blasr →
5.3+0-2 →
armhf → 2018-03-22 05:35:16
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| blasr 5.3+0-2 (armhf) Thu, 22 Mar 2018 04:50:52 +0000 |
+==============================================================================+
Package: blasr
Version: 5.3+0-2
Source Version: 5.3+0-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-efd047b1-ec9b-4070-935a-f09493bcb242' 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 [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.4 MB]
Fetched 23.1 MB in 29s (809 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'blasr' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/blasr.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/blasr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1226 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main blasr 5.3+0-2 (dsc) [2028 B]
Get:2 http://172.17.0.1/private buster-staging/main blasr 5.3+0-2 (tar) [1211 kB]
Get:3 http://172.17.0.1/private buster-staging/main blasr 5.3+0-2 (diff) [13.4 kB]
Fetched 1226 kB in 0s (2490 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/blasr-zoMQVW/blasr-5.3+0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/blasr-zoMQVW' 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-Gd1y7b/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-Gd1y7b/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Gd1y7b/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-Gd1y7b/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (3017 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 4 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-Gd1y7b/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 (21.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15682 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), python, cmake, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev
Filtered Build-Depends: debhelper (>= 11~), python, cmake, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev (>= 0~20160912), libpbbam-dev
dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive/sbuild-build-depends-blasr-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-blasr-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ Sources [540 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ Packages [622 B]
Fetched 2495 B in 1s (3459 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install blasr build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd libsasl2-modules openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarchive13 libblasr libblasr-dev libboost-dev
libboost1.62-dev libbsd0 libcroco3 libcurl3 libcurl3-gnutls
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgssapi-krb5-2
libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhts-dev libhts2 libicu57
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev liblzo2-2 libmagic-mgc
libmagic1 libnghttp2-14 libpbbam libpbbam-dev libpbdata libpbdata-dev
libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib librhash0 librtmp1 libsigsegv2
libssh2-1 libssl-dev libssl1.0.2 libsz2 libtimedate-perl libtool libuv1
libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build dh-make dwz gettext-doc libasprintf-dev
libgettextpo-dev groff lrzip libboost-doc libboost1.62-doc
libboost-atomic1.62-dev libboost-chrono1.62-dev libboost-context1.62-dev
libboost-coroutine1.62-dev libboost-date-time1.62-dev
libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-regex1.62-dev
libboost-serialization1.62-dev libboost-signals1.62-dev
libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user
libhdf5-doc liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl python-doc python-tk
python2.7-doc binfmt-support
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libssl-doc libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-strip-nondeterminism file gettext gettext-base
groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libarchive13 libblasr libblasr-dev libboost-dev
libboost1.62-dev libbsd0 libcroco3 libcurl3 libcurl3-gnutls
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgssapi-krb5-2
libhdf5-100 libhdf5-cpp-100 libhdf5-dev libhts-dev libhts2 libicu57
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev liblzo2-2 libmagic-mgc
libmagic1 libnghttp2-14 libpbbam libpbbam-dev libpbdata libpbdata-dev
libpbihdf libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib
libpython2.7-minimal libpython2.7-stdlib librhash0 librtmp1 libsigsegv2
libssh2-1 libssl-dev libssl1.0.2 libsz2 libtimedate-perl libtool libuv1
libxml2 m4 man-db mime-support po-debconf python python-minimal python2.7
python2.7-minimal sbuild-build-depends-blasr-dummy zlib1g-dev
0 upgraded, 84 newly installed, 0 to remove and 4 not upgraded.
Need to get 24.9 MB/46.5 MB of archives.
After this operation, 261 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Gd1y7b/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [908 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.2-1 [1145 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.14-7 [393 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.14-7 [1077 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.14-4 [41.0 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.14-7 [1842 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.14-7 [293 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.14-4 [20.4 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.14-4 [155 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2n-1 [887 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf cmake-data all 3.10.2-1 [1349 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libarchive13 armhf 3.2.2-3.1 [251 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.58.0-2 [276 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf librhash0 armhf 1.3.5-1 [95.9 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libuv1 armhf 1.18.0-3 [86.1 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf cmake armhf 3.10.2-1 [2463 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 16 [16.3 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.5 [1007 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-4 [36.0 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libpbbam armhf 0.7.4+ds-1+rpi1+b1 [395 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libpbdata armhf 0~20161219-2 [107 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-11 [191 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-4 [118 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libpbihdf armhf 0~20161219-2 [142 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libblasr armhf 0~20161219-2 [828 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libblasr-dev armhf 0~20161219-2 [1670 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:49 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-4 [2109 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.0g-2 [1371 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.7.4+ds-1+rpi1+b1 [90.2 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libpbdata-dev armhf 0~20161219-2 [180 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libpbihdf-dev armhf 0~20161219-2 [250 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libpbseq-dev all 0~20161219-2 [4092 B]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.27-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-7+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-11 gcc-7_7.3.0-11 libc6-dev_2.27-2+rpi1 libstdc++-7-dev_7.3.0-11 libstdc++6_8-20180218-1+rpi1 linux-libc-dev_4.15.4-1+rpi1
