Raspbian Package Auto-Building

Build log for blasr (5.3.3+dfsg-2) on armhf

blasr → 5.3.3+dfsg-2 → armhf → 2019-09-06 05:09:46 

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01

+==============================================================================+
| blasr 5.3.3+dfsg-2 (armhf)                   Fri, 06 Sep 2019 04:58:03 +0000 |
+==============================================================================+

Package: blasr
Version: 5.3.3+dfsg-2
Source Version: 5.3.3+dfsg-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-74d7c279-00ec-433d-b5a8-bfe88f3a650a' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.5 MB in 9s (2740 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'blasr' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/blasr.git
Please use:
git clone https://salsa.debian.org/med-team/blasr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 138 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main blasr 5.3.3+dfsg-2 (dsc) [2118 B]
Get:2 http://172.17.0.1/private bullseye-staging/main blasr 5.3.3+dfsg-2 (tar) [124 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main blasr 5.3.3+dfsg-2 (diff) [12.3 kB]
Fetched 138 kB in 0s (1243 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/blasr-1kTmse/blasr-5.3.3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/blasr-1kTmse' 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-c1jJcR/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-c1jJcR/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-c1jJcR/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (8242 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 95 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-c1jJcR/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12050 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-compat (= 12), python, meson, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev (>= 0.18.0~), libpbdata-dev, libgtest-dev, libblasr-dev (>= 5.3.1+dfsg-2)
Filtered Build-Depends: debhelper-compat (= 12), python, meson, pkg-config, libboost-dev, libhdf5-dev, zlib1g-dev, libpbseq-dev, libpbbam-dev (>= 0.18.0~), libpbdata-dev, libgtest-dev, libblasr-dev (>= 5.3.1+dfsg-2)
dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/<<BUILDDIR>>/resolver-c1jJcR/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-c1jJcR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ Sources [575 B]
Get:5 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ Packages [660 B]
Fetched 2568 B in 0s (9950 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 package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gcc-9-base gettext
  gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev
  libaec0 libarchive-zip-perl libblasr libblasr-dev libboost-dev
  libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1
  libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
  libgnutls30 libgssapi-krb5-2 libgtest-dev libhdf5-103 libhdf5-cpp-103
  libhdf5-dev libhts-dev libhts2 libicu63 libjpeg-dev libjpeg62-turbo
  libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
  liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6 libncursesw6
  libnghttp2-14 libpbbam-dev libpbbam0.19.0 libpbdata libpbdata-dev libpbihdf
  libpbihdf-dev libpbseq-dev libpipeline1 libpsl5 libpython-stdlib
  libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
  libpython3.7-minimal libpython3.7-stdlib libreadline8 librtmp1 libsigsegv2
  libssh2-1 libssl-dev libssl1.1 libsub-override-perl libsz2 libtasn1-6
  libtinfo5 libtinfo6 libtool libuchardet0 libxml2 m4 man-db meson
  mime-support ninja-build pkg-config po-debconf python python-minimal python2
  python2-minimal python2.7 python2.7-minimal python3 python3-minimal
  python3-pkg-resources python3.7 python3.7-minimal sensible-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
  libboost-doc libboost1.67-doc libboost-atomic1.67-dev
  libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
  libboost-coroutine1.67-dev libboost-date-time1.67-dev
  libboost-exception1.67-dev libboost-fiber1.67-dev
  libboost-filesystem1.67-dev libboost-graph1.67-dev
  libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
  libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
  libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
  libboost-program-options1.67-dev libboost-python1.67-dev
  libboost-random1.67-dev libboost-regex1.67-dev
  libboost-serialization1.67-dev libboost-signals1.67-dev
  libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
  libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
  libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
  gnutls-bin krb5-doc krb5-user libhdf5-doc liblzma-doc libssl-doc libtool-doc
  gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  libmail-box-perl python-doc python-tk python2-doc python2.7-doc
  binfmt-support python3-doc python3-tk python3-venv python3-setuptools
  python3.7-venv python3.7-doc
Recommended packages:
  curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev
  libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gcc-9-base gettext
  gettext-base googletest groff-base hdf5-helpers intltool-debian libaec-dev
  libaec0 libarchive-zip-perl libblasr libblasr-dev libboost-dev
  libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls libdeflate0 libelf1
  libexpat1 libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
  libgssapi-krb5-2 libgtest-dev libhdf5-103 libhdf5-cpp-103 libhdf5-dev
  libhts-dev libhts2 libicu63 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc
  libmagic1 libmpdec2 libncurses6 libnghttp2-14 libpbbam-dev libpbbam0.19.0
  libpbdata libpbdata-dev libpbihdf libpbihdf-dev libpbseq-dev libpipeline1
  libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal
  libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal
  libpython3.7-stdlib libreadline8 librtmp1 libsigsegv2 libssh2-1 libssl-dev
  libssl1.1 libsub-override-perl libsz2 libtinfo5 libtool libuchardet0 libxml2
  m4 man-db meson mime-support ninja-build pkg-config po-debconf python
  python-minimal python2 python2-minimal python2.7 python2.7-minimal python3
  python3-minimal python3-pkg-resources python3.7 python3.7-minimal
  sbuild-build-depends-blasr-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
  libgnutls30 libncursesw6 libtasn1-6 libtinfo6
4 upgraded, 103 newly installed, 0 to remove and 91 not upgraded.
Need to get 55.4 MB of archives.
After this operation, 295 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-c1jJcR/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [948 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20190803-1 [314 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.8.7-3 [1254 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-minimal armhf 2.7.16-3 [395 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf python2.7-minimal armhf 2.7.16-3 [1090 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python-minimal armhf 2.7.16-1 [21.0 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1c-1 [1259 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.63 [37.7 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.7-1 [77.2 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.1+20190803-1 [318 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.1+20190803-1 [104 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libreadline8 armhf 8.0-3 [138 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-stdlib armhf 2.7.16-3 [1845 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python2.7 armhf 2.7.16-3 [305 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf python2 armhf 2.7.16-1 [41.6 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf python armhf 2.7.16-1 [22.8 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.4-3 [584 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.4-3 [1462 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.3-1 [36.6 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.4-3 [1673 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.4-3 [340 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.3-1 [20.0 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.3-1 [61.5 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libtasn1-6 armhf 4.14-2 [48.2 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libgnutls30 armhf 3.6.9-4 [1081 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf gcc-9-base armhf 9.2.1-4+rpi1 [192 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-5 [253 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-5 [111 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-5 [66.2 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.5.0-1 [22.8 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.5.0-1 [14.1 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-1 [69.7 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.60.6-2 [1109 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20190803-1 [79.3 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.5.4 [1035 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf googletest armhf 1.9.0.20190831-1 [622 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf hdf5-helpers armhf 1.10.4+repack-10 [35.2 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libaec0 armhf 1.0.4-1 [20.0 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libsz2 armhf 1.0.4-1 [6664 B]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libaec-dev armhf 1.0.4-1 [17.8 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.39.2-1 [71.3 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.65.3-1 [298 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.2-1 [48.4 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-11 [255 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libpbbam0.19.0 armhf 0.19.0+dfsg-4+rpi1 [455 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libpbdata armhf 5.3.1+dfsg-2.1 [106 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-4+rpi1 [231 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-103 armhf 1.10.4+repack-10 [1259 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-cpp-103 armhf 1.10.4+repack-10 [121 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libpbihdf armhf 5.3.1+dfsg-2.1 [138 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libblasr armhf 5.3.1+dfsg-2.1 [832 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libpbdata-dev armhf 5.3.1+dfsg-2.1 [175 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libblasr-dev armhf 5.3.1+dfsg-2.1 [1664 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2 [4184 B]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libgtest-dev armhf 1.9.0.20190831-1 [208 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-dev armhf 1.10.4+repack-10 [2221 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.9-11 [4286 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1c-1 [1563 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libpbbam-dev armhf 0.19.0+dfsg-4+rpi1 [93.4 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libpbihdf-dev armhf 5.3.1+dfsg-2.1 [243 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libpbseq-dev all 5.3.1+dfsg-2.1 [4612 B]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf ninja-build armhf 1.9.0-3 [79.6 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 41.1.0-1 [154 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf meson all 0.51.2-1 [336 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 55.4 MB in 10s (5370 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 12050 files and directories currently installed.)
Preparing to unpack .../00-libbsd0_0.10.0-1_armhf.deb ...
Unpacking libbsd0:armhf (0.10.0-1) ...
Selecting previously unselected package libtinfo5:armhf.
Preparing to unpack .../01-libtinfo5_6.1+20190803-1_armhf.deb ...
Unpacking libtinfo5:armhf (6.1+20190803-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../02-bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../03-libuchardet0_0.0.6-3_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.6-3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../04-groff-base_1.22.4-3_armhf.deb ...
Unpacking groff-base (1.22.4-3) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../05-libpipeline1_1.5.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../06-man-db_2.8.7-3_armhf.deb ...
