.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c ChangeListID.cpp -o ChangeListID.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/BitUtils.cpp -o BitUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/SMRTTitle.cpp -o SMRTTitle.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c utils/TimeUtils.cpp -o TimeUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c StringUtils.cpp -o StringUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c SMRTSequence.cpp -o SMRTSequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c BlasrFASTQReader.cpp -o BlasrFASTQReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c BlasrFASTAReader.cpp -o BlasrFASTAReader.shared.o
In file included from SMRTSequence.cpp:3:
SMRTSequence.cpp: In member function 'float SMRTSequence::HQRegionSnr(char) const':
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \
^~~
SMRTSequence.cpp:329:9: note: in expansion of macro 'BLASR_THROW'
BLASR_THROW("Base must be in A, C, G, T");
^~~~~~~~~~~
SMRTSequence.cpp:328:5: note: some parts of macro expansion are not guarded by this 'else' clause
else
^~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c FASTASequence.cpp -o FASTASequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c loadpulses/MetricField.cpp -o MetricField.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c NucConversion.cpp -o NucConversion.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c qvs/QualityTransform.cpp -o QualityTransform.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c qvs/BlasrQualityValue.cpp -o BlasrQualityValue.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c MD5Utils.cpp -o MD5Utils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c alignment/CmpAlignment.cpp -o CmpAlignment.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c metagenome/TitleTable.cpp -o TitleTable.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c CommandLineParser.cpp -o CommandLineParser.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c CCSSequence.cpp -o CCSSequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c amos/AfgBasWriter.cpp -o AfgBasWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionAnnotations.cpp -o RegionAnnotations.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/HoleXY.cpp -o HoleXY.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/PulseFile.cpp -o PulseFile.shared.o
In file included from reads/RegionAnnotations.cpp:3:
reads/RegionAnnotations.cpp: In member function 'RegionAnnotation RegionAnnotations::TheHQRegion() const':
../pbdata/PrettyException.hpp:8:5: warning: macro expands to multiple statements [-Wmultistatement-macros]
std::cerr << "Exception in file '" << __FILE__ << "', on line '" << __LINE__ \
^~~
reads/RegionAnnotations.cpp:67:9: note: in expansion of macro 'BLASR_THROW'
BLASR_THROW("Zmw has more than one HQRegion");
^~~~~~~~~~~
reads/RegionAnnotations.cpp:66:5: note: some parts of macro expansion are not guarded by this 'else' clause
else
^~~~
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionTypeMap.cpp -o RegionTypeMap.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ReadType.cpp -o ReadType.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/AcqParams.cpp -o AcqParams.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/ScanData.cpp -o ScanData.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/BaseFile.cpp -o BaseFile.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionTable.cpp -o RegionTable.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c reads/RegionAnnotation.cpp -o RegionAnnotation.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c FASTQSequence.cpp -o FASTQSequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c GFFFile.cpp -o GFFFile.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c ReverseCompressIndex.cpp -o ReverseCompressIndex.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/RefInfo.cpp -o RefInfo.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/MovieInfo.cpp -o MovieInfo.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/AlnGroup.cpp -o AlnGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c saf/RefGroup.cpp -o RefGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c DNASequence.cpp -o DNASequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c PackedDNASequence.cpp -o PackedDNASequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/ReadGroup.cpp -o ReadGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/ReferenceSequence.cpp -o ReferenceSequence.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMHeader.cpp -o SAMHeader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -fPIC -c sam/SAMAlignment.cpp -o SAMAlignment.shared.o
ar rc libpbdata.a ChangeListID.o SMRTReadUtils.o BitUtils.o SMRTTitle.o TimeUtils.o StringUtils.o SMRTSequence.o BlasrFASTQReader.o BlasrFASTAReader.o FASTASequence.o MovieAlnIndexLookupTable.o MetricField.o NucConversion.o QualityTransform.o BlasrQualityValue.o MD5Utils.o CmpAlignment.o TitleTable.o CommandLineParser.o CCSSequence.o AfgBasWriter.o RegionAnnotations.o HoleXY.o PulseFile.o RegionTypeMap.o ReadType.o AcqParams.o ZMWGroupEntry.o PulseBaseCommon.o ScanData.o BaseFile.o RegionTable.o RegionAnnotation.o FASTQSequence.o GFFFile.o ReverseCompressIndex.o RefInfo.o MovieInfo.o AlnGroup.o RefGroup.o DNASequence.o PackedDNASequence.o ReadGroup.o ReferenceSequence.o SAMHeader.o SAMKeywordValuePair.o SAMAlignment.o
g++ -shared -Wl,-z,relro -Wl,-z,now -L/usr/lib -o libpbdata.so -Wl,-soname,libpbdata.so ChangeListID.shared.o SMRTReadUtils.shared.o BitUtils.shared.o SMRTTitle.shared.o TimeUtils.shared.o StringUtils.shared.o SMRTSequence.shared.o BlasrFASTQReader.shared.o BlasrFASTAReader.shared.o FASTASequence.shared.o MovieAlnIndexLookupTable.shared.o MetricField.shared.o NucConversion.shared.o QualityTransform.shared.o BlasrQualityValue.shared.o MD5Utils.shared.o CmpAlignment.shared.o TitleTable.shared.o CommandLineParser.shared.o CCSSequence.shared.o AfgBasWriter.shared.o RegionAnnotations.shared.o HoleXY.shared.o PulseFile.shared.o RegionTypeMap.shared.o ReadType.shared.o AcqParams.shared.o ZMWGroupEntry.shared.o PulseBaseCommon.shared.o ScanData.shared.o BaseFile.shared.o RegionTable.shared.o RegionAnnotation.shared.o FASTQSequence.shared.o GFFFile.shared.o ReverseCompressIndex.shared.o RefInfo.shared.o MovieInfo.shared.o AlnGroup.shared.o RefGroup.shared.o DNASequence.shared.o PackedDNASequence.shared.o ReadGroup.shared.o ReferenceSequence.shared.o SAMHeader.shared.o SAMKeywordValuePair.shared.o SAMAlignment.shared.o -lpbbam -lpbbam
make[4]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/pbdata'
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make libpbihdf
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//hdf all
make[4]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/hdf'
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAttributable.cpp -o HDFAttributable.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c BufferedHDFArray.cpp -o BufferedHDFArray.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFRegionsWriter.cpp -o HDFRegionsWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFScanDataReader.cpp -o HDFScanDataReader.o
HDFAttributable.cpp: In member function 'int HDFAttributable::ContainsAttribute(const string&)':
HDFAttributable.cpp:48:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFRegionTableReader.cpp -o HDFRegionTableReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFScanDataWriter.cpp -o HDFScanDataWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFWriterBase.cpp -o HDFWriterBase.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c DatasetCollection.cpp -o DatasetCollection.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFFile.cpp -o HDFFile.o
HDFFile.cpp: In member function 'void HDFFile::Open(std::__cxx11::string, unsigned int, const H5::FileAccPropList&)':
HDFFile.cpp:23:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
} catch (FileIException e) {
^
HDFFile.cpp:35:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
} catch (FileIException fileException) {
^~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFBaxWriter.cpp -o HDFBaxWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWMetricsWriter.hpp:7,
from HDFZMWMetricsWriter.cpp:3:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]':
HDFZMWMetricsWriter.cpp:54:27: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFZMWMetricsWriter.cpp:55:30: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseDataFile.cpp -o HDFPulseDataFile.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFCmpExperimentGroup.hpp:10,
from HDFCmpExperimentGroup.cpp:1:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned char]'
HDFCmpExperimentGroup.cpp:36:69: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = char; DSLength = long long unsigned int]':
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = char]'
HDFCmpExperimentGroup.cpp:199:72: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.o
HDFPulseCallsWriter.cpp: In member function 'virtual void HDFPulseCallsWriter::Close()':
HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAtom.cpp -o HDFAtom.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFWriterBase.hpp:12,
from ../hdf/HDFPulseCallsWriter.hpp:12,
from HDFPulseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFPulseCallsWriter.cpp:492:47: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long long unsigned int]':
HDFPulseCallsWriter.cpp:497:39: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
HDFPulseCallsWriter.cpp:498:49: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
In file included from HDFAtom.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:174:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^~~~~
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:175:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = char; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:176:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = unsigned char; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:177:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = long long unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:178:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = float; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:179:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::__cxx11::basic_string<char>; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:180:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<int>; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:181:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<unsigned int>; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:182:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:183:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
HDFBaseCallsWriter.cpp: In member function 'virtual void HDFBaseCallsWriter::Close()':
HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFWriterBase.hpp:12,
from ../hdf/HDFBaseCallsWriter.hpp:12,
from HDFBaseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFBaseCallsWriter.cpp:342:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long long unsigned int]':
HDFBaseCallsWriter.cpp:350:35: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWReader.cpp -o HDFZMWReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFZMWWriter.cpp -o HDFZMWWriter.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWWriter.hpp:11,
from HDFZMWWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
HDFZMWWriter.cpp:149:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFZMWWriter.cpp:151:28: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFNewBasReader.cpp -o HDFNewBasReader.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFPulseWriter.cpp -o HDFPulseWriter.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFGroup.cpp -o HDFGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFUtils.cpp -o HDFUtils.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c HDFData.cpp -o HDFData.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAttributable.cpp -o HDFAttributable.shared.o
HDFAttributable.cpp: In member function 'int HDFAttributable::ContainsAttribute(const string&)':
HDFAttributable.cpp:48:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c BufferedHDFArray.cpp -o BufferedHDFArray.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFRegionsWriter.cpp -o HDFRegionsWriter.shared.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFAlnGroupGroup.hpp:6,
from HDFAlnGroupGroup.cpp:1:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = std::__cxx11::basic_string<char>; DSLength = long long unsigned int]':
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]'
HDFAlnGroupGroup.cpp:16:29: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned int]'
HDFAlnGroupGroup.cpp:18:25: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataReader.cpp -o HDFScanDataReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFRegionTableReader.cpp -o HDFRegionTableReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFWriterBase.cpp -o HDFWriterBase.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c DatasetCollection.cpp -o DatasetCollection.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFFile.cpp -o HDFFile.shared.o
HDFFile.cpp: In member function 'void HDFFile::Open(std::__cxx11::string, unsigned int, const H5::FileAccPropList&)':
HDFFile.cpp:23:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
} catch (FileIException e) {
^
HDFFile.cpp:35:33: warning: catching polymorphic type 'class H5::FileIException' by value [-Wcatch-value=]
} catch (FileIException fileException) {
^~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaxWriter.cpp -o HDFBaxWriter.shared.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWMetricsWriter.hpp:7,
from HDFZMWMetricsWriter.cpp:3:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]':
HDFZMWMetricsWriter.cpp:54:27: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFZMWMetricsWriter.cpp:55:30: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.shared.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFCmpExperimentGroup.hpp:10,
from HDFCmpExperimentGroup.cpp:1:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned char]'
HDFCmpExperimentGroup.cpp:36:69: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = char; DSLength = long long unsigned int]':
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = char]'
HDFCmpExperimentGroup.cpp:199:72: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
HDFPulseCallsWriter.cpp: In member function 'virtual void HDFPulseCallsWriter::Close()':
HDFPulseCallsWriter.cpp:513:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFWriterBase.hpp:12,
from ../hdf/HDFPulseCallsWriter.hpp:12,
from HDFPulseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFPulseCallsWriter.cpp:492:47: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long long unsigned int]':
HDFPulseCallsWriter.cpp:497:39: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
HDFPulseCallsWriter.cpp:498:49: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
HDFBaseCallsWriter.cpp: In member function 'virtual void HDFBaseCallsWriter::Close()':
HDFBaseCallsWriter.cpp:364:28: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFWriterBase.hpp:12,
from ../hdf/HDFBaseCallsWriter.hpp:12,
from HDFBaseCallsWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFBaseCallsWriter.cpp:342:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long long unsigned int]':
HDFBaseCallsWriter.cpp:350:35: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAtom.cpp -o HDFAtom.shared.o
In file included from HDFAtom.cpp:1:
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:174:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
} catch (H5::Exception e) {
^~~~~
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:175:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = char; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:176:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = unsigned char; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:177:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = long long unsigned int; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:178:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = float; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:179:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::__cxx11::basic_string<char>; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:180:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<int>; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:181:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<unsigned int>; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:182:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
../hdf/HDFAtom.hpp: In instantiation of 'int HDFAtom<T>::Initialize(H5::H5File&, const string&) [with T = std::vector<std::__cxx11::basic_string<char> >; std::__cxx11::string = std::__cxx11::basic_string<char>]':
HDFAtom.cpp:183:16: required from here
../hdf/HDFAtom.hpp:52:11: warning: catching polymorphic type 'class H5::Exception' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWReader.cpp -o HDFZMWReader.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFZMWWriter.cpp -o HDFZMWWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFNewBasReader.cpp -o HDFNewBasReader.shared.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFZMWWriter.hpp:11,
from HDFZMWWriter.cpp:5:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
HDFZMWWriter.cpp:149:26: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]':
HDFZMWWriter.cpp:151:28: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFPulseWriter.cpp -o HDFPulseWriter.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFGroup.cpp -o HDFGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFUtils.cpp -o HDFUtils.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c HDFData.cpp -o HDFData.shared.o
g++ -std=c++14 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.shared.o