Package versions: adduser_3.117 apt_1.6~beta1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4.18-1.1 binutils_2.30-7+rpi1 binutils-arm-linux-gnueabihf_2.30-7+rpi1 binutils-common_2.30-7+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.4 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 cmake_3.10.2-1 cmake-data_3.10.2-1 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-11 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.1.5 debianutils_4.8.4 dh-autoreconf_16 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.0-1 e2fsprogs_1.44.0-1 e2fsprogs-l10n_1.44.0-1 fakeroot_1.22-2 fdisk_2.31.1-0.4 file_1:5.32-2 findutils_4.6.0+git+20170828-2 g++_4:7.2.0-1d1 g++-7_7.3.0-11 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_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-11 gcc-7-base_7.3.0-11 gcc-8-base_8-20180218-1+rpi1 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-4 hostname_3.20 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.12-3 libapt-pkg5.0_1.6~beta1 libarchive-zip-perl_1.60-1 libarchive13_3.2.2-3.1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-11 libassuan0_2.5.1-2 libatomic1_8-20180218-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-7+rpi1 libblasr_0~20161219-2 libblasr-dev_0~20161219-2 libblkid1_2.31.1-0.4 libboost-dev_1.62.0.1+b8 libboost1.62-dev_1.62.0+dfsg-5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-2+rpi1 libc-dev-bin_2.27-2+rpi1 libc6_2.27-2+rpi1 libc6-dev_2.27-2+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180218-1+rpi1 libcilkrts5_7.3.0-11 libcom-err2_1.44.0-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.1-1 libcryptsetup4_2:1.7.5-1 libcurl3_7.58.0-2 libcurl3-gnutls_7.58.0-2 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.241 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.90-1+rpi1 libdrm2_2.4.90-1+rpi1 libexpat1_2.2.5-3 libext2fs2_1.44.0-1 libfakeroot_1.22-2 libfdisk1_2.31.1-0.4 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.3.0-11 libgcc1_1:8-20180218-1+rpi1 libgcrypt20_1.8.1-4 libgdbm-compat4_1.14.1-4 libgdbm3_1.8.3-14 libgdbm5_1.14.1-4 libgfortran4_7.3.0-11 libglib2.0-0_2.54.3-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180218-1+rpi1 libgpg-error0_1.27-6 libgssapi-krb5-2_1.16-2 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_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu57_57.1-9 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-1 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.4 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncursesw5_6.1-1 libnettle6_3.4-1 libnghttp2-14_1.31.0-1 libnpth0_1.5-3 libnss-systemd_238-2 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-2 libpam0g_1.1.8-3.7 libpbbam_0.7.4+ds-1+rpi1+b1 libpbbam-dev_0.7.4+ds-1+rpi1+b1 libpbdata_0~20161219-2 libpbdata-dev_0~20161219-2 libpbihdf_0~20161219-2 libpbihdf-dev_0~20161219-2 libpbseq-dev_0~20161219-2 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.1-5 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-4 libpsl5_0.19.1-5 libpython-stdlib_2.7.14-4 libpython2.7-minimal_2.7.14-7 libpython2.7-stdlib_2.7.14-7 libreadline7_7.0-3 librhash0_1.3.5-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_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_2.12-1 libsmartcols1_2.31.1-0.4 libsqlite3-0_3.22.0-1 libss2_1.44.0-1 libssh2-1_1.8.0-1 libssl-dev_1.1.0g-2 libssl1.0.2_1.0.2n-1 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.3.0-11 libstdc++6_8-20180218-1+rpi1 libsystemd0_238-2 libsz2_1.0.2-1 libtasn1-6_4.13-2 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_6.1-1 libtool_2.4.6-2 libubsan0_7.3.0-11 libudev1_238-2 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.4 libuv1_1.18.0-3 libxml2_2.9.4+dfsg1-6.1 linux-base_4.5 linux-libc-dev_4.15.4-1+rpi1 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_2.8.2-1 mawk_1.3.3-17 mime-support_3.60 mount_2.31.1-0.4 multiarch-support_2.27-2+rpi1 nano_2.9.4-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 openssl_1.1.0g-2 passwd_1:4.5-1 patch_2.7.6-1 perl_5.26.1-5 perl-base_5.26.1-5 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-5 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-4 python_2.7.14-4 python-minimal_2.7.14-4 python2.7_2.7.14-7 python2.7-minimal_2.7.14-7 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-blasr-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-2 systemd-sysv_238-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018c-1 udev_238-2 util-linux_2.31.1-0.4 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 Sun Mar 11 17:10:30 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./blasr_5.3+0-2.dsc
dpkg-source: info: extracting blasr in /<<BUILDDIR>>/blasr-5.3+0
dpkg-source: info: unpacking blasr_5.3+0.orig.tar.gz
dpkg-source: info: unpacking blasr_5.3+0-2.debian.tar.xz
dpkg-source: info: applying disable-gtest.patch
dpkg-source: info: applying cmake-utils.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-efd047b1-ec9b-4070-935a-f09493bcb242
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package blasr
dpkg-buildpackage: info: source version 5.3+0-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build blasr-5.3+0
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
./configure.py --shared
`uname`
Linux
writing to '/<<BUILDDIR>>/blasr-5.3+0/defines.mk':
"""
HTSLIB_INC ?= /usr/include/htslib
HDF5_INC ?= /usr/include/hdf5/serial
PBBAM_INC ?= /usr/include
CXXFLAGS ?= -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security
LIBPBDATA_LIBFLAGS ?= -lpbdata
LIBPBIHDF_LIB ?= /usr/lib/arm-linux-gnueabihf
SHELL ?= bash
LIBPBDATA_INC ?= /usr/include/pbseq/pbdata
PBBAM_LIBFLAGS ?= -lpbbam
LIBPBIHDF_INC ?= /usr/include/pbseq/hdf
RT_LIBFLAGS ?= -lrt
ZLIB_LIBFLAGS ?= -lz
HTSLIB_LIB ?= /usr/lib/arm-linux-gnueabihf
PTHREAD_LIBFLAGS ?= -lpthread
LIBBLASR_LIBFLAGS ?= -lblasr
LIBPBDATA_LIB ?= /usr/lib/arm-linux-gnueabihf
HTSLIB_LIBFLAGS ?= -lhts
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5
DL_LIBFLAGS ?= -ldl
LIBPBIHDF_LIBFLAGS ?= -lpbihdf
LIBBLASR_INC ?= /usr/include/pbseq/alignment