Unpacking man-db (2.8.7-3) ...
Selecting previously unselected package libpython2.7-minimal:armhf.
Preparing to unpack .../07-libpython2.7-minimal_2.7.16-3_armhf.deb ...
Unpacking libpython2.7-minimal:armhf (2.7.16-3) ...
Selecting previously unselected package python2.7-minimal.
Preparing to unpack .../08-python2.7-minimal_2.7.16-3_armhf.deb ...
Unpacking python2.7-minimal (2.7.16-3) ...
Selecting previously unselected package python2-minimal.
Preparing to unpack .../09-python2-minimal_2.7.16-1_armhf.deb ...
Unpacking python2-minimal (2.7.16-1) ...
Selecting previously unselected package python-minimal.
Preparing to unpack .../10-python-minimal_2.7.16-1_armhf.deb ...
Unpacking python-minimal (2.7.16-1) ...
Selecting previously unselected package libssl1.1:armhf.
Preparing to unpack .../11-libssl1.1_1.1.1c-1_armhf.deb ...
Unpacking libssl1.1:armhf (1.1.1c-1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../12-mime-support_3.63_all.deb ...
Unpacking mime-support (3.63) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../13-libexpat1_2.2.7-1_armhf.deb ...
Unpacking libexpat1:armhf (2.2.7-1) ...
Preparing to unpack .../14-libtinfo6_6.1+20190803-1_armhf.deb ...
Unpacking libtinfo6:armhf (6.1+20190803-1) over (6.1+20181013-2) ...
Setting up libtinfo6:armhf (6.1+20190803-1) ...
(Reading database ... 12981 files and directories currently installed.)
Preparing to unpack .../libncursesw6_6.1+20190803-1_armhf.deb ...
Unpacking libncursesw6:armhf (6.1+20190803-1) over (6.1+20181013-2) ...
Setting up libncursesw6:armhf (6.1+20190803-1) ...
Selecting previously unselected package libreadline8:armhf.
(Reading database ... 12981 files and directories currently installed.)
Preparing to unpack .../libreadline8_8.0-3_armhf.deb ...
Unpacking libreadline8:armhf (8.0-3) ...
Selecting previously unselected package libpython2.7-stdlib:armhf.
Preparing to unpack .../libpython2.7-stdlib_2.7.16-3_armhf.deb ...
Unpacking libpython2.7-stdlib:armhf (2.7.16-3) ...
Selecting previously unselected package python2.7.
Preparing to unpack .../python2.7_2.7.16-3_armhf.deb ...
Unpacking python2.7 (2.7.16-3) ...
Selecting previously unselected package libpython2-stdlib:armhf.
Preparing to unpack .../libpython2-stdlib_2.7.16-1_armhf.deb ...
Unpacking libpython2-stdlib:armhf (2.7.16-1) ...
Selecting previously unselected package libpython-stdlib:armhf.
Preparing to unpack .../libpython-stdlib_2.7.16-1_armhf.deb ...
Unpacking libpython-stdlib:armhf (2.7.16-1) ...
Setting up libpython2.7-minimal:armhf (2.7.16-3) ...
Setting up python2.7-minimal (2.7.16-3) ...
Setting up python2-minimal (2.7.16-1) ...
Selecting previously unselected package python2.
(Reading database ... 13511 files and directories currently installed.)
Preparing to unpack .../python2_2.7.16-1_armhf.deb ...
Unpacking python2 (2.7.16-1) ...
Setting up python-minimal (2.7.16-1) ...
Selecting previously unselected package python.
(Reading database ... 13544 files and directories currently installed.)
Preparing to unpack .../python_2.7.16-1_armhf.deb ...
Unpacking python (2.7.16-1) ...
Selecting previously unselected package libpython3.7-minimal:armhf.
Preparing to unpack .../libpython3.7-minimal_3.7.4-3_armhf.deb ...
Unpacking libpython3.7-minimal:armhf (3.7.4-3) ...
Selecting previously unselected package python3.7-minimal.
Preparing to unpack .../python3.7-minimal_3.7.4-3_armhf.deb ...
Unpacking python3.7-minimal (3.7.4-3) ...
Setting up libssl1.1:armhf (1.1.1c-1) ...
Setting up libpython3.7-minimal:armhf (3.7.4-3) ...
Setting up libexpat1:armhf (2.2.7-1) ...
Setting up python3.7-minimal (3.7.4-3) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13798 files and directories currently installed.)
Preparing to unpack .../python3-minimal_3.7.3-1_armhf.deb ...
Unpacking python3-minimal (3.7.3-1) ...
Selecting previously unselected package libmpdec2:armhf.
Preparing to unpack .../libmpdec2_2.4.2-2_armhf.deb ...
Unpacking libmpdec2:armhf (2.4.2-2) ...
Selecting previously unselected package libpython3.7-stdlib:armhf.
Preparing to unpack .../libpython3.7-stdlib_3.7.4-3_armhf.deb ...
Unpacking libpython3.7-stdlib:armhf (3.7.4-3) ...
Selecting previously unselected package python3.7.
Preparing to unpack .../python3.7_3.7.4-3_armhf.deb ...
Unpacking python3.7 (3.7.4-3) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../libpython3-stdlib_3.7.3-1_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.7.3-1) ...
Setting up python3-minimal (3.7.3-1) ...
Selecting previously unselected package python3.
(Reading database ... 14211 files and directories currently installed.)
Preparing to unpack .../python3_3.7.3-1_armhf.deb ...
Unpacking python3 (3.7.3-1) ...
Preparing to unpack .../libtasn1-6_4.14-2_armhf.deb ...
Unpacking libtasn1-6:armhf (4.14-2) over (4.13-3) ...
Setting up libtasn1-6:armhf (4.14-2) ...
(Reading database ... 14244 files and directories currently installed.)
Preparing to unpack .../libgnutls30_3.6.9-4_armhf.deb ...
Unpacking libgnutls30:armhf (3.6.9-4) over (3.6.7-4) ...
Setting up libgnutls30:armhf (3.6.9-4) ...
Selecting previously unselected package gcc-9-base:armhf.
(Reading database ... 14244 files and directories currently installed.)
Preparing to unpack .../00-gcc-9-base_9.2.1-4+rpi1_armhf.deb ...
Unpacking gcc-9-base:armhf (9.2.1-4+rpi1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.12_all.deb ...
Unpacking sensible-utils (0.0.12) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.37-5_armhf.deb ...
Unpacking libmagic-mgc (1:5.37-5) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../03-libmagic1_1%3a5.37-5_armhf.deb ...
Unpacking libmagic1:armhf (1:5.37-5) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.37-5_armhf.deb ...
Unpacking file (1:5.37-5) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.19.8.1-9_armhf.deb ...
Unpacking gettext-base (0.19.8.1-9) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../06-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../07-m4_1.4.18-2_armhf.deb ...
Unpacking m4 (1.4.18-2) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../08-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../09-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../10-automake_1%3a1.16.1-4_all.deb ...
Unpacking automake (1:1.16.1-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../11-autopoint_0.19.8.1-9_all.deb ...
Unpacking autopoint (0.19.8.1-9) ...
Selecting previously unselected package libtool.
Preparing to unpack .../12-libtool_2.4.6-9_all.deb ...
Unpacking libtool (2.4.6-9) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../13-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../14-libarchive-zip-perl_1.64-1_all.deb ...
Unpacking libarchive-zip-perl (1.64-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../15-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../16-libfile-stripnondeterminism-perl_1.5.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.5.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../17-dh-strip-nondeterminism_1.5.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.5.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../18-libelf1_0.176-1.1_armhf.deb ...
Unpacking libelf1:armhf (0.176-1.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../19-dwz_0.13-1_armhf.deb ...
Unpacking dwz (0.13-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../20-libglib2.0-0_2.60.6-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.60.6-2) ...
Selecting previously unselected package libicu63:armhf.
Preparing to unpack .../21-libicu63_63.2-2_armhf.deb ...
Unpacking libicu63:armhf (63.2-2) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../22-libxml2_2.9.4+dfsg1-7+b2_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../23-libcroco3_0.6.13-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.13-1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../24-libncurses6_6.1+20190803-1_armhf.deb ...
Unpacking libncurses6:armhf (6.1+20190803-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../25-gettext_0.19.8.1-9_armhf.deb ...
Unpacking gettext (0.19.8.1-9) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../26-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../27-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../28-debhelper_12.5.4_all.deb ...
Unpacking debhelper (12.5.4) ...
Selecting previously unselected package googletest:armhf.
Preparing to unpack .../29-googletest_1.9.0.20190831-1_armhf.deb ...
Unpacking googletest:armhf (1.9.0.20190831-1) ...
Selecting previously unselected package hdf5-helpers.
Preparing to unpack .../30-hdf5-helpers_1.10.4+repack-10_armhf.deb ...
Unpacking hdf5-helpers (1.10.4+repack-10) ...
