pbseqlib →
0~20161219-2 →
armhf → 2017-11-15 07:12:10
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| pbseqlib 0~20161219-2 (armhf) Wed, 15 Nov 2017 06:00:13 +0000 |
+==============================================================================+
Package: pbseqlib
Version: 0~20161219-2
Source Version: 0~20161219-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-6471e882-7e69-44e9-8ca0-13bb291bb72e' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.1 MB]
Fetched 22.5 MB in 26s (851 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://anonscm.debian.org/git/debian-med/pbseqlib.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/pbseqlib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1351 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main pbseqlib 0~20161219-2 (dsc) [2498 B]
Get:2 http://172.17.0.1/private buster-staging/main pbseqlib 0~20161219-2 (tar) [1343 kB]
Get:3 http://172.17.0.1/private buster-staging/main pbseqlib 0~20161219-2 (diff) [5780 B]
Fetched 1351 kB in 0s (6920 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbseqlib-Nq1T7w/pbseqlib-0~20161219' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbseqlib-Nq1T7w' 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-tgmYET/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-tgmYET/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-tgmYET/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (3144 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
e2fsprogs-l10n
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 25 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13092 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 (>= 10), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev, libhts-dev, libgtest-dev
Filtered Build-Depends: debhelper (>= 10), dh-exec, python, zlib1g-dev, libhdf5-dev, libboost-dev, libpbbam-dev, libhts-dev, libgtest-dev
dpkg-deb: building package 'sbuild-build-depends-pbseqlib-dummy' in '/<<BUILDDIR>>/resolver-tgmYET/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-tgmYET/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ Sources [546 B]
Get:5 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ Packages [615 B]
Fetched 2494 B in 0s (3543 B/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 package was automatically installed and is no longer required:
e2fsprogs-l10n
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism file gettext gettext-base
googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libboost-dev libboost1.62-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libgfortran4
libglib2.0-0 libgssapi-krb5-2 libgtest-dev libhdf5-100 libhdf5-cpp-100
libhdf5-dev libhts-dev libhts2 libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbbam libpbbam-dev
libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
libsz2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf
python python-minimal python2.7 python2.7-minimal tabix zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
libboost-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user
libhdf5-doc liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx-cur ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales publicsuffix libssl-doc
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 file gettext gettext-base
googletest groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libboost-dev libboost1.62-dev libbsd0 libcroco3
libcurl3-gnutls libexpat1 libfile-stripnondeterminism-perl libgfortran4
libglib2.0-0 libgssapi-krb5-2 libgtest-dev libhdf5-100 libhdf5-cpp-100
libhdf5-dev libhts-dev libhts2 libicu57 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpbbam libpbbam-dev
libpipeline1 libpsl5 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
libsz2 libtimedate-perl libtool libxml2 m4 man-db mime-support po-debconf
python python-minimal python2.7 python2.7-minimal
sbuild-build-depends-pbseqlib-dummy tabix zlib1g-dev
0 upgraded, 74 newly installed, 0 to remove and 25 not upgraded.
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Get:1 copy:/<<BUILDDIR>>/resolver-tgmYET/apt_archive ./ sbuild-build-depends-pbseqlib-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-3 [95.9 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.14 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.14-2 [393 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.14-2 [1091 kB]
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Get:10 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.60 [36.7 kB]
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Get:16 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.14-1 [155 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
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Get:19 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
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Get:26 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
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Get:38 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
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Get:57 http://172.17.0.1/private buster-staging/main armhf libsz2 armhf 0.3.2-2 [6080 B]
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Get:60 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2 [110 kB]
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Get:64 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 0.3.2-2 [17.3 kB]
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Get:67 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.2-1.3 [284 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf tabix armhf 1.5-2 [246 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.5-2 [336 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libpbbam armhf 0.7.4+ds-1+rpi1+b1 [395 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.0g-2 [1371 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.7.4+ds-1+rpi1+b1 [90.2 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf dh-exec armhf 0.23 [24.9 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libgtest-dev armhf 1.8.0-6 [5110 B]
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Processing triggers for libc-bin (2.24-17) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29.1-6+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-12 gcc-7_7.2.0-12 libc6-dev_2.24-17 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha3 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-6+rpi1 binutils-arm-linux-gnueabihf_2.29.1-6+rpi1 binutils-common_2.29.1-6+rpi1 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-12 dash_0.5.8-2.5 debconf_1.5.64 debhelper_10.10.5 debianutils_4.8.2 dh-autoreconf_14 dh-exec_0.23 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.1-5 dmsetup_2:1.02.142-1 dpkg_1.19.0.4 dpkg-dev_1.19.0.4 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 e2fsprogs-l10n_1.43.7-1 fakeroot_1.22-1 fdisk_2.30.2-0.1 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6-base_6.4.0-6 gcc-7_7.2.0-12 gcc-7-base_7.2.0-12 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-5 gnupg-l10n_2.2.1-5 gnupg-utils_2.2.1-5 googletest_1.8.0-6 gpg_2.2.1-5 gpg-agent_2.2.1-5 gpg-wks-client_2.2.1-5 gpg-wks-server_2.2.1-5 gpgconf_2.2.1-5 gpgsm_2.2.1-5 gpgv_2.2.1-5 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-4 hostname_3.18 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libaec-dev_0.3.2-2 libaec0_0.3.2-2 libapparmor1_2.11.1-2 libapt-pkg5.0_1.6~alpha3 libarchive-zip-perl_1.59-1 libasan4_7.2.0-12 libassuan0_2.4.3-3 libatomic1_7.2.0-12 libattr1_1:2.4.47-2 libaudit-common_1:2.8.1-1 libaudit1_1:2.8.1-1 libbinutils_2.29.1-6+rpi1 libblkid1_2.30.2-0.1 libboost-dev_1.62.0.1+b8 libboost1.62-dev_1.62.0+dfsg-4+b2 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-17 libc-dev-bin_2.24-17 libc6_2.24-17 libc6-dev_2.24-17 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-12 libcilkrts5_7.2.0-12 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.56.1-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.22-1 libdebconfclient0_0.232 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.19.0.4 libdrm-common_2.4.84-2+rpi1 libdrm2_2.4.84-2+rpi1 libexpat1_2.2.3-2 libfakeroot_1.22-1 libfdisk1_2.30.2-0.1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-12 libgcc1_1:7.2.0-12 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libgfortran4_7.2.0-12 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-12 libgpg-error0_1.27-4 libgssapi-krb5-2_1.15.2-2 libgtest-dev_1.8.0-6 libhdf5-100_1.10.0-patch1+docs-4 libhdf5-cpp-100_1.10.0-patch1+docs-4 libhdf5-dev_1.10.0-patch1+docs-4 libhogweed4_3.3-2 libhts-dev_1.5-2 libhts2_1.5-2 libicu57_57.1-8 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2 libjpeg62-turbo-dev_1:1.5.2-2 libk5crypto3_1.15.2-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.2-2 libkrb5support0_1.15.2-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnghttp2-14_1.27.