ar rc libpbihdf.a HDFAttributable.o BufferedHDFArray.o HDFRegionsWriter.o HDFScanDataReader.o HDFRegionTableReader.o HDFScanDataWriter.o HDFWriterBase.o DatasetCollection.o HDFFile.o HDFZMWMetricsWriter.o HDFBaxWriter.o HDFCmpExperimentGroup.o HDFPulseDataFile.o HDFPulseCallsWriter.o HDFBaseCallsWriter.o HDFCmpSupportedFields.o HDFAtom.o HDFZMWReader.o HDFZMWWriter.o HDFPulseH5Writer.o HDFAlnInfoGroup.o HDFNewBasReader.o HDFPulseWriter.o HDFGroup.o HDFUtils.o HDFAlnGroupGroup.o HDFData.o BufferedHDF2DArray.o
In file included from ../hdf/BufferedHDFArray.hpp:217,
from ../hdf/HDFArray.hpp:9,
from ../hdf/HDFAlnGroupGroup.hpp:6,
from HDFAlnGroupGroup.cpp:1:
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = std::__cxx11::basic_string<char>; DSLength = long long unsigned int]':
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]'
HDFAlnGroupGroup.cpp:16:29: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/BufferedHDFArrayImpl.hpp: In instantiation of 'void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]':
../hdf/HDFArray.hpp:67:9: required from 'void HDFArray<T>::Write(const T*, int) [with T = unsigned int]'
HDFAlnGroupGroup.cpp:18:25: required from here
../hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
g++ -shared -Wl,-z,relro -Wl,-z,now -L/usr/lib -L../pbdata/ -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o libpbihdf.so -Wl,-soname,libpbihdf.so HDFAttributable.shared.o BufferedHDFArray.shared.o HDFRegionsWriter.shared.o HDFScanDataReader.shared.o HDFRegionTableReader.shared.o HDFScanDataWriter.shared.o HDFWriterBase.shared.o DatasetCollection.shared.o HDFFile.shared.o HDFZMWMetricsWriter.shared.o HDFBaxWriter.shared.o HDFCmpExperimentGroup.shared.o HDFPulseDataFile.shared.o HDFPulseCallsWriter.shared.o HDFBaseCallsWriter.shared.o HDFCmpSupportedFields.shared.o HDFAtom.shared.o HDFZMWReader.shared.o HDFZMWWriter.shared.o HDFPulseH5Writer.shared.o HDFAlnInfoGroup.shared.o HDFNewBasReader.shared.o HDFPulseWriter.shared.o HDFGroup.shared.o HDFUtils.shared.o HDFAlnGroupGroup.shared.o HDFData.shared.o BufferedHDF2DArray.shared.o -lpbbam -lpbbam -lpbdata -lhdf5 -lhdf5_cpp
make[4]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/hdf'
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make libblasr
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//alignment all
make[4]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/alignment'
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/FileOfFileNames.cpp -o FileOfFileNames.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/RangeUtils.cpp -o RangeUtils.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/RegionUtils.cpp -o RegionUtils.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/BlasrFileUtils.cpp -o BlasrFileUtils.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/LogUtils.cpp -o LogUtils.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c utils/PhredUtils.cpp -o PhredUtils.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/BaseSequenceIO.cpp -o BaseSequenceIO.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/CCSIterator.cpp -o CCSIterator.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/ReaderAgglomerate.cpp -o ReaderAgglomerate.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::Initialize(bool, bool)':
files/ReaderAgglomerate.cpp:267:37: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
} catch (std::exception e) {
^
In file included from ../alignment/files/ReaderAgglomerate.hpp:8,
from files/ReaderAgglomerate.cpp:1:
../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(FASTASequence&) [with T_Sequence = SMRTSequence]':
files/ReaderAgglomerate.cpp:360:50: required from here
../hdf/HDFBasReader.hpp:602:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]':
files/ReaderAgglomerate.cpp:401:50: required from here
../hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]':
files/ReaderAgglomerate.cpp:516:50: required from here
../hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNextBases(SMRTSequence&, bool) [with T_Sequence = SMRTSequence]':
files/ReaderAgglomerate.cpp:611:64: required from here
../hdf/HDFBasReader.hpp:691:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
In file included from ../alignment/files/ReaderAgglomerate.hpp:9,
from files/ReaderAgglomerate.cpp:1:
../hdf/HDFCCSReader.hpp: In instantiation of 'int HDFCCSReader<T_Sequence>::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]':
files/ReaderAgglomerate.cpp:664:50: required from here
../hdf/HDFCCSReader.hpp:270:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c files/FragmentCCSIterator.cpp -o FragmentCCSIterator.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c qvs/QualityValueProfile.cpp -o QualityValueProfile.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c MappingMetrics.cpp -o MappingMetrics.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNextBases(SMRTSequence&, bool)':
files/ReaderAgglomerate.cpp:624:81: warning: this statement may fall through [-Wimplicit-fallthrough=]
std::cout << "ERROR! Can not GetNextBases from a BAM File." << std::endl;
^~~~
files/ReaderAgglomerate.cpp:626:9: note: here
case FileType::Fourbit:
^~~~
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNext(CCSSequence&)':
files/ReaderAgglomerate.cpp:669:83: warning: this statement may fall through [-Wimplicit-fallthrough=]
std::cout << "ERROR! Could not read BamRecord as CCSSequence" << std::endl;
^~~~
files/ReaderAgglomerate.cpp:671:9: note: here
case FileType::Fourbit:
^~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/CmpFile.cpp -o CmpFile.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/Alignment.cpp -o Alignment.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/ClusterList.cpp -o ClusterList.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.o
In file included from /usr/include/c++/8/vector:69,
from ../alignment/datastructures/alignment/Alignment.hpp:5,
from ../alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
from ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp:7,
from datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp:1:
/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 AlignmentCandidate<FASTASequence, FASTASequence>&}; _Tp = AlignmentCandidate<>; _Alloc = std::allocator<AlignmentCandidate<> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<AlignmentCandidate<> >::iterator' {aka '__gnu_cxx::__normal_iterator<AlignmentCandidate<>*, std::vector<AlignmentCandidate<> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../alignment/datastructures/alignment/Alignment.hpp:5,
from ../alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
from ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp:7,
from datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In function 'void SAMAlignmentsToCandidates(SAMAlignment&, std::vector<FASTASequence>&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<AlignmentCandidate<> >&, bool, bool, bool)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignmentCandidate<>*, std::vector<AlignmentCandidate<> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c datastructures/anchoring/MatchPos.cpp -o MatchPos.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c simulator/LengthHistogram.cpp -o LengthHistogram.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c simulator/ContextSet.cpp -o ContextSet.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c simulator/ContextSample.cpp -o ContextSample.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c simulator/QualitySample.cpp -o QualitySample.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c statistics/StatUtils.cpp -o StatUtils.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c statistics/pdfs.cpp -o pdfs.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c statistics/cdfs.cpp -o cdfs.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/IntervalPrinter.cpp -o IntervalPrinter.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/SummaryPrinter.cpp -o SummaryPrinter.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/SAMPrinter.cpp -o SAMPrinter.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/KBandAlign.cpp -o KBandAlign.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/qsufsort.cpp -o qsufsort.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/Coordinate.cpp -o Coordinate.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c algorithms/anchoring/BWTSearch.cpp -o BWTSearch.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c tuples/DNATuple.cpp -o DNATuple.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c tuples/TupleMetrics.cpp -o TupleMetrics.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c tuples/BaseTuple.cpp -o BaseTuple.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c query/SequentialZmwGroupQuery.cpp -o SequentialZmwGroupQuery.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -c query/PbiFilterZmwGroupQuery.cpp -o PbiFilterZmwGroupQuery.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/FileOfFileNames.cpp -o FileOfFileNames.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/RangeUtils.cpp -o RangeUtils.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/RegionUtils.cpp -o RegionUtils.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/BlasrFileUtils.cpp -o BlasrFileUtils.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/LogUtils.cpp -o LogUtils.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c utils/PhredUtils.cpp -o PhredUtils.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c files/BaseSequenceIO.cpp -o BaseSequenceIO.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c files/CCSIterator.cpp -o CCSIterator.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c files/ReaderAgglomerate.cpp -o ReaderAgglomerate.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c files/FragmentCCSIterator.cpp -o FragmentCCSIterator.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c qvs/QualityValueProfile.cpp -o QualityValueProfile.shared.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::Initialize(bool, bool)':