Selecting previously unselected package libaec0:armhf.
Preparing to unpack .../31-libaec0_1.0.4-1_armhf.deb ...
Unpacking libaec0:armhf (1.0.4-1) ...
Selecting previously unselected package libsz2:armhf.
Preparing to unpack .../32-libsz2_1.0.4-1_armhf.deb ...
Unpacking libsz2:armhf (1.0.4-1) ...
Selecting previously unselected package libaec-dev:armhf.
Preparing to unpack .../33-libaec-dev_1.0.4-1_armhf.deb ...
Unpacking libaec-dev:armhf (1.0.4-1) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../34-libkeyutils1_1.6-6_armhf.deb ...
Unpacking libkeyutils1:armhf (1.6-6) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../35-libkrb5support0_1.17-6+b1_armhf.deb ...
Unpacking libkrb5support0:armhf (1.17-6+b1) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../36-libk5crypto3_1.17-6+b1_armhf.deb ...
Unpacking libk5crypto3:armhf (1.17-6+b1) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../37-libkrb5-3_1.17-6+b1_armhf.deb ...
Unpacking libkrb5-3:armhf (1.17-6+b1) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../38-libgssapi-krb5-2_1.17-6+b1_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.17-6+b1) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../39-libnghttp2-14_1.39.2-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.39.2-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../40-libpsl5_0.20.2-2_armhf.deb ...
Unpacking libpsl5:armhf (0.20.2-2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../41-librtmp1_2.4+20151223.gitfa8646d.1-2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../42-libssh2-1_1.8.0-2.1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-2.1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../43-libcurl3-gnutls_7.65.3-1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.65.3-1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../44-libdeflate0_1.2-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.2-1) ...
Selecting previously unselected package libhts2:armhf.
Preparing to unpack .../45-libhts2_1.9-11_armhf.deb ...
Unpacking libhts2:armhf (1.9-11) ...
Selecting previously unselected package libpbbam0.19.0:armhf.
Preparing to unpack .../46-libpbbam0.19.0_0.19.0+dfsg-4+rpi1_armhf.deb ...
Unpacking libpbbam0.19.0:armhf (0.19.0+dfsg-4+rpi1) ...
Selecting previously unselected package libpbdata:armhf.
Preparing to unpack .../47-libpbdata_5.3.1+dfsg-2.1_armhf.deb ...
Unpacking libpbdata:armhf (5.3.1+dfsg-2.1) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../48-libgfortran5_9.2.1-4+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (9.2.1-4+rpi1) ...
Selecting previously unselected package libhdf5-103:armhf.
Preparing to unpack .../49-libhdf5-103_1.10.4+repack-10_armhf.deb ...
Unpacking libhdf5-103:armhf (1.10.4+repack-10) ...
Selecting previously unselected package libhdf5-cpp-103:armhf.
Preparing to unpack .../50-libhdf5-cpp-103_1.10.4+repack-10_armhf.deb ...
Unpacking libhdf5-cpp-103:armhf (1.10.4+repack-10) ...
Selecting previously unselected package libpbihdf:armhf.
Preparing to unpack .../51-libpbihdf_5.3.1+dfsg-2.1_armhf.deb ...
Unpacking libpbihdf:armhf (5.3.1+dfsg-2.1) ...
Selecting previously unselected package libblasr:armhf.
Preparing to unpack .../52-libblasr_5.3.1+dfsg-2.1_armhf.deb ...
Unpacking libblasr:armhf (5.3.1+dfsg-2.1) ...
Selecting previously unselected package libpbdata-dev:armhf.
Preparing to unpack .../53-libpbdata-dev_5.3.1+dfsg-2.1_armhf.deb ...
Unpacking libpbdata-dev:armhf (5.3.1+dfsg-2.1) ...
Selecting previously unselected package libblasr-dev:armhf.
Preparing to unpack .../54-libblasr-dev_5.3.1+dfsg-2.1_armhf.deb ...
Unpacking libblasr-dev:armhf (5.3.1+dfsg-2.1) ...
Selecting previously unselected package libboost1.67-dev:armhf.
Preparing to unpack .../55-libboost1.67-dev_1.67.0-13_armhf.deb ...
Unpacking libboost1.67-dev:armhf (1.67.0-13) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../56-libboost-dev_1.67.0.2_armhf.deb ...
Unpacking libboost-dev:armhf (1.67.0.2) ...
Selecting previously unselected package libgtest-dev:armhf.
Preparing to unpack .../57-libgtest-dev_1.9.0.20190831-1_armhf.deb ...
Unpacking libgtest-dev:armhf (1.9.0.20190831-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../58-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../59-libjpeg62-turbo_1%3a1.5.2-2+b1_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Selecting previously unselected package libjpeg62-turbo-dev:armhf.
Preparing to unpack .../60-libjpeg62-turbo-dev_1%3a1.5.2-2+b1_armhf.deb ...
Unpacking libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Selecting previously unselected package libjpeg-dev.
Preparing to unpack .../61-libjpeg-dev_1%3a1.5.2-2_all.deb ...
Unpacking libjpeg-dev (1:1.5.2-2) ...
Selecting previously unselected package libhdf5-dev.
Preparing to unpack .../62-libhdf5-dev_1.10.4+repack-10_armhf.deb ...
Unpacking libhdf5-dev (1.10.4+repack-10) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../63-liblzma-dev_5.2.4-1_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.4-1) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../64-libhts-dev_1.9-11_armhf.deb ...
Unpacking libhts-dev:armhf (1.9-11) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../65-libssl-dev_1.1.1c-1_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.1c-1) ...
Selecting previously unselected package libpbbam-dev.
Preparing to unpack .../66-libpbbam-dev_0.19.0+dfsg-4+rpi1_armhf.deb ...
Unpacking libpbbam-dev (0.19.0+dfsg-4+rpi1) ...
Selecting previously unselected package libpbihdf-dev:armhf.
Preparing to unpack .../67-libpbihdf-dev_5.3.1+dfsg-2.1_armhf.deb ...
Unpacking libpbihdf-dev:armhf (5.3.1+dfsg-2.1) ...
Selecting previously unselected package libpbseq-dev.
Preparing to unpack .../68-libpbseq-dev_5.3.1+dfsg-2.1_all.deb ...
Unpacking libpbseq-dev (5.3.1+dfsg-2.1) ...
Selecting previously unselected package ninja-build.
Preparing to unpack .../69-ninja-build_1.9.0-3_armhf.deb ...
Unpacking ninja-build (1.9.0-3) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../70-python3-pkg-resources_41.1.0-1_all.deb ...
Unpacking python3-pkg-resources (41.1.0-1) ...
Selecting previously unselected package meson.
Preparing to unpack .../71-meson_0.51.2-1_all.deb ...
Unpacking meson (0.51.2-1) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../72-pkg-config_0.29-6_armhf.deb ...
Unpacking pkg-config (0.29-6) ...
Selecting previously unselected package sbuild-build-depends-blasr-dummy.
Preparing to unpack .../73-sbuild-build-depends-blasr-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-blasr-dummy (0.invalid.0) ...
Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up libkeyutils1:armhf (1.6-6) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up mime-support (3.63) ...
Setting up hdf5-helpers (1.10.4+repack-10) ...
Setting up libmagic-mgc (1:5.37-5) ...
Setting up libarchive-zip-perl (1.64-1) ...
Setting up libglib2.0-0:armhf (2.60.6-2) ...
No schema files found: doing nothing.
Setting up libreadline8:armhf (8.0-3) ...
Setting up libnghttp2-14:armhf (1.39.2-1) ...
Setting up libmagic1:armhf (1:5.37-5) ...
Setting up libdeflate0:armhf (1.2-1) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up file (1:5.37-5) ...
Setting up googletest:armhf (1.9.0.20190831-1) ...
Setting up libaec0:armhf (1.0.4-1) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up ninja-build (1.9.0-3) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up libpython2.7-stdlib:armhf (2.7.16-3) ...
Setting up autotools-dev (20180224.1) ...
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up libncurses6:armhf (6.1+20190803-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libssl-dev:armhf (1.1.1c-1) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up pkg-config (0.29-6) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libboost-dev:armhf (1.67.0.2) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20190803-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Setting up libsz2:armhf (1.0.4-1) ...
Setting up gcc-9-base:armhf (9.2.1-4+rpi1) ...
Setting up libfile-stripnondeterminism-perl (1.5.0-1) ...
Setting up libpython3.7-stdlib:armhf (3.7.4-3) ...
Setting up libgtest-dev:armhf (1.9.0.20190831-1) ...
Setting up python2.7 (2.7.16-3) ...
Setting up libtool (2.4.6-9) ...
Setting up libpython2-stdlib:armhf (2.7.16-1) ...
Setting up libaec-dev:armhf (1.0.4-1) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up m4 (1.4.18-2) ...
Setting up python2 (2.7.16-1) ...
Setting up libpython-stdlib:armhf (2.7.16-1) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up libgfortran5:armhf (9.2.1-4+rpi1) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.13-1) ...