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpbbam_0.7.4+ds-1+rpi1+b1 libpbbam-dev_0.7.4+ds-1+rpi1+b1 libpcre3_2:8.39-4 libperl5.26_5.26.1-2 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libpsl5_0.18.0-4 libpython-stdlib_2.7.14-1 libpython2.7-minimal_2.7.14-2 libpython2.7-stdlib_2.7.14-2 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.20.1-2 libss2_1.43.7-1 libssh2-1_1.8.0-1 libssl-dev_1.1.0g-2 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 libsystemd0_235-2 libsz2_0.3.2-2 libtasn1-6_4.12-2.1 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-12 libudev1_235-2 libunistring2_0.9.7-2 libuuid1_2.30.2-0.1 libxml2_2.9.4+dfsg1-5 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mime-support_3.60 mount_2.30.2-0.1 mountall_2.54 multiarch-support_2.24-17 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-2 perl-base_5.26.1-2 perl-modules-5.26_5.26.1-2 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 python_2.7.14-1 python-minimal_2.7.14-1 python2.7_2.7.14-2 python2.7-minimal_2.7.14-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbseqlib-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_235-2 sysvinit-utils_2.88dsf-59.10 tabix_1.5-2 tar_1.29b-2 tzdata_2017c-1 udev_235-2 util-linux_2.30.2-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Nov 10 03:51:02 2017 UTC
gpgv: using RSA key EAB723A266F627E68055615F59B2306F3AF9DDC1
gpgv: issuer "afif@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pbseqlib_0~20161219-2.dsc
dpkg-source: info: extracting pbseqlib in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking pbseqlib_0~20161219.orig.tar.gz
dpkg-source: info: unpacking pbseqlib_0~20161219-2.debian.tar.xz
dpkg-source: info: applying hdf5-1.10.1-support.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-6471e882-7e69-44e9-8ca0-13bb291bb72e
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbseqlib
dpkg-buildpackage: info: source version 0~20161219-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build pbseqlib-0~20161219
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C /<<PKGBUILDDIR>>//pbdata clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/pbdata'
rm -f libpbdata.a libpbdata.so *.o *.d
make[3]: Leaving directory '/<<PKGBUILDDIR>>/pbdata'
make -C /<<PKGBUILDDIR>>//hdf clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/hdf'
rm -f libpbihdf.a libpbihdf.so *.o *.d
make[3]: Leaving directory '/<<PKGBUILDDIR>>/hdf'
make -C /<<PKGBUILDDIR>>//alignment clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/alignment'
rm -f libblasr.a libblasr.so *.o *.d
make[3]: Leaving directory '/<<PKGBUILDDIR>>/alignment'
make -C /<<PKGBUILDDIR>>//unittest clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/unittest'
rm -f -r *.o libblasr-test-runner
make[3]: Leaving directory '/<<PKGBUILDDIR>>/unittest'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
find -name defines.mk -delete
rm -f pbdata/libconfig.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_autoreconf_clean
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 '/<<PKGBUILDDIR>>'
./configure.py PREFIX=/usr/
uname -s
uname='Linux'
writing to '/<<PKGBUILDDIR>>/pbdata/libconfig.h'
"""
#define USE_PBBAM
"""
writing to 'defines.mk'
"""
CXXFLAGS := -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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}
LIBS += ${PREFIX_LIB}
"""
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make libpbdata
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C /<<PKGBUILDDIR>>//pbdata libconfig.h
make[3]: Entering directory '/<<PKGBUILDDIR>>/pbdata'
make[3]: 'libconfig.h' is up to date.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/pbdata'
make -C /<<PKGBUILDDIR>>//pbdata all
make[3]: Entering directory '/<<PKGBUILDDIR>>/pbdata'
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c CCSSequence.cpp -o CCSSequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c ChangeListID.cpp -o ChangeListID.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c CommandLineParser.cpp -o CommandLineParser.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c DNASequence.cpp -o DNASequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c FASTAReader.cpp -o FASTAReader.o
CommandLineParser.cpp: In member function 'CommandLineParser::ErrorValue CommandLineParser::ParseOption(int, int&, int, char**)':
CommandLineParser.cpp:362:5: warning: 'ev' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (ev == CLGood) {
^~
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c FASTASequence.cpp -o FASTASequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c FASTQReader.cpp -o FASTQReader.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c FASTQSequence.cpp -o FASTQSequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c GFFFile.cpp -o GFFFile.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c MD5Utils.cpp -o MD5Utils.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c NucConversion.cpp -o NucConversion.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c PackedDNASequence.cpp -o PackedDNASequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c ReverseCompressIndex.cpp -o ReverseCompressIndex.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c SMRTSequence.cpp -o SMRTSequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c StringUtils.cpp -o StringUtils.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c alignment/CmpAlignment.cpp -o CmpAlignment.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c amos/AfgBasWriter.cpp -o AfgBasWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c loadpulses/MetricField.cpp -o MetricField.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c metagenome/TitleTable.cpp -o TitleTable.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c qvs/QualityTransform.cpp -o QualityTransform.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c qvs/QualityValue.cpp -o QualityValue.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/AcqParams.cpp -o AcqParams.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/BaseFile.cpp -o BaseFile.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/HoleXY.cpp -o HoleXY.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/PulseFile.cpp -o PulseFile.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/ReadType.cpp -o ReadType.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/RegionAnnotation.cpp -o RegionAnnotation.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/RegionAnnotations.cpp -o RegionAnnotations.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/RegionTable.cpp -o RegionTable.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/RegionTypeMap.cpp -o RegionTypeMap.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/ScanData.cpp -o ScanData.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c saf/AlnGroup.cpp -o AlnGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c saf/MovieInfo.cpp -o MovieInfo.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c saf/RefGroup.cpp -o RefGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c saf/RefInfo.cpp -o RefInfo.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c sam/ReadGroup.cpp -o ReadGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c sam/ReferenceSequence.cpp -o ReferenceSequence.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c sam/SAMAlignment.cpp -o SAMAlignment.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c sam/SAMHeader.cpp -o SAMHeader.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c utils/BitUtils.cpp -o BitUtils.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c utils/SMRTTitle.cpp -o SMRTTitle.o