files/ReaderAgglomerate.cpp:267:37: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
} catch (std::exception e) {
^
In file included from ../alignment/files/ReaderAgglomerate.hpp:8,
from files/ReaderAgglomerate.cpp:1:
../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(FASTASequence&) [with T_Sequence = SMRTSequence]':
files/ReaderAgglomerate.cpp:360:50: required from here
../hdf/HDFBasReader.hpp:602:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(FASTQSequence&) [with T_Sequence = SMRTSequence]':
files/ReaderAgglomerate.cpp:401:50: required from here
../hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = SMRTSequence]':
files/ReaderAgglomerate.cpp:516:50: required from here
../hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
../hdf/HDFBasReader.hpp: In instantiation of 'int T_HDFBasReader<T_Sequence>::GetNextBases(SMRTSequence&, bool) [with T_Sequence = SMRTSequence]':
files/ReaderAgglomerate.cpp:611:64: required from here
../hdf/HDFBasReader.hpp:691:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
In file included from ../alignment/files/ReaderAgglomerate.hpp:9,
from files/ReaderAgglomerate.cpp:1:
../hdf/HDFCCSReader.hpp: In instantiation of 'int HDFCCSReader<T_Sequence>::GetNext(T_Sequence&) [with T_Sequence = CCSSequence]':
files/ReaderAgglomerate.cpp:664:50: required from here
../hdf/HDFCCSReader.hpp:270:11: warning: catching polymorphic type 'class H5::DataSetIException' by value [-Wcatch-value=]
} catch (H5::DataSetIException e) {
^~~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c MappingMetrics.cpp -o MappingMetrics.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.shared.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNextBases(SMRTSequence&, bool)':
files/ReaderAgglomerate.cpp:624:81: warning: this statement may fall through [-Wimplicit-fallthrough=]
std::cout << "ERROR! Can not GetNextBases from a BAM File." << std::endl;
^~~~
files/ReaderAgglomerate.cpp:626:9: note: here
case FileType::Fourbit:
^~~~
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNext(CCSSequence&)':
files/ReaderAgglomerate.cpp:669:83: warning: this statement may fall through [-Wimplicit-fallthrough=]
std::cout << "ERROR! Could not read BamRecord as CCSSequence" << std::endl;
^~~~
files/ReaderAgglomerate.cpp:671:9: note: here
case FileType::Fourbit:
^~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/CmpFile.cpp -o CmpFile.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/Alignment.cpp -o Alignment.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/ClusterList.cpp -o ClusterList.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.shared.o
In file included from /usr/include/c++/8/vector:69,
from ../alignment/datastructures/alignment/Alignment.hpp:5,
from ../alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
from ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp:7,
from datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp:1:
/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 AlignmentCandidate<FASTASequence, FASTASequence>&}; _Tp = AlignmentCandidate<>; _Alloc = std::allocator<AlignmentCandidate<> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<AlignmentCandidate<> >::iterator' {aka '__gnu_cxx::__normal_iterator<AlignmentCandidate<>*, std::vector<AlignmentCandidate<> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/MatchPos.cpp -o MatchPos.shared.o
In file included from /usr/include/c++/8/vector:64,
from ../alignment/datastructures/alignment/Alignment.hpp:5,
from ../alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
from ../alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp:7,
from datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp:1:
/usr/include/c++/8/bits/stl_vector.h: In function 'void SAMAlignmentsToCandidates(SAMAlignment&, std::vector<FASTASequence>&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<AlignmentCandidate<> >&, bool, bool, bool)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AlignmentCandidate<>*, std::vector<AlignmentCandidate<> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c simulator/LengthHistogram.cpp -o LengthHistogram.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c simulator/ContextSet.cpp -o ContextSet.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c simulator/ContextSample.cpp -o ContextSample.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c simulator/QualitySample.cpp -o QualitySample.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c statistics/StatUtils.cpp -o StatUtils.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c statistics/pdfs.cpp -o pdfs.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c statistics/cdfs.cpp -o cdfs.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/IntervalPrinter.cpp -o IntervalPrinter.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/SummaryPrinter.cpp -o SummaryPrinter.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/SAMPrinter.cpp -o SAMPrinter.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/KBandAlign.cpp -o KBandAlign.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/qsufsort.cpp -o qsufsort.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/Coordinate.cpp -o Coordinate.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/BWTSearch.cpp -o BWTSearch.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c tuples/DNATuple.cpp -o DNATuple.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c tuples/TupleMetrics.cpp -o TupleMetrics.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c tuples/BaseTuple.cpp -o BaseTuple.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c query/SequentialZmwGroupQuery.cpp -o SequentialZmwGroupQuery.shared.o
g++ -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I.. -I../pbdata -I/usr/include/hdf5/serial -fPIC -c query/PbiFilterZmwGroupQuery.cpp -o PbiFilterZmwGroupQuery.shared.o
ar rc libblasr.a FileOfFileNames.o RangeUtils.o RegionUtils.o BlasrFileUtils.o LogUtils.o PhredUtils.o BaseSequenceIO.o CCSIterator.o ReaderAgglomerate.o FragmentCCSIterator.o QualityValueProfile.o MappingMetrics.o SAMQVConversion.o SAMSupplementalQVList.o CmpFile.o Alignment.o AlignmentContext.o FilterCriteria.o AlignmentStats.o AlignmentCandidate.o SAMToAlignmentCandidateAdapter.o AlignmentMap.o ClusterList.o WeightedInterval.o AnchorParameters.o MatchPos.o LengthHistogram.o ContextSet.o ContextSample.o QualitySample.o StatUtils.o pdfs.o LookupAnchorDistribution.o cdfs.o CompareSequencesPrinter.o IntervalPrinter.o SummaryPrinter.o SAMPrinter.o SAMHeaderPrinter.o GuidedAlign.o StringToScoreMatrix.o KBandAlign.o ExtendAlign.o ScoreMatrices.o AlignmentUtils.o IDSScoreFunction.o QualityValueScoreFunction.o BaseScoreFunction.o SparseDynamicProgramming.o SDPFragment.o MultikeyQuicksort.o LightweightSuffixArray.o qsufsort.o DifferenceCovers.o FindMaxInterval.o Coordinate.o ClusterProbability.o BWTSearch.o DNATuple.o TupleMetrics.o BaseTuple.o SequentialZmwGroupQuery.o PbiFilterZmwGroupQuery.o
g++ -shared -Wl,-z,relro -Wl,-z,now -L/usr/lib -L../pbdata/ -L../hdf/ -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o libblasr.so -Wl,-soname,libblasr.so FileOfFileNames.shared.o RangeUtils.shared.o RegionUtils.shared.o BlasrFileUtils.shared.o LogUtils.shared.o PhredUtils.shared.o BaseSequenceIO.shared.o CCSIterator.shared.o ReaderAgglomerate.shared.o FragmentCCSIterator.shared.o QualityValueProfile.shared.o MappingMetrics.shared.o SAMQVConversion.shared.o SAMSupplementalQVList.shared.o CmpFile.shared.o Alignment.shared.o AlignmentContext.shared.o FilterCriteria.shared.o AlignmentStats.shared.o AlignmentCandidate.shared.o SAMToAlignmentCandidateAdapter.shared.o AlignmentMap.shared.o ClusterList.shared.o WeightedInterval.shared.o AnchorParameters.shared.o MatchPos.shared.o LengthHistogram.shared.o ContextSet.shared.o ContextSample.shared.o QualitySample.shared.o StatUtils.shared.o pdfs.shared.o LookupAnchorDistribution.shared.o cdfs.shared.o CompareSequencesPrinter.shared.o IntervalPrinter.shared.o SummaryPrinter.shared.o SAMPrinter.shared.o SAMHeaderPrinter.shared.o GuidedAlign.shared.o StringToScoreMatrix.shared.o KBandAlign.shared.o ExtendAlign.shared.o ScoreMatrices.shared.o AlignmentUtils.shared.o IDSScoreFunction.shared.o QualityValueScoreFunction.shared.o BaseScoreFunction.shared.o SparseDynamicProgramming.shared.o SDPFragment.shared.o MultikeyQuicksort.shared.o LightweightSuffixArray.shared.o qsufsort.shared.o DifferenceCovers.shared.o FindMaxInterval.shared.o Coordinate.shared.o ClusterProbability.shared.o BWTSearch.shared.o DNATuple.shared.o TupleMetrics.shared.o BaseTuple.shared.o SequentialZmwGroupQuery.shared.o PbiFilterZmwGroupQuery.shared.o -lpbbam -lpbbam -lpbdata -lpbihdf