Setting up groff-base (1.22.4-3) ...
Setting up python (2.7.16-1) ...
Setting up libpython3-stdlib:armhf (3.7.3-1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.7 (3.7.4-3) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libcurl3-gnutls:armhf (7.65.3-1) ...
Setting up python3 (3.7.3-1) ...
Setting up man-db (2.8.7-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhdf5-103:armhf (1.10.4+repack-10) ...
Setting up python3-pkg-resources (41.1.0-1) ...
Setting up libhts2:armhf (1.9-11) ...
Setting up po-debconf (1.0.21) ...
Setting up libhdf5-cpp-103:armhf (1.10.4+repack-10) ...
Setting up libhts-dev:armhf (1.9-11) ...
Setting up meson (0.51.2-1) ...
Setting up libhdf5-dev (1.10.4+repack-10) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libpbbam0.19.0:armhf (0.19.0+dfsg-4+rpi1) ...
Setting up libpbbam-dev (0.19.0+dfsg-4+rpi1) ...
Setting up libpbdata:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbihdf:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbdata-dev:armhf (5.3.1+dfsg-2.1) ...
Setting up libblasr:armhf (5.3.1+dfsg-2.1) ...
Setting up libblasr-dev:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbihdf-dev:armhf (5.3.1+dfsg-2.1) ...
Setting up libpbseq-dev (5.3.1+dfsg-2.1) ...
Setting up debhelper (12.5.4) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.5.0-1) ...
Setting up sbuild-build-depends-blasr-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-10+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.15.0-58-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-16+rpi1 dpkg-dev_1.19.7 g++-8_8.3.0-6+rpi1 gcc-8_8.3.0-6+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16+rpi1 binutils-arm-linux-gnueabihf_2.31.1-16+rpi1 binutils-common_2.31.1-16+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.1 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-6+rpi1 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.5.4 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.5.0-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.37-5 findutils_4.6.0+git+20190209-2 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-6+rpi1 gcc_4:8.3.0-1+rpi2 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-6+rpi1 gcc-8-base_8.3.0-6+rpi1 gcc-9-base_9.2.1-4+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 googletest_1.9.0.20190831-1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hdf5-helpers_1.10.4+repack-10 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-6+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-6+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi1 libblasr_5.3.1+dfsg-2.1 libblasr-dev_5.3.1+dfsg-2.1 libblkid1_2.33.1-0.1 libboost-dev_1.67.0.2 libboost1.67-dev_1.67.0-13 libbsd0_0.10.0-1 libbz2-1.0_1.0.6-9.1 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-6+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.13-1 libcurl3-gnutls_7.65.3-1 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdeflate0_1.2-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.7-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.5.0-1 libgcc-8-dev_8.3.0-6+rpi1 libgcc1_1:8.3.0-6+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libgfortran5_9.2.1-4+rpi1 libglib2.0-0_2.60.6-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.9-4 libgomp1_8.3.0-6+rpi1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-6+b1 libgtest-dev_1.9.0.20190831-1 libhdf5-103_1.10.4+repack-10 libhdf5-cpp-103_1.10.4+repack-10 libhdf5-dev_1.10.4+repack-10 libhogweed4_3.4.1-1 libhts-dev_1.9-11 libhts2_1.9-11 libicu63_63.2-2 libidn2-0_2.0.5-1 libisl19_0.20-2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-5 libmagic1_1:5.37-5 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20190803-1 libncursesw6_6.1+20190803-1 libnettle6_3.4.1-1 libnghttp2-14_1.39.2-1 libnpth0_1.6-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpbbam-dev_0.19.0+dfsg-4+rpi1 libpbbam0.19.0_0.19.0+dfsg-4+rpi1 libpbdata_5.3.1+dfsg-2.1 libpbdata-dev_5.3.1+dfsg-2.1 libpbihdf_5.3.1+dfsg-2.1 libpbihdf-dev_5.3.1+dfsg-2.1 libpbseq-dev_5.3.1+dfsg-2.1 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpsl5_0.20.2-2 libpython-stdlib_2.7.16-1 libpython2-stdlib_2.7.16-1 libpython2.7-minimal_2.7.16-3 libpython2.7-stdlib_2.7.16-3 libpython3-stdlib_3.7.3-1 libpython3.7-minimal_3.7.4-3 libpython3.7-stdlib_3.7.4-3 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3 libss2_1.44.5-1 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1c-1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_241-5+rpi1 libsz2_1.0.4-1 libtasn1-6_4.14-2 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20190803-1 libtinfo6_6.1+20190803-1 libtool_2.4.6-9 libubsan1_8.3.0-6+rpi1 libuchardet0_0.0.6-3 libudev1_241-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b2 libzstd1_1.3.8+dfsg-3+rpi1 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.7-3 mawk_1.3.3-17 meson_0.51.2-1 mime-support_3.63 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 ninja-build_1.9.0-3 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 pkg-config_0.29-6 po-debconf_1.0.21 python_2.7.16-1 python-minimal_2.7.16-1 python2_2.7.16-1 python2-minimal_2.7.16-1 python2.7_2.7.16-3 python2.7-minimal_2.7.16-3 python3_3.7.3-1 python3-minimal_3.7.3-1 python3-pkg-resources_41.1.0-1 python3.7_3.7.4-3 python3.7-minimal_3.7.4-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-blasr-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Sep  1 05:58:18 2019 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./blasr_5.3.3+dfsg-2.dsc
dpkg-source: info: extracting blasr in /<<BUILDDIR>>/blasr-5.3.3+dfsg
dpkg-source: info: unpacking blasr_5.3.3+dfsg.orig.tar.xz
dpkg-source: info: unpacking blasr_5.3.3+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_pblibs.patch
dpkg-source: info: applying 2to3.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-74d7c279-00ec-433d-b5a8-bfe88f3a650a
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package blasr
dpkg-buildpackage: info: source version 5.3.3+dfsg-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean --buildsystem=meson
   dh_auto_clean -O--buildsystem=meson
   dh_autoreconf_clean -O--buildsystem=meson
   dh_clean -O--buildsystem=meson
 debian/rules build-arch
dh build-arch --buildsystem=meson
   dh_update_autotools_config -a -O--buildsystem=meson
   dh_autoreconf -a -O--buildsystem=meson
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3.3+dfsg'
LDFLAGS="-L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lhdf5_cpp -lhdf5" CPPFLAGS="-isystem /usr/include/hdf5/serial" meson -Dtests=false -Dprefix=/usr build .