LIBBLASR_LIB ?= /usr/lib/arm-linux-gnueabihf
PBBAM_LIB ?= /usr/lib/arm-linux-gnueabihf
BOOST_INC ?= /usr/include/boost
"""
----
/usr/bin/make clean
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
make[2]: git: Command not found
rm -f blasr Blasr.o Blasr.d blasr.d
/usr/bin/make -C utils clean
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[4]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
make[4]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
make[4]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
make[4]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
/usr/bin/make -C extrautils clean
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/extrautils'
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/extrautils'
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
/usr/bin/make -C utils/bam2bax clean
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
/usr/bin/make -C utils/bax2bam clean
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
# This is created by configure.py
rm -f defines.mk
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
./configure.py --shared
`uname`
Linux
writing to '/<<BUILDDIR>>/blasr-5.3+0/defines.mk':
"""
HTSLIB_INC ?= /usr/include/htslib
HDF5_INC ?= /usr/include/hdf5/serial
PBBAM_INC ?= /usr/include
CXXFLAGS ?= -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security
LIBPBDATA_LIBFLAGS ?= -lpbdata
LIBPBIHDF_LIB ?= /usr/lib/arm-linux-gnueabihf
SHELL ?= bash
LIBPBDATA_INC ?= /usr/include/pbseq/pbdata
PBBAM_LIBFLAGS ?= -lpbbam
LIBPBIHDF_INC ?= /usr/include/pbseq/hdf
RT_LIBFLAGS ?= -lrt
ZLIB_LIBFLAGS ?= -lz
HTSLIB_LIB ?= /usr/lib/arm-linux-gnueabihf
PTHREAD_LIBFLAGS ?= -lpthread
LIBBLASR_LIBFLAGS ?= -lblasr
LIBPBDATA_LIB ?= /usr/lib/arm-linux-gnueabihf
HTSLIB_LIBFLAGS ?= -lhts
HDF5_LIB ?= /usr/lib/arm-linux-gnueabihf/hdf5/serial
HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5
DL_LIBFLAGS ?= -ldl
LIBPBIHDF_LIBFLAGS ?= -lpbihdf
LIBBLASR_INC ?= /usr/include/pbseq/alignment
LIBBLASR_LIB ?= /usr/lib/arm-linux-gnueabihf
PBBAM_LIB ?= /usr/lib/arm-linux-gnueabihf
BOOST_INC ?= /usr/include/boost
"""
----
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
dh_auto_build
make -j4 -O "INSTALL=install --strip-program=true"
make -C utils
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o PulseToFasta.o PulseToFasta.cpp
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SamToCmpH5.o SamToCmpH5.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:6,
from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:4,
from SamToCmpH5.cpp:3:
/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 = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator {aka __gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_Alignment>::RearrangeReferences(std::vector<FASTASequence>&) [with T_ReferenceSequence = SAMFullReferenceSequence; T_ReadGroup = SAMReadGroup; T_Alignment = SAMPosAlignment]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<std::__cxx11::basic_string<char> > SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::ReadHeader(AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>&) [with T_ReferenceSequence = SAMFullReferenceSequence; T_ReadGroup = SAMReadGroup; T_SAMAlignment = SAMPosAlignment]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SamToM4.o SamToM4.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/pbbam/Frames.h:46,
from /usr/include/pbbam/BamRecord.h:46,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from SamToM4.cpp:19:
/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 = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator {aka __gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_Alignment>::RearrangeReferences(std::vector<FASTASequence>&) [with T_ReferenceSequence = SAMFullReferenceSequence; T_ReadGroup = SAMReadGroup; T_Alignment = SAMAlignment]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SamFilter.o SamFilter.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/pbbam/Frames.h:46,
from /usr/include/pbbam/BamRecord.h:46,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from SamFilter.cpp:31:
/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 = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator {aka __gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator {aka __gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_Alignment>::RearrangeReferences(std::vector<FASTASequence>&) [with T_ReferenceSequence = SAMFullReferenceSequence; T_ReadGroup = SAMReadGroup; T_Alignment = SAMAlignment]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'std::vector<std::__cxx11::basic_string<char> > SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::ReadHeader(AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>&) [with T_ReferenceSequence = SAMFullReferenceSequence; T_ReadGroup = SAMReadGroup; T_SAMAlignment = SAMAlignment]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o LoadPulses.o LoadPulses.cpp
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SAWriter.o SAWriter.cpp
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o ToAfg.o ToAfg.cpp
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -o loadPulses LoadPulses.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"loadPulses.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
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g++ -o pls2fasta PulseToFasta.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"pls2fasta.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -o samtoh5 SamToCmpH5.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"samtoh5.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -o samtom4 SamToM4.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"samtom4.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
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g++ -o samFilter SamFilter.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"samFilter.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -o toAfg ToAfg.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"toAfg.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -o sawriter SAWriter.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"sawriter.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o SDPMatcher.o SDPMatcher.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /usr/include/pbbam/Frames.h:46,
from /usr/include/pbbam/BamRecord.h:46,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:5,
from SDPMatcher.cpp:7:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PositionDNATuple&}; _Tp = PositionDNATuple; _Alloc = std::allocator<PositionDNATuple>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator {aka __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /usr/include/pbbam/Frames.h:46,
from /usr/include/pbbam/BamRecord.h:46,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:5,