sam/SAMAlignment.cpp: In member function 'bool SAMAlignment::StoreValues(std::__cxx11::string&, int)':
sam/SAMAlignment.cpp:110:139: warning: 'field' may be used uninitialized in this function [-Wmaybe-uninitialized]
std::cout << "Error parsing alignment line " << lineNumber << ". Missing or error in field " << SAMAlignmentRequiredFieldNames[field] << std::endl;
^
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -c utils/TimeUtils.cpp -o TimeUtils.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c CCSSequence.cpp -o CCSSequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c ChangeListID.cpp -o ChangeListID.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c CommandLineParser.cpp -o CommandLineParser.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c DNASequence.cpp -o DNASequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c FASTAReader.cpp -o FASTAReader.shared.o
CommandLineParser.cpp: In member function 'CommandLineParser::ErrorValue CommandLineParser::ParseOption(int, int&, int, char**)':
CommandLineParser.cpp:365:12: warning: 'ev' may be used uninitialized in this function [-Wmaybe-uninitialized]
return ev;
^~
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c FASTASequence.cpp -o FASTASequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c FASTQReader.cpp -o FASTQReader.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c FASTQSequence.cpp -o FASTQSequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c GFFFile.cpp -o GFFFile.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c MD5Utils.cpp -o MD5Utils.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c NucConversion.cpp -o NucConversion.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c PackedDNASequence.cpp -o PackedDNASequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c ReverseCompressIndex.cpp -o ReverseCompressIndex.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c SMRTSequence.cpp -o SMRTSequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c StringUtils.cpp -o StringUtils.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c alignment/CmpAlignment.cpp -o CmpAlignment.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c amos/AfgBasWriter.cpp -o AfgBasWriter.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c loadpulses/MetricField.cpp -o MetricField.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c loadpulses/MovieAlnIndexLookupTable.cpp -o MovieAlnIndexLookupTable.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c metagenome/TitleTable.cpp -o TitleTable.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c qvs/QualityTransform.cpp -o QualityTransform.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c qvs/QualityValue.cpp -o QualityValue.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/AcqParams.cpp -o AcqParams.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/BaseFile.cpp -o BaseFile.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/HoleXY.cpp -o HoleXY.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/PulseBaseCommon.cpp -o PulseBaseCommon.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/PulseFile.cpp -o PulseFile.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/ReadType.cpp -o ReadType.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/RegionAnnotation.cpp -o RegionAnnotation.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/RegionAnnotations.cpp -o RegionAnnotations.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/RegionTable.cpp -o RegionTable.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/RegionTypeMap.cpp -o RegionTypeMap.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/ScanData.cpp -o ScanData.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c reads/ZMWGroupEntry.cpp -o ZMWGroupEntry.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c saf/AlnGroup.cpp -o AlnGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c saf/MovieInfo.cpp -o MovieInfo.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c saf/RefGroup.cpp -o RefGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c saf/RefInfo.cpp -o RefInfo.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c sam/ReadGroup.cpp -o ReadGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c sam/ReferenceSequence.cpp -o ReferenceSequence.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c sam/SAMAlignment.cpp -o SAMAlignment.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c sam/SAMHeader.cpp -o SAMHeader.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c sam/SAMKeywordValuePair.cpp -o SAMKeywordValuePair.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c utils/BitUtils.cpp -o BitUtils.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c utils/SMRTReadUtils.cpp -o SMRTReadUtils.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c utils/SMRTTitle.cpp -o SMRTTitle.shared.o
sam/SAMAlignment.cpp: In member function 'bool SAMAlignment::StoreValues(std::__cxx11::string&, int)':
sam/SAMAlignment.cpp:110:139: warning: 'field' may be used uninitialized in this function [-Wmaybe-uninitialized]
std::cout << "Error parsing alignment line " << lineNumber << ". Missing or error in field " << SAMAlignmentRequiredFieldNames[field] << std::endl;
^
g++ -std=c++11 -pedantic -Wall -Wextra -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -fPIC -c utils/TimeUtils.cpp -o TimeUtils.shared.o
ar rc libpbdata.a CCSSequence.o ChangeListID.o CommandLineParser.o DNASequence.o FASTAReader.o FASTASequence.o FASTQReader.o FASTQSequence.o GFFFile.o MD5Utils.o NucConversion.o PackedDNASequence.o ReverseCompressIndex.o SMRTSequence.o StringUtils.o CmpAlignment.o AfgBasWriter.o MetricField.o MovieAlnIndexLookupTable.o TitleTable.o QualityTransform.o QualityValue.o AcqParams.o BaseFile.o HoleXY.o PulseBaseCommon.o PulseFile.o ReadType.o RegionAnnotation.o RegionAnnotations.o RegionTable.o RegionTypeMap.o ScanData.o ZMWGroupEntry.o AlnGroup.o MovieInfo.o RefGroup.o RefInfo.o ReadGroup.o ReferenceSequence.o SAMAlignment.o SAMHeader.o SAMKeywordValuePair.o BitUtils.o SMRTReadUtils.o SMRTTitle.o TimeUtils.o
g++ -shared -Wl,-z,relro -L/usr/lib -o libpbdata.so -Wl,-soname,libpbdata.so CCSSequence.shared.o ChangeListID.shared.o CommandLineParser.shared.o DNASequence.shared.o FASTAReader.shared.o FASTASequence.shared.o FASTQReader.shared.o FASTQSequence.shared.o GFFFile.shared.o MD5Utils.shared.o NucConversion.shared.o PackedDNASequence.shared.o ReverseCompressIndex.shared.o SMRTSequence.shared.o StringUtils.shared.o CmpAlignment.shared.o AfgBasWriter.shared.o MetricField.shared.o MovieAlnIndexLookupTable.shared.o TitleTable.shared.o QualityTransform.shared.o QualityValue.shared.o AcqParams.shared.o BaseFile.shared.o HoleXY.shared.o PulseBaseCommon.shared.o PulseFile.shared.o ReadType.shared.o RegionAnnotation.shared.o RegionAnnotations.shared.o RegionTable.shared.o RegionTypeMap.shared.o ScanData.shared.o ZMWGroupEntry.shared.o AlnGroup.shared.o MovieInfo.shared.o RefGroup.shared.o RefInfo.shared.o ReadGroup.shared.o ReferenceSequence.shared.o SAMAlignment.shared.o SAMHeader.shared.o SAMKeywordValuePair.shared.o BitUtils.shared.o SMRTReadUtils.shared.o SMRTTitle.shared.o TimeUtils.shared.o -lpbbam