The Meson build system
Version: 0.51.2
Source dir: /<<BUILDDIR>>/blasr-5.3.3+dfsg
Build dir: /<<BUILDDIR>>/blasr-5.3.3+dfsg/build
Build type: native build
Project name: blasr
Project version: 5.3.3
Appending CXXFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1'
Appending LDFLAGS from environment: '-L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lhdf5_cpp -lhdf5'
Appending CPPFLAGS from environment: '-isystem /usr/include/hdf5/serial'
Appending CXXFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pbseq -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1'
Appending LDFLAGS from environment: '-L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -lhdf5_cpp -lhdf5'
Appending CPPFLAGS from environment: '-isystem /usr/include/hdf5/serial'
C++ compiler for the host machine: c++ (gcc 8.3.0 "c++ (Raspbian 8.3.0-6+rpi1) 8.3.0")
Build machine cpu family: arm
Build machine cpu: armv8l
Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor -Wdelete-non-virtual-dtor: YES 
Compiler for C++ supports arguments -Wno-non-virtual-dtor -Wnon-virtual-dtor: YES 
Compiler for C++ supports arguments -Wno-unused-but-set-variable -Wunused-but-set-variable: YES 
Compiler for C++ supports arguments -Wno-unused-variable -Wunused-variable: YES 
Run-time dependency threads found: YES 
Run-time dependency Boost found: YES 1.67
Found pkg-config: /usr/bin/pkg-config (0.29)
Run-time dependency pbbam found: YES 0.19.0
Run-time dependency libblasr found: YES 5.3.1
Run-time dependency zlib found: YES 1.2.11
Library pbdata found: YES
Library pbihdf found: YES
Configuring BlasrVersion.h using configuration
Build targets in project: 5
Found ninja-1.9.0 at /usr/bin/ninja
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3.3+dfsg'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3.3+dfsg'
ln -s build obj-arm-linux-gnueabihf
dh_auto_build
	cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v
[1/25] /usr/bin/meson --internal vcstagger ../BlasrGitHash.h.in BlasrGitHash.h '' /<<BUILDDIR>>/blasr-5.3.3+dfsg @BLASR_GIT_SHA1@ '(.*)' /<<BUILDDIR>>/blasr-5.3.3+dfsg/git describe --always '--dirty=*'
[2/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -MF 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o.d' -o 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' -c ../extrautils/BwtToSuffixArray.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/bwt/Occ.hpp:8,
                 from /usr/include/pbseq/alignment/bwt/BWT.hpp:7,
                 from ../extrautils/BwtToSuffixArray.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[3/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SAModify.cpp.o' -MF 'blasr_impl@sta/extrautils_SAModify.cpp.o.d' -o 'blasr_impl@sta/extrautils_SAModify.cpp.o' -c ../extrautils/SAModify.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21,
                 from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8,
                 from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13,
                 from ../extrautils/SAModify.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[4/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -MF 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o.d' -o 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' -c ../extrautils/SuffixArrayToBWT.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/bwt/Occ.hpp:8,
                 from /usr/include/pbseq/alignment/bwt/BWT.hpp:7,
                 from ../extrautils/SuffixArrayToBWT.cpp:4:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from ../extrautils/SuffixArrayToBWT.cpp:4:
/usr/include/pbseq/alignment/bwt/BWT.hpp: In member function ‘void Bwt<T_BWT_Sequence, T_DNASequence>::InitializeDNACharacterCount() [with T_BWT_Sequence = PackedDNASequence; T_DNASequence = FASTASequence]’:
/usr/include/pbseq/alignment/bwt/BWT.hpp:192:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
                     charCount[0]++;
                     ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:193:17: note: here
                 case 0:  //A
                 ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:194:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
                     charCount[1]++;
                     ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:195:17: note: here
                 case 1:  //C
                 ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:196:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
                     charCount[2]++;
                     ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:197:17: note: here
                 case 2:  //G
                 ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:198:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
                     charCount[3]++;
                     ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:199:17: note: here
                 case 3:  //T
                 ^~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:200:21: warning: this statement may fall through [-Wimplicit-fallthrough=]
                     charCount[4]++;
                     ^~~~~~~~~
/usr/include/pbseq/alignment/bwt/BWT.hpp:201:17: note: here
                 case 4:  //N
                 ^~~~
[5/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -MF 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o.d' -o 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' -c ../extrautils/ExciseRepeats.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
                 from /usr/include/pbseq/pbdata/FASTAReader.hpp:7,
                 from ../extrautils/ExciseRepeats.cpp:3:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[6/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_Evolve.cpp.o' -MF 'blasr_impl@sta/extrautils_Evolve.cpp.o.d' -o 'blasr_impl@sta/extrautils_Evolve.cpp.o' -c ../extrautils/Evolve.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
                 from /usr/include/pbseq/pbdata/FASTAReader.hpp:7,
                 from ../extrautils/Evolve.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[7/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -MF 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o.d' -o 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' -c ../extrautils/SimpleShredder.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
                 from /usr/include/pbseq/pbdata/FASTAReader.hpp:7,
                 from ../extrautils/SimpleShredder.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[8/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -MF 'blasr_impl@sta/extrautils_SWMatcher.cpp.o.d' -o 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' -c ../extrautils/SWMatcher.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../extrautils/SWMatcher.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[9/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_SALS.cpp.o' -MF 'blasr_impl@sta/extrautils_SALS.cpp.o.d' -o 'blasr_impl@sta/extrautils_SALS.cpp.o' -c ../extrautils/SALS.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/sorting/MultikeyQuicksort.hpp:21,
                 from /usr/include/pbseq/alignment/algorithms/sorting/LightweightSuffixArray.hpp:8,
                 from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:13,
                 from ../extrautils/SALS.cpp:4:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[10/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -MF 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o.d' -o 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' -c ../extrautils/BuildSequenceDB.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/pbdata/FASTASequence.hpp:13,
                 from /usr/include/pbseq/pbdata/FASTAReader.hpp:7,
                 from ../extrautils/BuildSequenceDB.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[11/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -MF 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o.d' -o 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' -c ../extrautils/PrintTupleCountTable.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/tuples/DNATuple.hpp:15,
                 from /usr/include/pbseq/alignment/tuples/CompressedDNATuple.hpp:4,
                 from ../extrautils/PrintTupleCountTable.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[12/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -MF 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o.d' -o 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' -c ../extrautils/StoreQualityByContextFromCmpH5.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19,
                 from /usr/include/pbseq/hdf/HDFArray.hpp:9,
                 from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
                 from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
                 from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217,
                 from /usr/include/pbseq/hdf/HDFArray.hpp:9,
                 from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
                 from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
                 from ../extrautils/StoreQualityByContextFromCmpH5.cpp:2:
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = std::__cxx11::basic_string<char>; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:67:9:   required from ‘void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]’
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
     } catch (H5::DataSetIException e) {
       ^~~~~
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:67:9:   required from ‘void HDFArray<T>::Write(const T*, int) [with T = unsigned int]’
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:51:9:   required from ‘void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’
/usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
[13/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToM4.cpp.o' -MF 'blasr_impl@sta/utils_SamToM4.cpp.o.d' -o 'blasr_impl@sta/utils_SamToM4.cpp.o' -c ../utils/SamToM4.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SamToM4.cpp:21:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from /usr/include/c++/8/vector:69,
                 from /usr/include/pbbam/BamRecord.h:15,
                 from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SamToM4.cpp:21:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’ changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
[14/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamFilter.cpp.o' -MF 'blasr_impl@sta/utils_SamFilter.cpp.o.d' -o 'blasr_impl@sta/utils_SamFilter.cpp.o' -c ../utils/SamFilter.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SamFilter.cpp:32:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from /usr/include/c++/8/vector:69,
                 from /usr/include/pbbam/BamRecord.h:15,
                 from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SamFilter.cpp:32:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’ changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
[15/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_PulseToFasta.cpp.o' -MF 'blasr_impl@sta/utils_PulseToFasta.cpp.o.d' -o 'blasr_impl@sta/utils_PulseToFasta.cpp.o' -c ../utils/PulseToFasta.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19,
                 from /usr/include/pbseq/hdf/HDFArray.hpp:9,