from SDPMatcher.cpp:7:
/usr/include/c++/7/bits/stl_vector.h: In function 'int SequenceToTupleList(Sequence&, TupleMetrics&, TupleList<PositionDNATuple>&) [with Sequence = DNASequence]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:5,
from SDPMatcher.cpp:7:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:5,
from SDPMatcher.cpp:7:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Distance = int; _Tp = PositionDNATuple; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbseq/pbdata/DNASequence.hpp:15,
from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
from /usr/include/pbseq/pbdata/FASTAReader.hpp:5,
from SDPMatcher.cpp:7:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTASequence; T_TargetSequence = FASTASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, DNASequence>; T_TupleList = TupleList<PositionDNATuple>]':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
g++ -o sdpMatcher SDPMatcher.o -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wextra -Wno-overloaded-virtual -MMD -MP -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"sdpMatcher.d" -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils'
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -c -o Blasr.o Blasr.cpp
In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29:0,
from iblasr/BlasrHeaders.h:100,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In instantiation of 'void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]':
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:164:25: required from 'void BAMOutput::PrintAlignment(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::IRecordWriter&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]'
iblasr/BlasrUtilsImpl.hpp:974:182: required from here
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:24:44: warning: the compiler can assume that the address of 'read' will never be NULL [-Waddress]
if (dynamic_cast<SMRTSequence*>(&read) == NULL) {
^
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:43:0,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp: In instantiation of 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]':
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:129:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
while (refPos + 1 < reference.length and
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:130:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
queryPos + 1 < read.length and
~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:5:0,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp: In instantiation of 'int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]':
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:53:19: required from 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:1068:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
index[l] + lcpLength >= targetLength or // This shouldn't
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp: In instantiation of 'long int SuffixArray<T, Sigma, Compare, Tuple>::SearchLeftBound(T*, long int, DNALength, T, long int, long int) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]':
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:1056:32: required from 'int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:53:19: required from 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:763:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen == targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:773:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen < targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/7/cassert:44:0,
from /usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/../tuples/../../pbdata/CompressedSequence.hpp:3,
from /usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/../tuples/CompressedDNATuple.hpp:5,
from /usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:20,
from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:5,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:781:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
assert(index[m]+targetOffset < targetLength);
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:5:0,
from iblasr/BlasrHeaders.h:59,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp: In instantiation of 'long int SuffixArray<T, Sigma, Compare, Tuple>::SearchRightBound(T*, long int, DNALength, T, long int, long int) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]':
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:1057:33: required from 'int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:53:19: required from 'int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]'
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:224:36: required from 'int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]'
iblasr/BlasrAlignImpl.hpp:37:32: required from 'void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]'
Blasr.cpp:395:27: required from here
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:813:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen == targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/../../suffixarray/SuffixArray.hpp:817:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (targetSufLen < targetOffset) {
~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29:0,
from iblasr/BlasrHeaders.h:100,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In function 'void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence]':
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:24:5: warning: nonnull argument 'read' compared to NULL [-Wnonnull-compare]
if (dynamic_cast<SMRTSequence*>(&read) == NULL) {
^~
In file included from /usr/include/c++/7/vector:69:0,
from iblasr/BlasrHeaders.h:8,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/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 PositionDNATuple&}; _Tp = PositionDNATuple; _Alloc = std::allocator<PositionDNATuple>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator {aka __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from iblasr/BlasrHeaders.h:8,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/c++/7/bits/stl_vector.h: In function 'int SequenceToTupleList(Sequence&, TupleMetrics&, TupleList<PositionDNATuple>&) [with Sequence = DNASequence]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbbam/BamWriter.h:46,
from iblasr/BlasrHeaders.h:26,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbbam/BamWriter.h:46,
from iblasr/BlasrHeaders.h:26,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Distance = int; _Tp = PositionDNATuple; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from /usr/include/pbbam/internal/QualityValues.inl:43,
from /usr/include/pbbam/QualityValues.h:198,
from /usr/include/pbbam/BamRecordImpl.h:49,