make[3]: Leaving directory '/<<PKGBUILDDIR>>/pbdata'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make libpbihdf
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C /<<PKGBUILDDIR>>//hdf all
make[3]: Entering directory '/<<PKGBUILDDIR>>/hdf'
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFAttributable.cpp -o HDFAttributable.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFBaxWriter.cpp -o HDFBaxWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFWriterBase.cpp -o HDFWriterBase.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c DatasetCollection.cpp -o DatasetCollection.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFRegionTableReader.cpp -o HDFRegionTableReader.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c BufferedHDFArray.cpp -o BufferedHDFArray.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFAtom.cpp -o HDFAtom.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFPulseDataFile.cpp -o HDFPulseDataFile.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.o
HDFPulseCallsWriter.cpp: In member function 'bool HDFPulseCallsWriter::InitializeQVGroups()':
HDFPulseCallsWriter.cpp:234:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (_HasQV(PacBio::BAM::BaseFeature::PULSE_CALL))
^~
HDFPulseCallsWriter.cpp:236:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ret *= isPulseArray_.Initialize(pulsecallsGroup_, PacBio::GroupNames::ispulse);
^~~
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFZMWReader.cpp -o HDFZMWReader.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFFile.cpp -o HDFFile.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFScanDataReader.cpp -o HDFScanDataReader.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFRegionsWriter.cpp -o HDFRegionsWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFScanDataWriter.cpp -o HDFScanDataWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFNewBasReader.cpp -o HDFNewBasReader.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFPulseWriter.cpp -o HDFPulseWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFGroup.cpp -o HDFGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFUtils.cpp -o HDFUtils.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFData.cpp -o HDFData.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFZMWWriter.cpp -o HDFZMWWriter.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFAttributable.cpp -o HDFAttributable.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFBaxWriter.cpp -o HDFBaxWriter.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFWriterBase.cpp -o HDFWriterBase.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c DatasetCollection.cpp -o DatasetCollection.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFRegionTableReader.cpp -o HDFRegionTableReader.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c BufferedHDFArray.cpp -o BufferedHDFArray.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFAtom.cpp -o HDFAtom.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFZMWMetricsWriter.cpp -o HDFZMWMetricsWriter.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFPulseCallsWriter.cpp -o HDFPulseCallsWriter.shared.o
HDFPulseCallsWriter.cpp: In member function 'bool HDFPulseCallsWriter::InitializeQVGroups()':
HDFPulseCallsWriter.cpp:234:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
if (_HasQV(PacBio::BAM::BaseFeature::PULSE_CALL))
^~
HDFPulseCallsWriter.cpp:236:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
ret *= isPulseArray_.Initialize(pulsecallsGroup_, PacBio::GroupNames::ispulse);
^~~
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFBaseCallsWriter.cpp -o HDFBaseCallsWriter.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFZMWReader.cpp -o HDFZMWReader.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFFile.cpp -o HDFFile.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFScanDataReader.cpp -o HDFScanDataReader.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFRegionsWriter.cpp -o HDFRegionsWriter.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFNewBasReader.cpp -o HDFNewBasReader.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFPulseWriter.cpp -o HDFPulseWriter.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFGroup.cpp -o HDFGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFUtils.cpp -o HDFUtils.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFData.cpp -o HDFData.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFZMWWriter.cpp -o HDFZMWWriter.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c HDFPulseH5Writer.cpp -o HDFPulseH5Writer.shared.o
g++ -std=c++11 -pedantic -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.shared.o
ar rc libpbihdf.a HDFAttributable.o HDFBaxWriter.o HDFWriterBase.o DatasetCollection.o HDFRegionTableReader.o BufferedHDFArray.o HDFAtom.o HDFCmpExperimentGroup.o HDFZMWMetricsWriter.o HDFPulseDataFile.o HDFPulseCallsWriter.o HDFCmpSupportedFields.o HDFBaseCallsWriter.o HDFZMWReader.o HDFFile.o HDFScanDataReader.o HDFAlnInfoGroup.o HDFRegionsWriter.o HDFScanDataWriter.o HDFNewBasReader.o HDFPulseWriter.o HDFGroup.o HDFUtils.o HDFAlnGroupGroup.o HDFData.o HDFZMWWriter.o HDFPulseH5Writer.o BufferedHDF2DArray.o
g++ -shared -Wl,-z,relro -L/usr/lib -L../pbdata/ -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o libpbihdf.so -Wl,-soname,libpbihdf.so HDFAttributable.shared.o HDFBaxWriter.shared.o HDFWriterBase.shared.o DatasetCollection.shared.o HDFRegionTableReader.shared.o BufferedHDFArray.shared.o HDFAtom.shared.o HDFCmpExperimentGroup.shared.o HDFZMWMetricsWriter.shared.o HDFPulseDataFile.shared.o HDFPulseCallsWriter.shared.o HDFCmpSupportedFields.shared.o HDFBaseCallsWriter.shared.o HDFZMWReader.shared.o HDFFile.shared.o HDFScanDataReader.shared.o HDFAlnInfoGroup.shared.o HDFRegionsWriter.shared.o HDFScanDataWriter.shared.o HDFNewBasReader.shared.o HDFPulseWriter.shared.o HDFGroup.shared.o HDFUtils.shared.o HDFAlnGroupGroup.shared.o HDFData.shared.o HDFZMWWriter.shared.o HDFPulseH5Writer.shared.o BufferedHDF2DArray.shared.o -lpbbam -lpbdata -lhdf5 -lhdf5_cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/hdf'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make libblasr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make -C /<<PKGBUILDDIR>>//alignment all
make[3]: Entering directory '/<<PKGBUILDDIR>>/alignment'
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c MappingMetrics.cpp -o MappingMetrics.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/KBandAlign.cpp -o KBandAlign.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/anchoring/BWTSearch.cpp -o BWTSearch.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/anchoring/Coordinate.cpp -o Coordinate.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c algorithms/sorting/qsufsort.cpp -o qsufsort.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignment/Alignment.cpp -o Alignment.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignment/CmpFile.cpp -o CmpFile.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.o
In file included from /usr/include/c++/7/vector:69:0,
from datastructures/alignment/../../../pbdata/utils/SMRTTitle.hpp:4,
from datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp:2:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++/7/vector:64:0,
from datastructures/alignment/../../../pbdata/utils/SMRTTitle.hpp:4,
from datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp:2:
/usr/include/c++/7/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++/7/bits/stl_vector.h:948:21: 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++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/anchoring/ClusterList.cpp -o ClusterList.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/anchoring/MatchPos.cpp -o MatchPos.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c files/BaseSequenceIO.cpp -o BaseSequenceIO.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c files/CCSIterator.cpp -o CCSIterator.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c files/FragmentCCSIterator.cpp -o FragmentCCSIterator.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c files/ReaderAgglomerate.cpp -o ReaderAgglomerate.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c format/IntervalPrinter.cpp -o IntervalPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c format/SAMPrinter.cpp -o SAMPrinter.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNextBases(SMRTSequence&, bool)':
files/ReaderAgglomerate.cpp:588:68: warning: this statement may fall through [-Wimplicit-fallthrough=]
cout << "ERROR! Can not GetNextBases from a BAM File." << endl;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
files/ReaderAgglomerate.cpp:590:9: note: here
case FileType::Fourbit:
^~~~
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNext(CCSSequence&)':
files/ReaderAgglomerate.cpp:631:70: warning: this statement may fall through [-Wimplicit-fallthrough=]
cout << "ERROR! Could not read BamRecord as CCSSequence" << endl;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
files/ReaderAgglomerate.cpp:633:9: note: here
case FileType::Fourbit:
^~~~
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c format/SummaryPrinter.cpp -o SummaryPrinter.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c query/PbiFilterZmwGroupQuery.cpp -o PbiFilterZmwGroupQuery.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c query/SequentialZmwGroupQuery.cpp -o SequentialZmwGroupQuery.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c qvs/QualityValueProfile.cpp -o QualityValueProfile.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c simulator/ContextSample.cpp -o ContextSample.o
query/PbiFilterZmwGroupQuery.cpp: In member function 'bool PacBio::BAM::PbiFilterZmwGroupQuery::PbiFilterZmwGroupQueryPrivate::GetNext(std::vector<PacBio::BAM::BamRecord>&)':
query/PbiFilterZmwGroupQuery.cpp:46:53: warning: 'holeNumber' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (record.MovieName() == movieName and record.HoleNumber() == holeNumber)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c simulator/ContextSet.cpp -o ContextSet.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c simulator/LengthHistogram.cpp -o LengthHistogram.o
query/SequentialZmwGroupQuery.cpp: In member function 'virtual bool PacBio::BAM::SequentialZmwGroupQuery::GetNext(std::vector<PacBio::BAM::BamRecord>&)':
query/SequentialZmwGroupQuery.cpp:44:53: warning: 'holeNumber' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (record.MovieName() == movieName and record.HoleNumber() == holeNumber)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
query/SequentialZmwGroupQuery.cpp:25:17: note: 'holeNumber' was declared here
int32_t holeNumber;
^~~~~~~~~~
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c simulator/QualitySample.cpp -o QualitySample.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c statistics/StatUtils.cpp -o StatUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c statistics/cdfs.cpp -o cdfs.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c statistics/pdfs.cpp -o pdfs.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c tuples/BaseTuple.cpp -o BaseTuple.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c tuples/DNATuple.cpp -o DNATuple.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c tuples/TupleMetrics.cpp -o TupleMetrics.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c utils/FileOfFileNames.cpp -o FileOfFileNames.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c utils/FileUtils.cpp -o FileUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c utils/LogUtils.cpp -o LogUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c utils/PhredUtils.cpp -o PhredUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c utils/RangeUtils.cpp -o RangeUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -c utils/RegionUtils.cpp -o RegionUtils.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c MappingMetrics.cpp -o MappingMetrics.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/AlignmentUtils.cpp -o AlignmentUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/BaseScoreFunction.cpp -o BaseScoreFunction.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/ExtendAlign.cpp -o ExtendAlign.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/GuidedAlign.cpp -o GuidedAlign.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/IDSScoreFunction.cpp -o IDSScoreFunction.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/KBandAlign.cpp -o KBandAlign.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/QualityValueScoreFunction.cpp -o QualityValueScoreFunction.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/ScoreMatrices.cpp -o ScoreMatrices.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/StringToScoreMatrix.cpp -o StringToScoreMatrix.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/sdp/SDPFragment.cpp -o SDPFragment.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o SparseDynamicProgramming.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/BWTSearch.cpp -o BWTSearch.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/ClusterProbability.cpp -o ClusterProbability.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/Coordinate.cpp -o Coordinate.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/anchoring/FindMaxInterval.cpp -o FindMaxInterval.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/DifferenceCovers.cpp -o DifferenceCovers.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/LightweightSuffixArray.cpp -o LightweightSuffixArray.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/MultikeyQuicksort.cpp -o MultikeyQuicksort.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c algorithms/sorting/qsufsort.cpp -o qsufsort.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/Alignment.cpp -o Alignment.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentCandidate.cpp -o AlignmentCandidate.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentContext.cpp -o AlignmentContext.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentMap.cpp -o AlignmentMap.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/AlignmentStats.cpp -o AlignmentStats.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/CmpFile.cpp -o CmpFile.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/FilterCriteria.cpp -o FilterCriteria.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o SAMToAlignmentCandidateAdapter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignmentset/SAMQVConversion.cpp -o SAMQVConversion.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o SAMSupplementalQVList.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/AnchorParameters.cpp -o AnchorParameters.shared.o
In file included from /usr/include/c++/7/vector:69:0,
from datastructures/alignment/../../../pbdata/utils/SMRTTitle.hpp:4,
from datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp:2:
/usr/include/c++/7/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++/7/bits/vector.tcc:394:7: 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++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/ClusterList.cpp -o ClusterList.shared.o
In file included from /usr/include/c++/7/vector:64:0,
from datastructures/alignment/../../../pbdata/utils/SMRTTitle.hpp:4,
from datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp:2:
/usr/include/c++/7/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++/7/bits/stl_vector.h:948:21: 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++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/MatchPos.cpp -o MatchPos.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c datastructures/anchoring/WeightedInterval.cpp -o WeightedInterval.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c files/BaseSequenceIO.cpp -o BaseSequenceIO.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c files/CCSIterator.cpp -o CCSIterator.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c files/FragmentCCSIterator.cpp -o FragmentCCSIterator.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c files/ReaderAgglomerate.cpp -o ReaderAgglomerate.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c format/CompareSequencesPrinter.cpp -o CompareSequencesPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c format/IntervalPrinter.cpp -o IntervalPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c format/SAMHeaderPrinter.cpp -o SAMHeaderPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c format/SAMPrinter.cpp -o SAMPrinter.shared.o
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNextBases(SMRTSequence&, bool)':
files/ReaderAgglomerate.cpp:588:68: warning: this statement may fall through [-Wimplicit-fallthrough=]
cout << "ERROR! Can not GetNextBases from a BAM File." << endl;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
files/ReaderAgglomerate.cpp:590:9: note: here
case FileType::Fourbit:
^~~~
files/ReaderAgglomerate.cpp: In member function 'int ReaderAgglomerate::GetNext(CCSSequence&)':
files/ReaderAgglomerate.cpp:631:70: warning: this statement may fall through [-Wimplicit-fallthrough=]
cout << "ERROR! Could not read BamRecord as CCSSequence" << endl;
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
files/ReaderAgglomerate.cpp:633:9: note: here
case FileType::Fourbit:
^~~~
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c format/SummaryPrinter.cpp -o SummaryPrinter.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c query/PbiFilterZmwGroupQuery.cpp -o PbiFilterZmwGroupQuery.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c query/SequentialZmwGroupQuery.cpp -o SequentialZmwGroupQuery.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c qvs/QualityValueProfile.cpp -o QualityValueProfile.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c simulator/ContextSample.cpp -o ContextSample.shared.o
query/SequentialZmwGroupQuery.cpp: In member function 'virtual bool PacBio::BAM::SequentialZmwGroupQuery::GetNext(std::vector<PacBio::BAM::BamRecord>&)':
query/SequentialZmwGroupQuery.cpp:44:53: warning: 'holeNumber' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (record.MovieName() == movieName and record.HoleNumber() == holeNumber)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
query/SequentialZmwGroupQuery.cpp:25:17: note: 'holeNumber' was declared here
int32_t holeNumber;
^~~~~~~~~~
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c simulator/ContextSet.cpp -o ContextSet.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c simulator/LengthHistogram.cpp -o LengthHistogram.shared.o
query/PbiFilterZmwGroupQuery.cpp: In member function 'bool PacBio::BAM::PbiFilterZmwGroupQuery::PbiFilterZmwGroupQueryPrivate::GetNext(std::vector<PacBio::BAM::BamRecord>&)':
query/PbiFilterZmwGroupQuery.cpp:46:53: warning: 'holeNumber' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (record.MovieName() == movieName and record.HoleNumber() == holeNumber)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c simulator/QualitySample.cpp -o QualitySample.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c statistics/LookupAnchorDistribution.cpp -o LookupAnchorDistribution.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c statistics/StatUtils.cpp -o StatUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c statistics/cdfs.cpp -o cdfs.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c statistics/pdfs.cpp -o pdfs.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c tuples/BaseTuple.cpp -o BaseTuple.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c tuples/DNATuple.cpp -o DNATuple.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c tuples/TupleMetrics.cpp -o TupleMetrics.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c utils/FileOfFileNames.cpp -o FileOfFileNames.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c utils/FileUtils.cpp -o FileUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c utils/LogUtils.cpp -o LogUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c utils/PhredUtils.cpp -o PhredUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c utils/RangeUtils.cpp -o RangeUtils.shared.o
g++ -std=c++11 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/hdf5/serial -fPIC -c utils/RegionUtils.cpp -o RegionUtils.shared.o
ar rc libblasr.a MappingMetrics.o AlignmentUtils.o BaseScoreFunction.o ExtendAlign.o GuidedAlign.o IDSScoreFunction.o KBandAlign.o QualityValueScoreFunction.o ScoreMatrices.o StringToScoreMatrix.o SDPFragment.o SparseDynamicProgramming.o BWTSearch.o ClusterProbability.o Coordinate.o FindMaxInterval.o DifferenceCovers.o LightweightSuffixArray.o MultikeyQuicksort.o qsufsort.o Alignment.o AlignmentCandidate.o AlignmentContext.o AlignmentMap.o AlignmentStats.o CmpFile.o FilterCriteria.o SAMToAlignmentCandidateAdapter.o SAMQVConversion.o SAMSupplementalQVList.o AnchorParameters.o ClusterList.o MatchPos.o WeightedInterval.o BaseSequenceIO.o CCSIterator.o FragmentCCSIterator.o ReaderAgglomerate.o CompareSequencesPrinter.o IntervalPrinter.o SAMHeaderPrinter.o SAMPrinter.o SummaryPrinter.o PbiFilterZmwGroupQuery.o SequentialZmwGroupQuery.o QualityValueProfile.o ContextSample.o ContextSet.o LengthHistogram.o QualitySample.o LookupAnchorDistribution.o StatUtils.o cdfs.o pdfs.o BaseTuple.o DNATuple.o TupleMetrics.o FileOfFileNames.o FileUtils.o LogUtils.o PhredUtils.o RangeUtils.o RegionUtils.o
g++ -shared -Wl,-z,relro -L/usr/lib -L../pbdata/ -L../hdf/ -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -o libblasr.so -Wl,-soname,libblasr.so MappingMetrics.shared.o AlignmentUtils.shared.o BaseScoreFunction.shared.o ExtendAlign.shared.o GuidedAlign.shared.o IDSScoreFunction.shared.o KBandAlign.shared.o QualityValueScoreFunction.shared.o ScoreMatrices.shared.o StringToScoreMatrix.shared.o SDPFragment.shared.o SparseDynamicProgramming.shared.o BWTSearch.shared.o ClusterProbability.shared.o Coordinate.shared.o FindMaxInterval.shared.o DifferenceCovers.shared.o LightweightSuffixArray.shared.o MultikeyQuicksort.shared.o qsufsort.shared.o Alignment.shared.o AlignmentCandidate.shared.o AlignmentContext.shared.o AlignmentMap.shared.o AlignmentStats.shared.o CmpFile.shared.o FilterCriteria.shared.o SAMToAlignmentCandidateAdapter.shared.o SAMQVConversion.shared.o SAMSupplementalQVList.shared.o AnchorParameters.shared.o ClusterList.shared.o MatchPos.shared.o WeightedInterval.shared.o BaseSequenceIO.shared.o CCSIterator.shared.o FragmentCCSIterator.shared.o ReaderAgglomerate.shared.o CompareSequencesPrinter.shared.o IntervalPrinter.shared.o SAMHeaderPrinter.shared.o SAMPrinter.shared.o SummaryPrinter.shared.o PbiFilterZmwGroupQuery.shared.o SequentialZmwGroupQuery.shared.o QualityValueProfile.shared.o ContextSample.shared.o ContextSet.shared.o LengthHistogram.shared.o QualitySample.shared.o LookupAnchorDistribution.shared.o StatUtils.shared.o cdfs.shared.o pdfs.shared.o BaseTuple.shared.o DNATuple.shared.o TupleMetrics.shared.o FileOfFileNames.shared.o FileUtils.shared.o LogUtils.shared.o PhredUtils.shared.o RangeUtils.shared.o RegionUtils.shared.o -lpbbam -lpbdata -lpbihdf
make[3]: Leaving directory '/<<PKGBUILDDIR>>/alignment'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -k gtest
make[2]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -C /<<PKGBUILDDIR>>//unittest gtest