                 from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
                 from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
                 from ../utils/PulseToFasta.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from ../utils/PulseToFasta.cpp:8:
/usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’:
/usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
         } catch (DataSetIException e) {
                                    ^
In file included from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
                 from ../utils/PulseToFasta.cpp:5:
/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’:
../utils/PulseToFasta.cpp:157:41:   required from here
/usr/include/pbseq/hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
         } catch (H5::DataSetIException e) {
           ^~~~~
/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader<T_Sequence>::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’:
/usr/include/pbseq/hdf/HDFBasReader.hpp:726:25:   required from ‘int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’
../utils/PulseToFasta.cpp:157:41:   required from here
/usr/include/pbseq/hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
         } catch (H5::DataSetIException e) {
           ^~~~~
[16/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -MF 'blasr_impl@sta/utils_SamToCmpH5.cpp.o.d' -o 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' -c ../utils/SamToCmpH5.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:9,
                 from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
                 from ../utils/SamToCmpH5.cpp:3:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217,
                 from /usr/include/pbseq/hdf/HDFArray.hpp:9,
                 from /usr/include/pbseq/hdf/HDFAlnGroupGroup.hpp:6,
                 from /usr/include/pbseq/hdf/HDFCmpFile.hpp:12,
                 from /usr/include/pbseq/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp:7,
                 from ../utils/SamToCmpH5.cpp:5:
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = std::__cxx11::basic_string<char>; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:67:9:   required from ‘void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]’
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
     } catch (H5::DataSetIException e) {
       ^~~~~
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:67:9:   required from ‘void HDFArray<T>::Write(const T*, int) [with T = unsigned int]’
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:51:9:   required from ‘void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’
/usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
In file included from /usr/include/c++/8/vector:69,
                 from /usr/include/pbseq/alignment/datastructures/alignment/Alignment.hpp:5,
                 from /usr/include/pbseq/alignment/datastructures/alignment/AlignmentCandidate.hpp:6,
                 from ../utils/SamToCmpH5.cpp:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {SAMFullReferenceSequence}; _Tp = SAMFullReferenceSequence; _Alloc = std::allocator<SAMFullReferenceSequence>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<SAMFullReferenceSequence*, std::vector<SAMFullReferenceSequence, std::allocator<SAMFullReferenceSequence> > >’ changed in GCC 7.1
    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
    ^~~~~~~~~~~~~~~~~
[17/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -MF 'blasr_impl@sta/utils_SDPMatcher.cpp.o.d' -o 'blasr_impl@sta/utils_SDPMatcher.cpp.o' -c ../utils/SDPMatcher.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SDPMatcher.cpp:8:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from /usr/include/c++/8/vector:69,
                 from /usr/include/pbbam/BamRecord.h:15,
                 from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PositionDNATuple&}; _Tp = PositionDNATuple; _Alloc = std::allocator<PositionDNATuple>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
                 from /usr/include/pbbam/BamRecord.h:15,
                 from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/bits/stl_vector.h: In function ‘int SequenceToTupleList(Sequence&, TupleMetrics&, TupleList<PositionDNATuple>&) [with Sequence = DNASequence]’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from /usr/include/pbbam/internal/QualityValues.inl:8,
                 from /usr/include/pbbam/QualityValues.h:132,
                 from /usr/include/pbbam/BamRecordImpl.h:20,
                 from /usr/include/pbbam/BamRecord.h:19,
                 from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from /usr/include/pbbam/internal/QualityValues.inl:8,
                 from /usr/include/pbbam/QualityValues.h:132,
                 from /usr/include/pbbam/BamRecordImpl.h:20,
                 from /usr/include/pbbam/BamRecord.h:19,
                 from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Distance = int; _Tp = PositionDNATuple; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from /usr/include/pbbam/internal/QualityValues.inl:8,
                 from /usr/include/pbbam/QualityValues.h:132,
                 from /usr/include/pbbam/BamRecordImpl.h:20,
                 from /usr/include/pbbam/BamRecord.h:19,
                 from /usr/include/pbseq/pbdata/DNASequence.hpp:17,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from ../utils/SDPMatcher.cpp:8:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __heap_select(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __comp);
       ~~~~~~~                     
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
       std::__heap_select(__first, __middle, __last, __comp);
       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTASequence; T_TargetSequence = FASTASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, DNASequence>; T_TupleList = TupleList<PositionDNATuple>]’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[18/25] c++ -Isawriter@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'sawriter@exe/utils_SAWriter.cpp.o' -MF 'sawriter@exe/utils_SAWriter.cpp.o.d' -o 'sawriter@exe/utils_SAWriter.cpp.o' -c ../utils/SAWriter.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/algorithms/sorting/Karkkainen.hpp:4,
                 from ../utils/SAWriter.cpp:5:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
[19/25] c++ -ItoAfg@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'toAfg@exe/utils_ToAfg.cpp.o' -MF 'toAfg@exe/utils_ToAfg.cpp.o.d' -o 'toAfg@exe/utils_ToAfg.cpp.o' -c ../utils/ToAfg.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:19,
                 from /usr/include/pbseq/hdf/HDFArray.hpp:9,
                 from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
                 from /usr/include/pbseq/alignment/files/ReaderAgglomerate.hpp:8,
                 from ../utils/ToAfg.cpp:6:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from ../utils/ToAfg.cpp:9:
/usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’:
/usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
         } catch (DataSetIException e) {
                                    ^
[20/25] c++ -Iblasr_impl@sta -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -fPIC -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -MD -MQ 'blasr_impl@sta/utils_LoadPulses.cpp.o' -MF 'blasr_impl@sta/utils_LoadPulses.cpp.o.d' -o 'blasr_impl@sta/utils_LoadPulses.cpp.o' -c ../utils/LoadPulses.cpp
In file included from /usr/include/pbseq/pbdata/DNASequence.hpp:4,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp:13,
                 from /usr/include/pbseq/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp:42,
                 from /usr/include/pbseq/alignment/algorithms/alignment/AlignmentUtils.hpp:6,
                 from /usr/include/pbseq/alignment/datastructures/alignment/ByteAlignment.h:6,
                 from ../utils/LoadPulses.cpp:11:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from ../utils/LoadPulses.cpp:19:
/usr/include/pbseq/hdf/HDFPlsReader.hpp: In member function ‘int HDFPlsReader::GetNextFlattenedToBase(SMRTSequence&, int*)’:
/usr/include/pbseq/hdf/HDFPlsReader.hpp:549:36: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
         } catch (DataSetIException e) {
                                    ^
In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217,
                 from /usr/include/pbseq/hdf/HDFArray.hpp:9,
                 from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
                 from ../utils/LoadPulses.cpp:16:
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = std::__cxx11::basic_string<char>; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:67:9:   required from ‘void HDFArray<T>::Write(const T*, int) [with T = std::__cxx11::basic_string<char>]’
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:36:43:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
     } catch (H5::DataSetIException e) {
       ^~~~~
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned int; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:67:9:   required from ‘void HDFArray<T>::Write(const T*, int) [with T = unsigned int]’
/usr/include/pbseq/hdf/HDFFileLogGroup.hpp:44:29:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = float; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:51:9:   required from ‘void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = float; UInt = unsigned int]’
/usr/include/pbseq/hdf/HDFMovieInfoGroup.hpp:81:60:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
In file included from ../utils/LoadPulses.cpp:16:
/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’:
/usr/include/pbseq/hdf/HDFBasReader.hpp:135:28:   required from ‘DNALength T_HDFBasReader<T_Sequence>::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]’
../utils/LoadPulses.cpp:680:59:   required from here
/usr/include/pbseq/hdf/HDFBasReader.hpp:760:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
         } catch (H5::DataSetIException e) {
           ^~~~~
In file included from /usr/include/pbseq/hdf/BufferedHDFArray.hpp:217,
                 from /usr/include/pbseq/hdf/HDFArray.hpp:9,
                 from /usr/include/pbseq/hdf/HDFBasReader.hpp:13,
                 from ../utils/LoadPulses.cpp:16:
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = unsigned char; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:51:9:   required from ‘void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = unsigned char; UInt = unsigned int]’
../utils/LoadPulses.cpp:1525:62:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
     } catch (H5::DataSetIException e) {
       ^~~~~
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = char; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:51:9:   required from ‘void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = char; UInt = unsigned int]’
../utils/LoadPulses.cpp:1537:64:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp: In instantiation of ‘void BufferedHDFArray<T>::Flush(bool, DSLength) [with T = short unsigned int; DSLength = long long unsigned int]’:
/usr/include/pbseq/hdf/HDFArray.hpp:51:9:   required from ‘void HDFArray<T>::WriteToPos(const T*, int, UInt) [with T = short unsigned int; UInt = unsigned int]’