from /usr/include/pbbam/BamRecord.h:47,
from /usr/include/pbbam/BamWriter.h:46,
from iblasr/BlasrHeaders.h:26,
from iblasr/BlasrMiscs.hpp:4,
from Blasr.cpp:3:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1963:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
__sort(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~
/usr/include/c++/7/bits/stl_algo.h:1963:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>]':
/usr/include/c++/7/bits/stl_algo.h:4836:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:4836:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:4836:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>]':
/usr/include/c++/7/bits/stl_algo.h:4836:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:4836:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:4836:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_ScoreFn = IDSScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>]':
/usr/include/c++/7/bits/stl_algo.h:4836:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:4836:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:4836:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >' changed in GCC 7.1
std::__sort(__first, __last, __gnu_cxx::__ops::__iter_less_iter());
~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
g++ -o blasr -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -DSHA1_7=\"\" -std=c++0x -pedantic -Wall -Wextra -Wno-div-by-zero -Wno-overloaded-virtual -MMD -MP -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq/alignment -I/usr/include/pbseq/hdf -I/usr/include/pbseq/pbdata -I/usr/include -I/usr/include/hdf5/serial -I/usr/include/htslib -I/usr/include/boost -MF"blasr.d" Blasr.o -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -lpbihdf -lblasr -lpbihdf -lpbdata -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lrt -lpthread -ldl
LD_LIBRARY_PATH=/usr/lib/arm-linux-gnueabihf:/usr/lib/arm-linux-gnueabihf:/usr/lib/arm-linux-gnueabihf:/usr/lib/arm-linux-gnueabihf/hdf5/serial:/usr/lib/arm-linux-gnueabihf:/usr/lib/arm-linux-gnueabihf::
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
/usr/bin/make -C utils/bax2bam
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
Re-run cmake no build system arguments
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.8")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Performing Test HAS_NO_OVERLOADED_VIRTUAL
-- Performing Test HAS_NO_OVERLOADED_VIRTUAL - Success
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNINITIALIZED
-- Performing Test HAS_NO_UNINITIALIZED - Success
-- Performing Test HAS_NO_DEPRECATED_DECLARATIONS
-- Performing Test HAS_NO_DEPRECATED_DECLARATIONS - Success
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEF
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEF - Success
-- Configuring done
-- Generating done
-- Build files have been written to: /<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build'
make[4]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build'
make[5]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build'
Dependee "/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build/src/CMakeFiles/bax2bam.dir/DependInfo.cmake" is newer than depender "/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build/src/CMakeFiles/bax2bam.dir/depend.internal".
Dependee "/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build/src/CMakeFiles/bax2bam.dir/depend.internal".
Scanning dependencies of target bax2bam
make[5]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build'
make[5]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build'
[ 10%] Building CXX object src/CMakeFiles/bax2bam.dir/main.cpp.o
[ 20%] Building CXX object src/CMakeFiles/bax2bam.dir/Bax2Bam.cpp.o
[ 30%] Building CXX object src/CMakeFiles/bax2bam.dir/CcsConverter.cpp.o
[ 40%] Building CXX object src/CMakeFiles/bax2bam.dir/HqRegionConverter.cpp.o
[ 50%] Building CXX object src/CMakeFiles/bax2bam.dir/IConverter.cpp.o
[ 60%] Building CXX object src/CMakeFiles/bax2bam.dir/OptionParser.cpp.o
[ 70%] Building CXX object src/CMakeFiles/bax2bam.dir/PolymeraseReadConverter.cpp.o
[ 80%] Building CXX object src/CMakeFiles/bax2bam.dir/Settings.cpp.o
[ 90%] Building CXX object src/CMakeFiles/bax2bam.dir/SubreadConverter.cpp.o
[100%] Linking CXX executable ../../bin/bax2bam
/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wno-overloaded-virtual -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-declarations -Wno-unused-local-typedef -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -Wl,--no-as-needed -ldl -pthread -lrt -rdynamic CMakeFiles/bax2bam.dir/main.cpp.o CMakeFiles/bax2bam.dir/Bax2Bam.cpp.o CMakeFiles/bax2bam.dir/CcsConverter.cpp.o CMakeFiles/bax2bam.dir/HqRegionConverter.cpp.o CMakeFiles/bax2bam.dir/IConverter.cpp.o CMakeFiles/bax2bam.dir/OptionParser.cpp.o CMakeFiles/bax2bam.dir/PolymeraseReadConverter.cpp.o CMakeFiles/bax2bam.dir/Settings.cpp.o CMakeFiles/bax2bam.dir/SubreadConverter.cpp.o -o ../../bin/bax2bam -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lpbbam -lhts -lz -lpthread -lrt -ldl
make[5]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build'
[100%] Built target bax2bam
make[4]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build'
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam/build'
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bax2bam'
/usr/bin/make -C utils/bam2bax
make[2]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
Re-run cmake no build system arguments
-- The CXX compiler identification is GNU 7.3.0
-- The C compiler identification is GNU 7.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.8")
-- Performing Test HAS_NO_OVERLOADED_VIRTUAL
-- Performing Test HAS_NO_OVERLOADED_VIRTUAL - Success
-- Performing Test HAS_NO_UNUSED_VARIABLE
-- Performing Test HAS_NO_UNUSED_VARIABLE - Success
-- Performing Test HAS_NO_UNINITIALIZED
-- Performing Test HAS_NO_UNINITIALIZED - Success
-- Performing Test HAS_UNUSED_BUT_SET_VARIABLE
-- Performing Test HAS_UNUSED_BUT_SET_VARIABLE - Success
-- Performing Test HAS_NO_DEPRECATED_DECLARATIONS
-- Performing Test HAS_NO_DEPRECATED_DECLARATIONS - Success
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEF
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEF - Success
-- Configuring done
-- Generating done
-- Build files have been written to: /<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build
make[3]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
make[4]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
make[5]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
Dependee "/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build/src/CMakeFiles/bam2bax.dir/DependInfo.cmake" is newer than depender "/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build/src/CMakeFiles/bam2bax.dir/depend.internal".