make[3]: Entering directory '/<<PKGBUILDDIR>>/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++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CCSSequence_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/CCSSequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SeqUtils_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/SeqUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SMRTSequence_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/SMRTSequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o defs_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/defs_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o NucConversion_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/NucConversion_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o DNASequence_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/DNASequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o VectorUtils_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/VectorUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ScanData_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/ScanData_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ChangeListID_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/ChangeListID_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTQReader_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/FASTQReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o utils_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/utils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTASequence_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/FASTASequence_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FASTAReader_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/FASTAReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o StringUtils_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/StringUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SMRTTitle_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/utils/SMRTTitle_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o TitleTable_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/metagenome/TitleTable_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RefInfo_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/saf/RefInfo_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o AlnGroup_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/saf/AlnGroup_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o MovieInfo_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/saf/MovieInfo_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionAnnotations_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/reads/RegionAnnotations_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ReadType_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/reads/ReadType_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionTypeMap_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/reads/RegionTypeMap_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o QualityValueVector_gtest.o /<<PKGBUILDDIR>>/unittest/pbdata/qvs/QualityValueVector_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFScanDataReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFScanDataReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDF2DArray_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDF2DArray_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFScanDataWriter_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFScanDataWriter_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFCCSReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFCCSReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFUtils_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFPlsReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFPlsReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFBasReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFBasReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o HDFZMWReader_gtest.o /<<PKGBUILDDIR>>/unittest/hdf/HDFZMWReader_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RangeUtils_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/utils/RangeUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FileUtils_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/utils/FileUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o RegionUtils_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/utils/RegionUtils_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o PbiFilterZmwGroupQuery_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SequentialZmwGroupQuery_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o AlignmentMap_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CmpIndexedStringTable_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o CCSIterator_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/files/CCSIterator_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o ReaderAgglomerate_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/files/ReaderAgglomerate_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FragmentCCSIterator_other_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/files/FragmentCCSIterator_other_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o FragmentCCSIterator_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/files/FragmentCCSIterator_gtest.cpp
g++ -O3 -std=c++11 -Wno-div-by-zero -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/<<PKGBUILDDIR>>/unittest/ -I/<<PKGBUILDDIR>>/unittest//../alignment -I/usr/include -I../alignment -I../hdf -I../pbdata -I/usr/include/hdf5/serial -c -o SAMPrinter_gtest.o /<<PKGBUILDDIR>>/unittest/alignment/format/SAMPrinter_gtest.cpp
In file included from /<<PKGBUILDDIR>>/unittest//../alignment/format/SAMPrinter.hpp:4:0,
from /<<PKGBUILDDIR>>/unittest/alignment/format/SAMPrinter_gtest.cpp:24:
/usr/include/c++/7/sstream:300:7: error: 'struct std::__cxx11::basic_stringbuf<_CharT, _Traits, _Alloc>::__xfer_bufptrs' redeclared with different access
struct __xfer_bufptrs
^~~~~~
makefile:110: recipe for target 'SAMPrinter_gtest.o' failed
make[3]: *** [SAMPrinter_gtest.o] Error 1
make[3]: Target 'gtest' not remade because of errors.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/unittest'
makefile:27: recipe for target 'gtest' failed
make[2]: *** [gtest] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:31: recipe for target 'override_dh_auto_test' failed
make[1]: [override_dh_auto_test] Error 2 (ignored)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
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_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: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: 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_0~20161219-2_armhf.deb'.
dpkg-deb: building package 'libblasr-dev' in '../libblasr-dev_0~20161219-2_armhf.deb'.
dpkg-deb: building package 'libpbihdf-dev' in '../libpbihdf-dev_0~20161219-2_armhf.deb'.
dpkg-deb: building package 'libpbdata' in '../libpbdata_0~20161219-2_armhf.deb'.
dpkg-deb: building package 'libpbdata-dbgsym' in '../libpbdata-dbgsym_0~20161219-2_armhf.deb'.
dpkg-deb: building package 'libpbihdf' in '../libpbihdf_0~20161219-2_armhf.deb'.
dpkg-deb: building package 'libpbihdf-dbgsym' in '../libpbihdf-dbgsym_0~20161219-2_armhf.deb'.
dpkg-deb: building package 'libblasr' in '../libblasr_0~20161219-2_armhf.deb'.
dpkg-deb: building package 'libblasr-dbgsym' in '../libblasr-dbgsym_0~20161219-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pbseqlib_0~20161219-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build pbseqlib-0~20161219
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-11-15T07:10:35Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pbseqlib_0~20161219-2_armhf.changes:
------------------------------------
Format: 1.8
Date: Thu, 09 Nov 2017 22:48:55 -0500
Source: pbseqlib
Binary: libpbseq libpbseq-dev libpbdata-dev libpbdata libpbihdf-dev libpbihdf libblasr-dev libblasr
Architecture: armhf
Version: 0~20161219-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Afif Elghraoui <afif@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)
Closes: 880805
Changes:
pbseqlib (0~20161219-2) unstable; urgency=medium
.