../utils/LoadPulses.cpp:1547:76:   required from here
/usr/include/pbseq/hdf/BufferedHDFArrayImpl.hpp:146:7: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
In file included from ../utils/LoadPulses.cpp:16:
/usr/include/pbseq/hdf/HDFBasReader.hpp: In instantiation of ‘int T_HDFBasReader<T_Sequence>::GetNext(FASTQSequence&) [with T_Sequence = FASTASequence]’:
/usr/include/pbseq/hdf/HDFBasReader.hpp:726:25:   required from ‘int T_HDFBasReader<T_Sequence>::GetNext(SMRTSequence&) [with T_Sequence = FASTASequence]’
/usr/include/pbseq/hdf/HDFBasReader.hpp:135:28:   required from ‘DNALength T_HDFBasReader<T_Sequence>::GetReadAt(UInt, SMRTSequence&) [with T_Sequence = FASTASequence; DNALength = unsigned int; UInt = unsigned int]’
../utils/LoadPulses.cpp:680:59:   required from here
/usr/include/pbseq/hdf/HDFBasReader.hpp:647:11: warning: catching polymorphic type ‘class H5::DataSetIException’ by value [-Wcatch-value=]
         } catch (H5::DataSetIException e) {
           ^~~~~
[21/25] rm -f libblasr_impl.a && gcc-ar csrD libblasr_impl.a 'blasr_impl@sta/extrautils_SuffixArrayToBWT.cpp.o' 'blasr_impl@sta/extrautils_BwtToSuffixArray.cpp.o' 'blasr_impl@sta/extrautils_SWMatcher.cpp.o' 'blasr_impl@sta/extrautils_SAModify.cpp.o' 'blasr_impl@sta/extrautils_ExciseRepeats.cpp.o' 'blasr_impl@sta/extrautils_StoreQualityByContextFromCmpH5.cpp.o' 'blasr_impl@sta/extrautils_SALS.cpp.o' 'blasr_impl@sta/extrautils_SimpleShredder.cpp.o' 'blasr_impl@sta/extrautils_Evolve.cpp.o' 'blasr_impl@sta/extrautils_BuildSequenceDB.cpp.o' 'blasr_impl@sta/extrautils_PrintTupleCountTable.cpp.o' 'blasr_impl@sta/utils_SamToM4.cpp.o' 'blasr_impl@sta/utils_SamToCmpH5.cpp.o' 'blasr_impl@sta/utils_SDPMatcher.cpp.o' 'blasr_impl@sta/utils_LoadPulses.cpp.o' 'blasr_impl@sta/utils_PulseToFasta.cpp.o' 'blasr_impl@sta/utils_SamFilter.cpp.o'
[22/25] c++  -o sawriter 'sawriter@exe/utils_SAWriter.cpp.o' -I/usr/include/pbseq -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread /usr/lib/arm-linux-gnueabihf/libpbbam.so /usr/lib/arm-linux-gnueabihf/libhts.so -lblasr /usr/lib/arm-linux-gnueabihf/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<<BUILDDIR>>/blasr-5.3.3+dfsg/build/
[23/25] c++  -o toAfg 'toAfg@exe/utils_ToAfg.cpp.o' -I/usr/include/pbseq -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread /usr/lib/arm-linux-gnueabihf/libpbbam.so /usr/lib/arm-linux-gnueabihf/libhts.so -lblasr /usr/lib/arm-linux-gnueabihf/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<<BUILDDIR>>/blasr-5.3.3+dfsg/build/
[24/25] c++ -Iblasr@exe -I. -I.. -I/usr/include/pbseq -I/usr/include/pbseq/pbdata/ -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -isystem /usr/include/hdf5/serial -pthread -Wno-delete-non-virtual-dtor -Wno-non-virtual-dtor -Wno-unused-but-set-variable -Wno-unused-variable -DUSE_PBBAM=1 -DCMAKE_BUILD=1 -MD -MQ 'blasr@exe/Blasr.cpp.o' -MF 'blasr@exe/Blasr.cpp.o.d' -o 'blasr@exe/Blasr.cpp.o' -c ../Blasr.cpp
In file included from ../iblasr/BlasrHeaders.h:22,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/pbseq/pbdata/LibBlasrConfig.h:2: warning: "USE_PBBAM" redefined
 #define USE_PBBAM
 
<command-line>: note: this is the location of the previous definition
In file included from ../iblasr/BlasrUtils.hpp:138,
                 from ../iblasr/BlasrAlignImpl.hpp:4,
                 from ../iblasr/BlasrAlign.hpp:67,
                 from ../Blasr.cpp:3:
../iblasr/BlasrUtilsImpl.hpp: In function ‘void PrintAlignment(T_AlignmentCandidate&, SMRTSequence&, MappingParameters&, AlignmentContext&, std::ostream&, SMRTSequence&, PacBio::BAM::IRecordWriter*)’:
../iblasr/BlasrUtilsImpl.hpp:976:36: warning: catching polymorphic type ‘class std::ios_base::failure’ by value [-Wcatch-value=]
     } catch (std::ostream::failure f) {
                                    ^
../Blasr.cpp: In function ‘int main(int, char**)’:
../Blasr.cpp:1407:51: warning: cast between incompatible function types from ‘void (*)(MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>*)’ to ‘void* (*)(void*)’ [-Wcast-function-type]
                                (void *(*)(void *))MapReads, &mapdb[procIndex]);
                                                   ^~~~~~~~
../Blasr.cpp:1462:37: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
             } catch (std::exception e) {
                                     ^
In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29,
                 from ../iblasr/BlasrHeaders.h:60,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In instantiation of ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]’:
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:167:25:   required from ‘void BAMOutput::PrintAlignment(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::IRecordWriter&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence; T_AlignmentCandidate = AlignmentCandidate<DNASequence, FASTQSequence>]’
../iblasr/BlasrUtilsImpl.hpp:953:65:   required from here
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:45: warning: the compiler can assume that the address of ‘read’ will never be NULL [-Waddress]
     if (dynamic_cast<SMRTSequence *>(&read) == NULL) {
                                             ^
In file included from /usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArray.hpp:38,
                 from ../iblasr/BlasrHeaders.h:49,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp: In instantiation of ‘int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]’:
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:210:36:   required from ‘int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]’
../iblasr/BlasrAlignImpl.hpp:34:45:   required from ‘void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]’
../Blasr.cpp:371:27:   required from here
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:126:35: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
                 while (refPos + 1 < reference.length and queryPos + 1 < read.length and
                        ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:126:71: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
                 while (refPos + 1 < reference.length and queryPos + 1 < read.length and
                                                          ~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/pbseq/alignment/bwt/BWT.hpp:9,
                 from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:6,
                 from ../iblasr/BlasrHeaders.h:42,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp: In instantiation of ‘int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]’:
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:54:19:   required from ‘int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]’
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:210:36:   required from ‘int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]’
../iblasr/BlasrAlignImpl.hpp:34:45:   required from ‘void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]’
../Blasr.cpp:371:27:   required from here
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:1110:38: warning: comparison of integer expressions of different signedness: ‘SAIndex’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare]
                 index[l] + lcpLength >= targetLength or  // This shouldn't
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp: In instantiation of ‘long int SuffixArray<T, Sigma, Compare, Tuple>::SearchLeftBound(T*, long int, DNALength, T, long int, long int) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]’:
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:1099:17:   required from ‘int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]’
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:54:19:   required from ‘int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]’
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:210:36:   required from ‘int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]’
../iblasr/BlasrAlignImpl.hpp:34:45:   required from ‘void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]’
../Blasr.cpp:371:27:   required from here
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:807:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
             if (targetSufLen == targetOffset) {
                 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:817:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
             if (targetSufLen < targetOffset) {
                 ~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from /usr/include/pbseq/pbdata/CompressedSequence.hpp:4,
                 from /usr/include/pbseq/alignment/tuples/CompressedDNATuple.hpp:5,
                 from /usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:16,
                 from /usr/include/pbseq/alignment/bwt/BWT.hpp:9,
                 from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:6,
                 from ../iblasr/BlasrHeaders.h:42,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:824:48: warning: comparison of integer expressions of different signedness: ‘SAIndex’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare]
                 assert(index[m] + targetOffset < targetLength);
In file included from /usr/include/pbseq/alignment/bwt/BWT.hpp:9,
                 from /usr/include/pbseq/alignment/algorithms/anchoring/BWTSearch.hpp:6,
                 from ../iblasr/BlasrHeaders.h:42,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp: In instantiation of ‘long int SuffixArray<T, Sigma, Compare, Tuple>::SearchRightBound(T*, long int, DNALength, T, long int, long int) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]’:
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:1100:17:   required from ‘int SuffixArray<T, Sigma, Compare, Tuple>::StoreLCPBounds(T*, long int, T*, DNALength, bool, DNALength, std::vector<unsigned int>&, std::vector<unsigned int>&, bool) [with T = unsigned char; Sigma = std::vector<int>; Compare = DefaultCompareStrings<unsigned char>; Tuple = DNATuple; DNALength = unsigned int]’
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:54:19:   required from ‘int LocateAnchorBoundsInSuffixArray(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<unsigned int>&, std::vector<unsigned int>&, std::vector<unsigned int>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence]’
/usr/include/pbseq/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp:210:36:   required from ‘int MapReadToGenome(T_RefSequence&, T_SuffixArray&, T_Sequence&, unsigned int, std::vector<T_MatchPos>&, AnchorParameters&) [with T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_RefSequence = FASTASequence; T_Sequence = SMRTSequence; T_MatchPos = ChainedMatchPos]’
../iblasr/BlasrAlignImpl.hpp:34:45:   required from ‘void MapRead(T_Sequence&, T_Sequence&, T_RefSequence&, T_SuffixArray&, BWT&, SeqBoundaryFtr<FASTQSequence>&, T_TupleCountTable&, SequenceIndexDatabase<FASTQSequence>&, MappingParameters&, MappingMetrics&, std::vector<AlignmentCandidate<DNASequence, FASTQSequence>*>&, MappingBuffers&, MappingIPC*, MappingSemaphores&) [with T_Sequence = SMRTSequence; T_RefSequence = FASTASequence; T_SuffixArray = SuffixArray<unsigned char, std::vector<int> >; T_TupleCountTable = TupleCountTable<FASTASequence, DNATuple>; BWT = Bwt<PackedDNASequence, FASTASequence>; MappingIPC = MappingData<SuffixArray<unsigned char, std::vector<int> >, FASTASequence, DNATuple>]’