Dependee "/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build/src/CMakeFiles/bam2bax.dir/depend.internal".
Scanning dependencies of target bam2bax
make[5]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
make[5]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
[ 7%] Building CXX object src/CMakeFiles/bam2bax.dir/Bam2BaxMain.cpp.o
[ 14%] Building CXX object src/CMakeFiles/bam2bax.dir/Settings.cpp.o
[ 21%] Building CXX object src/CMakeFiles/bam2bax.dir/Converter.cpp.o
[ 28%] Building CXX object src/CMakeFiles/bam2bax.dir/Bam2Bax.cpp.o
[ 35%] Building CXX object src/CMakeFiles/bam2bax.dir/OptionParser.cpp.o
[ 42%] Building CXX object src/CMakeFiles/bam2bax.dir/MetadataWriter.cpp.o
[ 50%] Linking CXX executable ../../bin/bam2bax
/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wno-overloaded-virtual -Wno-unused-variable -Wno-uninitialized -Wunused-but-set-variable -Wno-deprecated-declarations -Wno-unused-local-typedef -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -Wl,--no-as-needed -ldl -pthread -lrt -rdynamic CMakeFiles/bam2bax.dir/Bam2BaxMain.cpp.o CMakeFiles/bam2bax.dir/Settings.cpp.o CMakeFiles/bam2bax.dir/Converter.cpp.o CMakeFiles/bam2bax.dir/Bam2Bax.cpp.o CMakeFiles/bam2bax.dir/OptionParser.cpp.o CMakeFiles/bam2bax.dir/MetadataWriter.cpp.o -o ../../bin/bam2bax -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lpbbam -lhts -lz -lrt
make[5]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
[ 50%] Built target bam2bax
make[5]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
Dependee "/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build/src/CMakeFiles/bam2plx.dir/DependInfo.cmake" is newer than depender "/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build/src/CMakeFiles/bam2plx.dir/depend.internal".
Dependee "/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build/src/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build/src/CMakeFiles/bam2plx.dir/depend.internal".
Scanning dependencies of target bam2plx
make[5]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
make[5]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
[ 57%] Building CXX object src/CMakeFiles/bam2plx.dir/Bam2PlxMain.cpp.o
[ 64%] Building CXX object src/CMakeFiles/bam2plx.dir/Settings.cpp.o
[ 71%] Building CXX object src/CMakeFiles/bam2plx.dir/Converter.cpp.o
[ 78%] Building CXX object src/CMakeFiles/bam2plx.dir/Bam2Bax.cpp.o
[ 85%] Building CXX object src/CMakeFiles/bam2plx.dir/OptionParser.cpp.o
[ 92%] Building CXX object src/CMakeFiles/bam2plx.dir/MetadataWriter.cpp.o
[100%] Linking CXX executable ../../bin/bam2plx
/usr/bin/c++ -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3+0=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -Wall -Wno-overloaded-virtual -Wno-unused-variable -Wno-uninitialized -Wunused-but-set-variable -Wno-deprecated-declarations -Wno-unused-local-typedef -Wl,-z,relro -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -L/usr/lib/arm-linux-gnueabihf -Wl,--no-as-needed -ldl -pthread -lrt -rdynamic CMakeFiles/bam2plx.dir/Bam2PlxMain.cpp.o CMakeFiles/bam2plx.dir/Settings.cpp.o CMakeFiles/bam2plx.dir/Converter.cpp.o CMakeFiles/bam2plx.dir/Bam2Bax.cpp.o CMakeFiles/bam2plx.dir/OptionParser.cpp.o CMakeFiles/bam2plx.dir/MetadataWriter.cpp.o -o ../../bin/bam2plx -lblasr -lpbihdf -lpbdata -lhdf5_cpp -lhdf5 -lpbbam -lhts -lz -lrt
make[5]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
[100%] Built target bam2plx
make[4]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
make[3]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax/build'
make[2]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0/utils/bam2bax'
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3+0'
make[1]: 'override_dh_auto_test' is up to date.