make[4]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/alignment'
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
/usr/bin/make -k gtest
make[2]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
/usr/bin/make -C /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg//unittest gtest
make[3]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest'
make[3]: *** No rule to make target 'gtest-all.o', needed by 'libblasr-test-runner'.
make[3]: *** No rule to make target 'gtest_main.o', needed by 'libblasr-test-runner'.
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CCSSequence_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/CCSSequence_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/CCSSequence_gtest.cpp:25:10: fatal error: pbdata/CCSSequence.hpp: No such file or directory
#include <pbdata/CCSSequence.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: CCSSequence_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SeqUtils_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/SeqUtils_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/SeqUtils_gtest.cpp:22:10: fatal error: pbdata/SeqUtils.hpp: No such file or directory
#include <pbdata/SeqUtils.hpp>
^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: SeqUtils_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SMRTSequence_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/SMRTSequence_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/SMRTSequence_gtest.cpp:24:10: fatal error: pbdata/SMRTSequence.hpp: No such file or directory
#include <pbdata/SMRTSequence.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: SMRTSequence_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o defs_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/defs_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/defs_gtest.cpp:21:10: fatal error: pbdata/defs.h: No such file or directory
#include <pbdata/defs.h>
^~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: defs_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o NucConversion_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/NucConversion_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/NucConversion_gtest.cpp:21:10: fatal error: pbdata/NucConversion.hpp: No such file or directory
#include <pbdata/NucConversion.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: NucConversion_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTQReader_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTQReader_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTQReader_gtest.cpp:22:10: fatal error: pbdata/FASTQReader.hpp: No such file or directory
#include <pbdata/FASTQReader.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: FASTQReader_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o VectorUtils_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/VectorUtils_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/VectorUtils_gtest.cpp:23:10: fatal error: pbdata/VectorUtils.hpp: No such file or directory
#include <pbdata/VectorUtils.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: VectorUtils_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ScanData_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/ScanData_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/ScanData_gtest.cpp:21:10: fatal error: pbdata/reads/ScanData.hpp: No such file or directory
#include <pbdata/reads/ScanData.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: ScanData_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ChangeListID_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/ChangeListID_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/ChangeListID_gtest.cpp:23:10: fatal error: pbdata/ChangeListID.hpp: No such file or directory
#include <pbdata/ChangeListID.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: ChangeListID_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o utils_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/utils_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/utils_gtest.cpp:24:10: fatal error: pbdata/utils.hpp: No such file or directory
#include <pbdata/utils.hpp>
^~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: utils_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTASequence_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTASequence_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTASequence_gtest.cpp:25:10: fatal error: pbdata/FASTASequence.hpp: No such file or directory
#include <pbdata/FASTASequence.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: FASTASequence_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o DNASequence_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/DNASequence_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/DNASequence_gtest.cpp:26:10: fatal error: pbdata/DNASequence.hpp: No such file or directory
#include <pbdata/DNASequence.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: DNASequence_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTAReader_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTAReader_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTAReader_gtest.cpp:22:10: fatal error: pbdata/FASTAReader.hpp: No such file or directory
#include <pbdata/FASTAReader.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: FASTAReader_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTQSequence_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTQSequence_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/FASTQSequence_gtest.cpp:25:10: fatal error: pbdata/FASTQSequence.hpp: No such file or directory
#include <pbdata/FASTQSequence.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: FASTQSequence_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o StringUtils_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/StringUtils_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/StringUtils_gtest.cpp:20:10: fatal error: pbdata/StringUtils.hpp: No such file or directory
#include <pbdata/StringUtils.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: StringUtils_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SMRTTitle_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/utils/SMRTTitle_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/utils/SMRTTitle_gtest.cpp:3:10: fatal error: pbdata/utils/SMRTTitle.hpp: No such file or directory
#include <pbdata/utils/SMRTTitle.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: SMRTTitle_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o TitleTable_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/metagenome/TitleTable_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/metagenome/TitleTable_gtest.cpp:22:10: fatal error: pbdata/metagenome/TitleTable.hpp: No such file or directory
#include <pbdata/metagenome/TitleTable.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: TitleTable_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RefInfo_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/RefInfo_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/RefInfo_gtest.cpp:21:10: fatal error: pbdata/saf/RefInfo.hpp: No such file or directory
#include <pbdata/saf/RefInfo.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: RefInfo_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o AlnGroup_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/AlnGroup_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/AlnGroup_gtest.cpp:21:10: fatal error: pbdata/saf/AlnGroup.hpp: No such file or directory
#include <pbdata/saf/AlnGroup.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: AlnGroup_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o MovieInfo_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/MovieInfo_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/saf/MovieInfo_gtest.cpp:21:10: fatal error: pbdata/Types.h: No such file or directory
#include <pbdata/Types.h>
^~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: MovieInfo_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionAnnotations_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/RegionAnnotations_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/RegionAnnotations_gtest.cpp:27:10: fatal error: pbdata/reads/ReadInterval.hpp: No such file or directory