* Add support for HDF5 1.10.1
Thanks to Gilles Filippini for the patches (Closes: #880805)
* Bump Standards-Version to 4.1.1
* Update copyright year
* Handle nocheck build profile
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libblasr-dbgsym_0~20161219-2_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 3954192 bytes: control archive=556 bytes.
402 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libblasr-dbgsym
Source: pbseqlib
Version: 0~20161219-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4014
Depends: libblasr (= 0~20161219-2)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libblasr
Build-Ids: 15cb6d4691b4951fbcb0fe87bcdb1e58c04e9ccd
drwxr-xr-x root/root 0 2017-11-10 03:48 ./
drwxr-xr-x root/root 0 2017-11-10 03:48 ./usr/
drwxr-xr-x root/root 0 2017-11-10 03:48 ./usr/lib/
drwxr-xr-x root/root 0 2017-11-10 03:48 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-11-10 03:48 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-11-10 03:48 ./usr/lib/debug/.build-id/15/
-rw-r--r-- root/root 4100028 2017-11-10 03:48 ./usr/lib/debug/.build-id/15/cb6d4691b4951fbcb0fe87bcdb1e58c04e9ccd.debug
drwxr-xr-x root/root 0 2017-11-10 03:48 ./usr/share/
drwxr-xr-x root/root 0 2017-11-10 03:48 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-11-10 03:48 ./usr/share/doc/libblasr-dbgsym -> libblasr
libblasr-dev_0~20161219-2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
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Package: libblasr-dev
Source: pbseqlib
Version: 0~20161219-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6460
Depends: libblasr (= 0~20161219-2)
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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-rw-r--r-- root/root 4679 2017-11-10 03:36 ./usr/share/doc/libblasr-dev/copyright
libblasr_0~20161219-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 828360 bytes: control archive=872 bytes.
748 bytes, 17 lines control
218 bytes, 3 lines md5sums
26 bytes, 1 lines triggers
Package: libblasr
Source: pbseqlib
Version: 0~20161219-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2269
Depends: libc6 (>= 2.17), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), libpbdata (= 0~20161219-2), libpbihdf (= 0~20161219-2), libpbbam
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 2017-11-10 03:48 ./
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-rw-r--r-- root/root 4679 2017-11-10 03:36 ./usr/share/doc/libblasr/copyright
libpbdata-dbgsym_0~20161219-2_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 1660088 bytes: control archive=560 bytes.
405 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libpbdata-dbgsym
Source: pbseqlib
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Auto-Built-Package: debug-symbols
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Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
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Depends: libpbdata (= 0~20161219-2)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libpbdata
Build-Ids: d2db7764b86ad856f941460b09799c18e3104826
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lrwxrwxrwx root/root 0 2017-11-10 03:48 ./usr/share/doc/libpbdata-dbgsym -> libpbdata
libpbdata-dev_0~20161219-2_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 179708 bytes: control archive=3084 bytes.
703 bytes, 18 lines control
6871 bytes, 86 lines md5sums
Package: libpbdata-dev
Source: pbseqlib
Version: 0~20161219-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1057
Depends: libpbdata (= 0~20161219-2)
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
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three sub-libraries, including pbdata, hdf and alignment.
.
This package contains the header files and static library for the pbdata
sublibrary.
drwxr-xr-x root/root 0 2017-11-10 03:48 ./
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-rw-r--r-- root/root 4679 2017-11-10 03:36 ./usr/share/doc/libpbdata-dev/copyright
libpbdata_0~20161219-2_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 107068 bytes: control archive=852 bytes.
672 bytes, 17 lines control
221 bytes, 3 lines md5sums
26 bytes, 1 lines triggers
Package: libpbdata
Source: pbseqlib
Version: 0~20161219-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 351
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), libpbbam
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 2017-11-10 03:48 ./
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libpbihdf-dbgsym_0~20161219-2_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 2319868 bytes: control archive=564 bytes.
405 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libpbihdf-dbgsym
Source: pbseqlib
Version: 0~20161219-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2404
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Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libpbihdf
Build-Ids: 9faa2f4597a758e09af8b095087d79581aeb3bc3
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drwxr-xr-x root/root 0 2017-11-10 03:48 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-11-10 03:48 ./usr/share/doc/libpbihdf-dbgsym -> libpbihdf
libpbihdf-dev_0~20161219-2_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 250192 bytes: control archive=2192 bytes.
701 bytes, 18 lines control
4232 bytes, 56 lines md5sums
Package: libpbihdf-dev
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Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1945
Depends: libpbihdf (= 0~20161219-2)
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 2017-11-10 03:48 ./
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libpbihdf_0~20161219-2_armhf.deb
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new Debian package, version 2.0.
size 142072 bytes: control archive=884 bytes.
740 bytes, 17 lines control
221 bytes, 3 lines md5sums
26 bytes, 1 lines triggers
Package: libpbihdf
Source: pbseqlib
Version: 0~20161219-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 539
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libhdf5-100, libhdf5-cpp-100 (>= 1.10.0), libstdc++6 (>= 5.2), libpbdata (= 0~20161219-2), libpbbam
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 2017-11-10 03:48 ./
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Build Architecture: armhf
Build-Space: 231960
Build-Time: 3632
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 542
Job: pbseqlib_0~20161219-2
Machine Architecture: armhf
Package: pbseqlib
Package-Time: 4222
Source-Version: 0~20161219-2
Space: 231960
Status: successful
Version: 0~20161219-2
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Finished at 2017-11-15T07:10:35Z
Build needed 01:10:22, 231960k disc space