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3+0'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_lintian -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: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/sdpMatcher contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/toAfg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samFilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/blasr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/bam2bax contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/sawriter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/pls2fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/loadPulses contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/bax2bam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samtoh5 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/bam2plx contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbbam.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/samtom4 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/blasr debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/samtom4 were not linked against libz.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/blasr debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/samtom4 were not linked against libhts.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/blasr debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/samtom4 were not linked against libdl.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/blasr debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/samtom4 were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sdpMatcher debian/blasr/usr/bin/toAfg debian/blasr/usr/bin/samFilter debian/blasr/usr/bin/blasr debian/blasr/usr/bin/bam2bax debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/pls2fasta debian/blasr/usr/bin/loadPulses debian/blasr/usr/bin/bax2bam debian/blasr/usr/bin/samtoh5 debian/blasr/usr/bin/bam2plx debian/blasr/usr/bin/samtom4 were not linked against librt.so.1 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3+0-2_armhf.deb'.
dpkg-deb: building package 'blasr' in '../blasr_5.3+0-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../blasr_5.3+0-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build blasr-5.3+0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-03-22T05:35:04Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
blasr_5.3+0-2_armhf.changes:
----------------------------
Format: 1.8
Date: Sun, 11 Mar 2018 18:02:22 +0100
Source: blasr
Binary: blasr
Architecture: armhf
Version: 5.3+0-2
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
blasr - mapping single-molecule sequencing reads
Closes: 892630
Changes:
blasr (5.3+0-2) unstable; urgency=low
.
* Team upload
.
[ Steffen Moeller ]
* debian/upstream/metadata: Added references to OMICtools and RRID
.
[ Afif Elghraoui ]
* Add README.source
.
[ Gilles Filippini ]
* Support for HDF5 1.10.1
Closes: #892630
.
[ Andreas Tille ]
* d/control:
- more cme-ish sequence of entries
- Standards-Version: 4.1.3
* debhelper 11
Checksums-Sha1:
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b333dd4a84c31420ae310c9fd51d0e0e4f3c4234 6545 blasr_5.3+0-2_armhf.buildinfo
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Checksums-Sha256:
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6df8d14d58b5abf20a32359d18257226a25b0b471c7d19de6236f1c281ad8eaf 542676 blasr_5.3+0-2_armhf.deb
Files:
d0dd53d6211dd382bff9cba656a046c1 10261724 debug optional blasr-dbgsym_5.3+0-2_armhf.deb
7ce12dc6a7369c08b198f714bbcd90d9 6545 science optional blasr_5.3+0-2_armhf.buildinfo
7b171fe2e2665a8426e55ea2b1fe31d3 542676 science optional blasr_5.3+0-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
blasr-dbgsym_5.3+0-2_armhf.deb
------------------------------
new Debian package, version 2.0.
size 10261724 bytes: control archive=1088 bytes.
815 bytes, 12 lines control
1272 bytes, 12 lines md5sums
Package: blasr-dbgsym
Source: blasr
Version: 5.3+0-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10684
Depends: blasr (= 5.3+0-2)
Section: debug
Priority: optional
Description: debug symbols for blasr
Build-Ids: 1607cc038e55c006f7e96731d1fd8122b54ba2e8 303cfad6b7a00cda9058ab574dca60dc0f1ccdab 479dc98e2df031b1e4ea50bcb113a531cb48ab09 576e0ab2c0fb8426d62603b6083386ab604d5ef1 6173de2cfb0fb2bcfe79ecb6ec6ce9f287aaefd3 672ea87d4870901ab2d9ba0b04325a7888ffc714 8bab58b69ba4edf3fd39f20d6caf9f632de6c1a4 96171de295a4c717080cb61671a66949c02559a3 c2402dc7cb84993f358d50261cae90fa28af8867 c5ce5a07b9f8303c130e16c833b6110f5011e861 d1fe3955eafc33e936fdff4cf549366291f0004d d9b575a550d4418e9746c8968a0d0a38fbb9d0cf
drwxr-xr-x root/root 0 2018-03-11 17:02 ./
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/16/
-rw-r--r-- root/root 947104 2018-03-11 17:02 ./usr/lib/debug/.build-id/16/07cc038e55c006f7e96731d1fd8122b54ba2e8.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/30/
-rw-r--r-- root/root 282168 2018-03-11 17:02 ./usr/lib/debug/.build-id/30/3cfad6b7a00cda9058ab574dca60dc0f1ccdab.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/47/
-rw-r--r-- root/root 407204 2018-03-11 17:02 ./usr/lib/debug/.build-id/47/9dc98e2df031b1e4ea50bcb113a531cb48ab09.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/57/
-rw-r--r-- root/root 2513072 2018-03-11 17:02 ./usr/lib/debug/.build-id/57/6e0ab2c0fb8426d62603b6083386ab604d5ef1.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/61/
-rw-r--r-- root/root 394292 2018-03-11 17:02 ./usr/lib/debug/.build-id/61/73de2cfb0fb2bcfe79ecb6ec6ce9f287aaefd3.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/67/
-rw-r--r-- root/root 497304 2018-03-11 17:02 ./usr/lib/debug/.build-id/67/2ea87d4870901ab2d9ba0b04325a7888ffc714.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/8b/
-rw-r--r-- root/root 270132 2018-03-11 17:02 ./usr/lib/debug/.build-id/8b/ab58b69ba4edf3fd39f20d6caf9f632de6c1a4.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/96/
-rw-r--r-- root/root 141436 2018-03-11 17:02 ./usr/lib/debug/.build-id/96/171de295a4c717080cb61671a66949c02559a3.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/c2/
-rw-r--r-- root/root 843056 2018-03-11 17:02 ./usr/lib/debug/.build-id/c2/402dc7cb84993f358d50261cae90fa28af8867.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/c5/
-rw-r--r-- root/root 576764 2018-03-11 17:02 ./usr/lib/debug/.build-id/c5/ce5a07b9f8303c130e16c833b6110f5011e861.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/d1/
-rw-r--r-- root/root 841712 2018-03-11 17:02 ./usr/lib/debug/.build-id/d1/fe3955eafc33e936fdff4cf549366291f0004d.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/lib/debug/.build-id/d9/
-rw-r--r-- root/root 3198024 2018-03-11 17:02 ./usr/lib/debug/.build-id/d9/b575a550d4418e9746c8968a0d0a38fbb9d0cf.debug
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/share/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-03-11 17:02 ./usr/share/doc/blasr-dbgsym -> blasr
blasr_5.3+0-2_armhf.deb
-----------------------
new Debian package, version 2.0.