#include <pbdata/reads/ReadInterval.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: RegionAnnotations_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ReadType_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/ReadType_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/ReadType_gtest.cpp:21:10: fatal error: pbdata/reads/ReadType.hpp: No such file or directory
#include <pbdata/reads/ReadType.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: ReadType_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionTypeMap_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/RegionTypeMap_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/reads/RegionTypeMap_gtest.cpp:25:10: fatal error: pbdata/reads/RegionTypeMap.hpp: No such file or directory
#include <pbdata/reads/RegionTypeMap.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: RegionTypeMap_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o QualityValueVector_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/qvs/QualityValueVector_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/pbdata/qvs/QualityValueVector_gtest.cpp:21:10: fatal error: pbdata/qvs/QualityValue.hpp: No such file or directory
#include <pbdata/qvs/QualityValue.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: QualityValueVector_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFUtils_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFUtils_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFUtils_gtest.cpp:22:10: fatal error: hdf/HDFUtils.hpp: No such file or directory
#include <hdf/HDFUtils.hpp>
^~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: HDFUtils_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFScanDataWriter_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFScanDataWriter_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFScanDataWriter_gtest.cpp:23:10: fatal error: hdf/HDFFile.hpp: No such file or directory
#include <hdf/HDFFile.hpp>
^~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: HDFScanDataWriter_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFCCSReader_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFCCSReader_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFCCSReader_gtest.cpp:22:10: fatal error: hdf/HDFCCSReader.hpp: No such file or directory
#include <hdf/HDFCCSReader.hpp>
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: HDFCCSReader_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFPlsReader_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFPlsReader_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFPlsReader_gtest.cpp:22:10: fatal error: hdf/HDFPlsReader.hpp: No such file or directory
#include <hdf/HDFPlsReader.hpp>
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: HDFPlsReader_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFScanDataReader_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFScanDataReader_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFScanDataReader_gtest.cpp:4:10: fatal error: hdf/HDFScanDataReader.hpp: No such file or directory
#include <hdf/HDFScanDataReader.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: HDFScanDataReader_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFBasReader_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFBasReader_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFBasReader_gtest.cpp:22:10: fatal error: hdf/HDFBasReader.hpp: No such file or directory
#include <hdf/HDFBasReader.hpp>
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: HDFBasReader_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDF2DArray_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDF2DArray_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDF2DArray_gtest.cpp:24:10: fatal error: hdf/HDF2DArray.hpp: No such file or directory
#include <hdf/HDF2DArray.hpp>
^~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: HDF2DArray_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFZMWReader_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFZMWReader_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/hdf/HDFZMWReader_gtest.cpp:22:10: fatal error: hdf/HDFZMWReader.hpp: No such file or directory
#include <hdf/HDFZMWReader.hpp>
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: HDFZMWReader_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RangeUtils_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/RangeUtils_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/RangeUtils_gtest.cpp:21:10: fatal error: alignment/utils/RangeUtils.hpp: No such file or directory
#include <alignment/utils/RangeUtils.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: RangeUtils_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FileUtils_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/FileUtils_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/FileUtils_gtest.cpp:21:10: fatal error: alignment/utils/FileUtils.hpp: No such file or directory
#include <alignment/utils/FileUtils.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: FileUtils_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionUtils_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/RegionUtils_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/utils/RegionUtils_gtest.cpp:22:10: fatal error: alignment/utils/RegionUtils.hpp: No such file or directory
#include <alignment/utils/RegionUtils.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: RegionUtils_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o PbiFilterZmwGroupQuery_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp:5:10: fatal error: alignment/query/PbiFilterZmwGroupQuery.h: No such file or directory
#include <alignment/query/PbiFilterZmwGroupQuery.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: PbiFilterZmwGroupQuery_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SequentialZmwGroupQuery_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp:5:10: fatal error: alignment/query/SequentialZmwGroupQuery.h: No such file or directory
#include <alignment/query/SequentialZmwGroupQuery.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: SequentialZmwGroupQuery_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o AlignmentMap_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp:25:10: fatal error: alignment/datastructures/alignment/AlignmentMap.hpp: No such file or directory
#include <alignment/datastructures/alignment/AlignmentMap.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: AlignmentMap_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CmpIndexedStringTable_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp:21:10: fatal error: alignment/datastructures/alignment/CmpIndexedStringTable.h: No such file or directory
#include <alignment/datastructures/alignment/CmpIndexedStringTable.h>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: CmpIndexedStringTable_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CCSIterator_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/files/CCSIterator_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/files/CCSIterator_gtest.cpp:22:10: fatal error: alignment/files/CCSIterator.hpp: No such file or directory
#include <alignment/files/CCSIterator.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: CCSIterator_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ReaderAgglomerate_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/files/ReaderAgglomerate_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/files/ReaderAgglomerate_gtest.cpp:25:10: fatal error: alignment/files/ReaderAgglomerate.hpp: No such file or directory
#include <alignment/files/ReaderAgglomerate.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: ReaderAgglomerate_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FragmentCCSIterator_other_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp:27:10: fatal error: alignment/files/CCSIterator.hpp: No such file or directory
#include <alignment/files/CCSIterator.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: FragmentCCSIterator_other_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FragmentCCSIterator_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/files/FragmentCCSIterator_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/files/FragmentCCSIterator_gtest.cpp:26:10: fatal error: alignment/files/FragmentCCSIterator.hpp: No such file or directory
#include <alignment/files/FragmentCCSIterator.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: FragmentCCSIterator_gtest.o] Error 1
g++ -O3 -std=c++14 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -DHAVE_HDF5_1_10_1 -I/usr/include -I../pbdata -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/ -I/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SAMPrinter_gtest.o /<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/format/SAMPrinter_gtest.cpp
/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest/alignment/format/SAMPrinter_gtest.cpp:29:10: fatal error: alignment/format/SAMPrinter.hpp: No such file or directory
#include <alignment/format/SAMPrinter.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [makefile:108: SAMPrinter_gtest.o] Error 1
make[3]: Target 'gtest' not remade because of errors.
make[3]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg/unittest'
make[2]: *** [makefile:27: gtest] Error 2
make[2]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
make[1]: [debian/rules:37: override_dh_auto_test] Error 2 (ignored)
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
mkdir -p debian/libpbdata-dev/usr/include/pbseq
cp -r pbdata debian/libpbdata-dev/usr/include/pbseq/
mkdir -p debian/libpbihdf-dev/usr/include/pbseq/
cp -r hdf debian/libpbihdf-dev/usr/include/pbseq/
mkdir -p debian/libblasr-dev/usr/include/pbseq/
cp -r alignment debian/libblasr-dev/usr/include/pbseq/
find -L debian/*/usr/include/ -type f -regextype posix-egrep -not -regex '.*(hpp|h)$' -delete
find debian/*/usr/include/ -name "*.mk" -delete
dh_auto_install
make[1]: Leaving directory '/<<BUILDDIR>>/pbseqlib-5.3.1+dfsg'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: cannot find library libpbdata.so needed by debian/libpbihdf/usr/lib/arm-linux-gnueabihf/libpbihdf.so (ELF format: 'elf32-littlearm' abi: '0101002800000000'; RPATH: '')
dpkg-shlibdeps: warning: cannot find library libpbdata.so needed by debian/libblasr/usr/lib/arm-linux-gnueabihf/libblasr.so (ELF format: 'elf32-littlearm' abi: '0101002800000000'; RPATH: '')
dpkg-shlibdeps: warning: cannot find library libpbihdf.so needed by debian/libblasr/usr/lib/arm-linux-gnueabihf/libblasr.so (ELF format: 'elf32-littlearm' abi: '0101002800000000'; RPATH: '')
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libpbdata/usr/lib/arm-linux-gnueabihf/libpbdata.so found in none of the libraries
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libpbdata-dev' in '../libpbdata-dev_5.3.1+dfsg-2.1_armhf.deb'.
dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_5.3.1+dfsg-2.1_armhf.deb'.
dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_5.3.1+dfsg-2.1_armhf.deb'.
dpkg-deb: building package 'libpbdata' in '../libpbdata_5.3.1+dfsg-2.1_armhf.deb'.
dpkg-deb: building package 'libpbdata-dbgsym' in '../libpbdata-dbgsym_5.3.1+dfsg-2.1_armhf.deb'.
dpkg-deb: building package 'libpbihdf' in '../libpbihdf_5.3.1+dfsg-2.1_armhf.deb'.
dpkg-deb: building package 'libpbihdf-dbgsym' in '../libpbihdf-dbgsym_5.3.1+dfsg-2.1_armhf.deb'.
dpkg-deb: building package 'libblasr' in '../libblasr_5.3.1+dfsg-2.1_armhf.deb'.
dpkg-deb: building package 'libblasr-dbgsym' in '../libblasr-dbgsym_5.3.1+dfsg-2.1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../pbseqlib_5.3.1+dfsg-2.1_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 2019-02-14T18:33:41Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pbseqlib_5.3.1+dfsg-2.1_armhf.changes:
--------------------------------------
Format: 1.8
Date: Wed, 06 Feb 2019 09:02:44 +0200
Source: pbseqlib
Binary: libpbseq libpbseq-dev libpbdata-dev libpbdata libpbihdf-dev libpbihdf libblasr-dev libblasr
Architecture: armhf
Version: 5.3.1+dfsg-2.1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Adrian Bunk <bunk@debian.org>
Description:
libblasr - tools for aligning PacBio reads to target sequences
libblasr-dev - tools for aligning PacBio reads to target sequences (development
libpbdata - tools for handling PacBio sequences
libpbdata-dev - tools for handling PacBio sequences (development files)
libpbihdf - tools for handling PacBio hdf5 files
libpbihdf-dev - tools for handling PacBio hdf5 files (development files)
libpbseq - library for analyzing PacBio sequencing data
libpbseq-dev - library for analyzing PacBio sequencing data (development files)
Changes:
pbseqlib (5.3.1+dfsg-2.1) unstable; urgency=medium
.
* Non-maintainer upload.
* Remove manual dependencies on libpbbam, version build
dependency on libpbbam-dev to ensure a proper dependency
is generated.
Checksums-Sha1:
6ed73bb2ad7241bf85b9c0224bde047d5dd4a6de 4065612 libblasr-dbgsym_5.3.1+dfsg-2.1_armhf.deb
2bed76eb4e2d55335c4c1cc55b0bb9d4084a4d31 1664336 libblasr-dev_5.3.1+dfsg-2.1_armhf.deb
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libblasr-dbgsym_5.3.1+dfsg-2.1_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 4065612 bytes: control archive=560 bytes.
406 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libblasr-dbgsym
Source: pbseqlib
Version: 5.3.1+dfsg-2.1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4131
Depends: libblasr (= 5.3.1+dfsg-2.1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libblasr
Build-Ids: 83307bd59b5317b3b7ee0dc74149a22679e97c3d
drwxr-xr-x root/root 0 2019-02-06 07:02 ./
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-02-06 07:02 ./usr/share/doc/libblasr-dbgsym -> libblasr
libblasr-dev_5.3.1+dfsg-2.1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 1664336 bytes: control archive=5320 bytes.
758 bytes, 18 lines control
16158 bytes, 167 lines md5sums
Package: libblasr-dev
Source: pbseqlib
Version: 5.3.1+dfsg-2.1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 7386
Depends: libblasr (= 5.3.1+dfsg-2.1), libpbdata-dev (= 5.3.1+dfsg-2.1)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for aligning PacBio reads to target sequences (development files)
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the header files and static library for the alignment
sublibrary.
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libblasr_5.3.1+dfsg-2.1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 832344 bytes: control archive=884 bytes.
777 bytes, 17 lines control
218 bytes, 3 lines md5sums
26 bytes, 1 lines triggers
Package: libblasr
Source: pbseqlib
Version: 5.3.1+dfsg-2.1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2275
Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.5), libpbbam0.19.0 (>= 0.19.0+dfsg), libstdc++6 (>= 5.2), libpbdata (= 5.3.1+dfsg-2.1), libpbihdf (= 5.3.1+dfsg-2.1)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for aligning PacBio reads to target sequences
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the alignment sublibrary.
drwxr-xr-x root/root 0 2019-02-06 07:02 ./
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/share/doc/libblasr/
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-rw-r--r-- root/root 4753 2019-01-28 10:27 ./usr/share/doc/libblasr/copyright
libpbdata-dbgsym_5.3.1+dfsg-2.1_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 1589956 bytes: control archive=564 bytes.
409 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libpbdata-dbgsym
Source: pbseqlib
Version: 5.3.1+dfsg-2.1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1651
Depends: libpbdata (= 5.3.1+dfsg-2.1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libpbdata
Build-Ids: 4e05e85e1eef0409cdfc63795cff000ac6c1b1c0
drwxr-xr-x root/root 0 2019-02-06 07:02 ./
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/debug/.build-id/
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-02-06 07:02 ./usr/share/doc/libpbdata-dbgsym -> libpbdata
libpbdata-dev_5.3.1+dfsg-2.1_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 175492 bytes: control archive=3116 bytes.