size 542676 bytes: control archive=1496 bytes.
764 bytes, 14 lines control
1684 bytes, 28 lines md5sums
Package: blasr
Version: 5.3+0-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2134
Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.5), libhdf5-100, libhdf5-cpp-100 (>= 1.10.0), libhts2 (>= 1.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), libpbseq (>= 0~20160912), libpbbam
Section: science
Priority: optional
Homepage: https://github.com/PacificBiosciences/blasr
Description: mapping single-molecule sequencing reads
Basic local alignment with successive refinement (BLASR) is a method
for mapping single-molecule sequencing reads against a reference genome.
Such reads are thousands of bases long, with divergence between them
and the genome being dominated by insertion and deletion error.
drwxr-xr-x root/root 0 2018-03-11 17:02 ./
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/bin/
-rwxr-xr-x root/root 145664 2018-03-11 17:02 ./usr/bin/bam2bax
-rwxr-xr-x root/root 145668 2018-03-11 17:02 ./usr/bin/bam2plx
-rwxr-xr-x root/root 494336 2018-03-11 17:02 ./usr/bin/bax2bam
-rwxr-xr-x root/root 478372 2018-03-11 17:02 ./usr/bin/blasr
-rwxr-xr-x root/root 285268 2018-03-11 17:02 ./usr/bin/loadPulses
-rwxr-xr-x root/root 104712 2018-03-11 17:02 ./usr/bin/pls2fasta
-rwxr-xr-x root/root 92256 2018-03-11 17:02 ./usr/bin/samFilter
-rwxr-xr-x root/root 133472 2018-03-11 17:02 ./usr/bin/samtoh5
-rwxr-xr-x root/root 55196 2018-03-11 17:02 ./usr/bin/samtom4
-rwxr-xr-x root/root 51004 2018-03-11 17:02 ./usr/bin/sawriter
-rwxr-xr-x root/root 75592 2018-03-11 17:02 ./usr/bin/sdpMatcher
-rwxr-xr-x root/root 79920 2018-03-11 17:02 ./usr/bin/toAfg
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/share/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/share/doc/blasr/
-rw-r--r-- root/root 193 2016-12-20 10:22 ./usr/share/doc/blasr/NEWS.Debian.gz
-rw-r--r-- root/root 1173 2016-12-16 01:59 ./usr/share/doc/blasr/README.MANUAL.md
-rw-r--r-- root/root 92 2016-12-16 01:59 ./usr/share/doc/blasr/README.md
-rw-r--r-- root/root 95 2016-12-20 10:22 ./usr/share/doc/blasr/TODO.Debian
-rw-r--r-- root/root 1046 2018-03-11 17:02 ./usr/share/doc/blasr/changelog.Debian.gz
-rw-r--r-- root/root 2007 2016-12-20 10:22 ./usr/share/doc/blasr/copyright
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/share/lintian/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 84 2016-12-20 10:22 ./usr/share/lintian/overrides/blasr
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/share/man/
drwxr-xr-x root/root 0 2018-03-11 17:02 ./usr/share/man/man1/
-rw-r--r-- root/root 5732 2018-03-11 17:02 ./usr/share/man/man1/blasr.1.gz
-rw-r--r-- root/root 936 2018-03-11 17:02 ./usr/share/man/man1/loadPulses.1.gz
-rw-r--r-- root/root 925 2018-03-11 17:02 ./usr/share/man/man1/pls2fasta.1.gz
-rw-r--r-- root/root 1397 2018-03-11 17:02 ./usr/share/man/man1/samFilter.1.gz
-rw-r--r-- root/root 925 2018-03-11 17:02 ./usr/share/man/man1/samtoh5.1.gz
-rw-r--r-- root/root 401 2018-03-11 17:02 ./usr/share/man/man1/samtom4.1.gz
-rw-r--r-- root/root 841 2018-03-11 17:02 ./usr/share/man/man1/sawriter.1.gz
-rw-r--r-- root/root 440 2018-03-11 17:02 ./usr/share/man/man1/sdpMatcher.1.gz
-rw-r--r-- root/root 311 2018-03-11 17:02 ./usr/share/man/man1/toAfg.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 118712
Build-Time: 1563
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 1029
Job: blasr_5.3+0-2
Machine Architecture: armhf
Package: blasr
Package-Time: 2652
Source-Version: 5.3+0-2
Space: 118712
Status: successful
Version: 5.3+0-2
--------------------------------------------------------------------------------
Finished at 2018-03-22T05:35:04Z
Build needed 00:44:12, 118712k disc space