707 bytes, 18 lines control
6955 bytes, 87 lines md5sums
Package: libpbdata-dev
Source: pbseqlib
Version: 5.3.1+dfsg-2.1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1039
Depends: libpbdata (= 5.3.1+dfsg-2.1)
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for handling PacBio sequences (development files)
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the header files and static library for the pbdata
sublibrary.
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libpbdata_5.3.1+dfsg-2.1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 106324 bytes: control archive=868 bytes.
697 bytes, 17 lines control
221 bytes, 3 lines md5sums
26 bytes, 1 lines triggers
Package: libpbdata
Source: pbseqlib
Version: 5.3.1+dfsg-2.1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 346
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libpbbam0.19.0 (>= 0.19.0+dfsg), libstdc++6 (>= 5.2)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for handling PacBio sequences
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the pbdata sublibrary.
drwxr-xr-x root/root 0 2019-02-06 07:02 ./
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 337564 2019-02-06 07:02 ./usr/lib/arm-linux-gnueabihf/libpbdata.so
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/share/
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/share/doc/
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-rw-r--r-- root/root 1343 2019-02-06 07:02 ./usr/share/doc/libpbdata/changelog.Debian.gz
-rw-r--r-- root/root 4753 2019-01-28 10:27 ./usr/share/doc/libpbdata/copyright
libpbihdf-dbgsym_5.3.1+dfsg-2.1_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 2566364 bytes: control archive=560 bytes.
409 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libpbihdf-dbgsym
Source: pbseqlib
Version: 5.3.1+dfsg-2.1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2674
Depends: libpbihdf (= 5.3.1+dfsg-2.1)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libpbihdf
Build-Ids: ca7d1ad5c11d61fa98242cc2277ad7c3c12ee643
drwxr-xr-x root/root 0 2019-02-06 07:02 ./
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/debug/.build-id/ca/
-rw-r--r-- root/root 2727436 2019-02-06 07:02 ./usr/lib/debug/.build-id/ca/7d1ad5c11d61fa98242cc2277ad7c3c12ee643.debug
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/share/
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-02-06 07:02 ./usr/share/doc/libpbihdf-dbgsym -> libpbihdf
libpbihdf-dev_5.3.1+dfsg-2.1_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 243464 bytes: control archive=2192 bytes.
718 bytes, 18 lines control
4232 bytes, 56 lines md5sums
Package: libpbihdf-dev
Source: pbseqlib
Version: 5.3.1+dfsg-2.1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1955
Depends: libpbihdf (= 5.3.1+dfsg-2.1), libhdf5-dev
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for handling PacBio hdf5 files (development files)
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the header files and static library for the hdf
sublibrary.
drwxr-xr-x root/root 0 2019-02-06 07:02 ./
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/include/
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/include/pbseq/hdf/
-rw-r--r-- root/root 5767 2019-02-06 07:02 ./usr/include/pbseq/hdf/BufferedHDF2DArray.hpp
-rw-r--r-- root/root 12469 2019-02-06 07:02 ./usr/include/pbseq/hdf/BufferedHDF2DArrayImpl.hpp
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-rw-r--r-- root/root 1129 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFAlnGroup.hpp
-rw-r--r-- root/root 481 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp
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-rw-r--r-- root/root 5816 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFAtom.hpp
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-rw-r--r-- root/root 6346 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFBaseCallsWriter.hpp
-rw-r--r-- root/root 3471 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFBaxWriter.hpp
-rw-r--r-- root/root 11599 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFCCSReader.hpp
-rw-r--r-- root/root 1002 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFCmpData.hpp
-rw-r--r-- root/root 2463 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFCmpExperimentGroup.hpp
-rw-r--r-- root/root 37131 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFCmpFile.hpp
-rw-r--r-- root/root 29734 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFCmpReader.hpp
-rw-r--r-- root/root 4075 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFCmpRefAlignmentGroup.hpp
-rw-r--r-- root/root 2186 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFCmpRootGroup.hpp
-rw-r--r-- root/root 226 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFCmpSupportedFields.hpp
-rw-r--r-- root/root 128 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFCommonFG.hpp
-rw-r--r-- root/root 174 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFConfig.hpp
-rw-r--r-- root/root 1465 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFData.hpp
-rw-r--r-- root/root 733 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFFile.hpp
-rw-r--r-- root/root 1851 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFFileLogGroup.hpp
-rw-r--r-- root/root 703 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFGroup.hpp
-rw-r--r-- root/root 2262 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp
-rw-r--r-- root/root 856 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFNewBasReader.hpp
-rw-r--r-- root/root 23134 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFPlsReader.hpp
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-rw-r--r-- root/root 2023 2019-02-06 07:02 ./usr/include/pbseq/hdf/HDFZMWMetricsWriter.hpp
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/
drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/arm-linux-gnueabihf/
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-rw-r--r-- root/root 1343 2019-02-06 07:02 ./usr/share/doc/libpbihdf-dev/changelog.Debian.gz
-rw-r--r-- root/root 4753 2019-01-28 10:27 ./usr/share/doc/libpbihdf-dev/copyright
libpbihdf_5.3.1+dfsg-2.1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 138264 bytes: control archive=900 bytes.
767 bytes, 17 lines control
221 bytes, 3 lines md5sums
26 bytes, 1 lines triggers
Package: libpbihdf
Source: pbseqlib
Version: 5.3.1+dfsg-2.1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 526
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libhdf5-103, libhdf5-cpp-103 (>= 1.10.4), libpbbam0.19.0 (>= 0.19.0+dfsg), libstdc++6 (>= 5.2), libpbdata (= 5.3.1+dfsg-2.1)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/PacificBiosciences/blasr_libcpp
Description: tools for handling PacBio hdf5 files
Blasr_libcpp is a library used by blasr and other executables such as
samtoh5, loadPulses for analyzing PacBio sequences. This library contains
three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the hdf sublibrary.
drwxr-xr-x root/root 0 2019-02-06 07:02 ./
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/lib/arm-linux-gnueabihf/
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drwxr-xr-x root/root 0 2019-02-06 07:02 ./usr/share/
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-rw-r--r-- root/root 1343 2019-02-06 07:02 ./usr/share/doc/libpbihdf/changelog.Debian.gz
-rw-r--r-- root/root 4753 2019-01-28 10:27 ./usr/share/doc/libpbihdf/copyright
+------------------------------------------------------------------------------+
| Post Build |
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| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 256760
Build-Time: 671
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 394
Job: pbseqlib_5.3.1+dfsg-2.1
Machine Architecture: armhf
Package: pbseqlib
Package-Time: 1081
Source-Version: 5.3.1+dfsg-2.1
Space: 256760
Status: successful
Version: 5.3.1+dfsg-2.1
--------------------------------------------------------------------------------
Finished at 2019-02-14T18:33:41Z
Build needed 00:18:01, 256760k disk space