../Blasr.cpp:371:27:   required from here
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:855:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
             if (targetSufLen == targetOffset) {
                 ~~~~~~~~~~~~~^~~~~~~~~~~~~~~
/usr/include/pbseq/alignment/suffixarray/SuffixArray.hpp:859:30: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘DNALength’ {aka ‘unsigned int’} [-Wsign-compare]
             if (targetSufLen < targetOffset) {
                 ~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/pbseq/alignment/format/BAMPrinter.hpp:29,
                 from ../iblasr/BlasrHeaders.h:60,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp: In function ‘void AlignmentToBamRecord(T_AlignmentCandidate&, T_Sequence&, T_Sequence&, PacBio::BAM::BamRecord&, AlignmentContext&, SupplementalQVList&, SAMOutput::Clipping, bool, bool) [with T_Sequence = SMRTSequence]’:
/usr/include/pbseq/alignment/format/BAMPrinterImpl.hpp:27:5: warning: nonnull argument ‘read’ compared to NULL [-Wnonnull-compare]
     if (dynamic_cast<SMRTSequence *>(&read) == NULL) {
     ^~
In file included from /usr/include/c++/8/vector:69,
                 from ../iblasr/BlasrHeaders.h:14,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PositionDNATuple&}; _Tp = PositionDNATuple; _Alloc = std::allocator<PositionDNATuple>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PositionDNATuple, std::allocator<PositionDNATuple> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’} changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
                 from ../iblasr/BlasrHeaders.h:14,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/c++/8/bits/stl_vector.h: In function ‘int SequenceToTupleList(Sequence&, TupleMetrics&, TupleList<PositionDNATuple>&) [with Sequence = DNASequence]’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from /usr/include/pbbam/internal/QualityValues.inl:8,
                 from /usr/include/pbbam/QualityValues.h:132,
                 from /usr/include/pbbam/BamRecordImpl.h:20,
                 from /usr/include/pbbam/BamRecord.h:19,
                 from /usr/include/pbbam/BamWriter.h:15,
                 from ../iblasr/BlasrHeaders.h:24,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b,
     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __unguarded_linear_insert(_RandomAccessIterator __last,
     ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __insertion_sort(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
                 from /usr/include/c++/8/algorithm:62,
                 from /usr/include/pbbam/internal/QualityValues.inl:8,
                 from /usr/include/pbbam/QualityValues.h:132,
                 from /usr/include/pbbam/BamRecordImpl.h:20,
                 from /usr/include/pbbam/BamRecord.h:19,
                 from /usr/include/pbbam/BamWriter.h:15,
                 from ../iblasr/BlasrHeaders.h:24,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/c++/8/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Distance = int; _Tp = PositionDNATuple; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
     ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
                 from /usr/include/pbbam/internal/QualityValues.inl:8,
                 from /usr/include/pbbam/QualityValues.h:132,
                 from /usr/include/pbbam/BamRecordImpl.h:20,
                 from /usr/include/pbbam/BamRecord.h:19,
                 from /usr/include/pbbam/BamWriter.h:15,
                 from ../iblasr/BlasrHeaders.h:24,
                 from ../iblasr/BlasrAlign.hpp:4,
                 from ../Blasr.cpp:3:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __heap_select(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1668:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
     __introsort_loop(_RandomAccessIterator __first,
     ^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
       std::__move_median_to_first(__first, __first + 1, __mid, __last - 1,
       ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __comp);
       ~~~~~~~                     
/usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__cut, __last, __depth_limit, __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1933:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
       std::__heap_select(__first, __middle, __last, __comp);
       ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = FASTQSequence; T_TargetSequence = DNASequence; T_ScoreFn = DistanceMatrixScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>]’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘int SDPAlign(T_QuerySequence&, T_TargetSequence&, T_ScoreFn&, int, int, int, float, blasr::Alignment&, std::vector<Fragment>&, std::vector<Fragment>&, std::vector<Fragment>&, T_TupleList&, T_TupleList&, T_TupleList&, std::vector<int>&, AlignmentType, bool, bool, DNALength, bool, unsigned int) [with T_QuerySequence = SMRTSequence; T_TargetSequence = DNASequence; T_ScoreFn = IDSScoreFunction<DNASequence, FASTQSequence>; T_TupleList = TupleList<PositionDNATuple>]’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__introsort_loop(__first, __last,
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
     std::__lg(__last - __first) * 2,
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     __comp);
     ~~~~~~~              
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
    std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PositionDNATuple*, std::vector<PositionDNATuple, std::allocator<PositionDNATuple> > >’ changed in GCC 7.1
  std::__insertion_sort(__first, __last, __comp);
  ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[25/25] c++  -o blasr 'blasr@exe/Blasr.cpp.o' -I/usr/include/pbseq -L/usr/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf/hdf5/serial -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/blasr-5.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DHAVE_HDF5_1_10_1 -Wl,--start-group -lhdf5_cpp -lhdf5 libblasr_impl.a -pthread /usr/lib/arm-linux-gnueabihf/libpbbam.so /usr/lib/arm-linux-gnueabihf/libhts.so -lblasr /usr/lib/arm-linux-gnueabihf/libz.so -lpbdata -lpbihdf -lblasr -lpbdata -lpbihdf -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<<BUILDDIR>>/blasr-5.3.3+dfsg/build/
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3.3+dfsg'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/blasr-5.3.3+dfsg'
echo Tests require data not available in the source distribution
Tests require data not available in the source distribution
make[1]: Leaving directory '/<<BUILDDIR>>/blasr-5.3.3+dfsg'
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary-arch
dh binary-arch --buildsystem=meson
   dh_testroot -a -O--buildsystem=meson
   dh_prep -a -O--buildsystem=meson
   dh_auto_install -a -O--buildsystem=meson
	cd obj-arm-linux-gnueabihf && DESTDIR=/<<BUILDDIR>>/blasr-5.3.3\+dfsg/debian/blasr LC_ALL=C.UTF-8 ninja install
[1/4] Generating BlasrGitHash.h with a custom command.
[1/2] Installing files.
Installing blasr to /<<BUILDDIR>>/blasr-5.3.3+dfsg/debian/blasr/usr/bin
Installing sawriter to /<<BUILDDIR>>/blasr-5.3.3+dfsg/debian/blasr/usr/bin
   dh_install -a -O--buildsystem=meson
   dh_installdocs -a -O--buildsystem=meson
   dh_installchangelogs -a -O--buildsystem=meson
   dh_installman -a -O--buildsystem=meson
   dh_installinit -a -O--buildsystem=meson
   dh_installsystemduser -a -O--buildsystem=meson
   dh_lintian -a -O--buildsystem=meson
   dh_perl -a -O--buildsystem=meson
   dh_link -a -O--buildsystem=meson
   dh_strip_nondeterminism -a -O--buildsystem=meson
   dh_compress -a -O--buildsystem=meson
   dh_fixperms -a -O--buildsystem=meson
   dh_missing -a -O--buildsystem=meson
   dh_dwz -a -O--buildsystem=meson
   dh_strip -a -O--buildsystem=meson
   dh_makeshlibs -a -O--buildsystem=meson
   dh_shlibdeps -a -O--buildsystem=meson
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/sawriter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libblasr.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbdata.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libpbihdf.so'
dpkg-shlibdeps: warning: debian/blasr/usr/bin/blasr contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/blasr/usr/bin/sawriter debian/blasr/usr/bin/blasr were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
   dh_installdeb -a -O--buildsystem=meson
   dh_gencontrol -a -O--buildsystem=meson
   dh_md5sums -a -O--buildsystem=meson
   dh_builddeb -a -O--buildsystem=meson
dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_5.3.3+dfsg-2_armhf.deb'.
dpkg-deb: building package 'blasr' in '../blasr_5.3.3+dfsg-2_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../blasr_5.3.3+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2019-09-06T05:09:42Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


blasr_5.3.3+dfsg-2_armhf.changes:
---------------------------------

Format: 1.8
Date: Sun, 01 Sep 2019 07:52:40 +0200
Source: blasr
Binary: blasr blasr-dbgsym
Architecture: armhf
Version: 5.3.3+dfsg-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 blasr      - mapping single-molecule sequencing reads
Closes: 936213
Changes:
 blasr (5.3.3+dfsg-2) unstable; urgency=medium
 .
   * Use 2to3 to port to Python3
     Closes: #936213
Checksums-Sha1:
 96f956545abe9d9f677856e951b6ff3a51fd0d61 3097316 blasr-dbgsym_5.3.3+dfsg-2_armhf.deb
 4aa1dc24a90efa1990708205fea336536481c4c1 6864 blasr_5.3.3+dfsg-2_armhf.buildinfo
 80f3fdf4937585dff1d7e15110f063808576ef58 178280 blasr_5.3.3+dfsg-2_armhf.deb
Checksums-Sha256:
 b3b811277167afdc375c234ad9add12217fd2e850771eea9f2752c608a0cea40 3097316 blasr-dbgsym_5.3.3+dfsg-2_armhf.deb
 9f329767225e9490612cf61c4c5b6b2212ada1fe16c9842589f668b00a064614 6864 blasr_5.3.3+dfsg-2_armhf.buildinfo
 34bd55280806064d864ab2f14a7aae5ac0e8d0b277da4a2a42a174c671aa2968 178280 blasr_5.3.3+dfsg-2_armhf.deb
Files:
 82bc8aae39462d5696df3ecd96666952 3097316 debug optional blasr-dbgsym_5.3.3+dfsg-2_armhf.deb
 d03fb21d6dfa999c765c7ad340b783e4 6864 science optional blasr_5.3.3+dfsg-2_armhf.buildinfo
 15d6111db609ebc3e83ba8b2840ae9ed 178280 science optional blasr_5.3.3+dfsg-2_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


blasr-dbgsym_5.3.3+dfsg-2_armhf.deb
-----------------------------------

 new Debian package, version 2.0.
 size 3097316 bytes: control archive=644 bytes.
     414 bytes,    12 lines      control              
     297 bytes,     3 lines      md5sums              
 Package: blasr-dbgsym
 Source: blasr
 Version: 5.3.3+dfsg-2
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3187
 Depends: blasr (= 5.3.3+dfsg-2)
 Section: debug
 Priority: optional
 Description: debug symbols for blasr
 Build-Ids: 7210ae7ebad817c49a03872696516796c25c2e56 7411258efd25fbf927776ae66bc1f6eb943d6f78

drwxr-xr-x root/root         0 2019-09-01 05:52 ./
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/lib/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/lib/debug/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/lib/debug/.build-id/72/
-rw-r--r-- root/root    130452 2019-09-01 05:52 ./usr/lib/debug/.build-id/72/10ae7ebad817c49a03872696516796c25c2e56.debug
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/lib/debug/.build-id/74/
-rw-r--r-- root/root   3081764 2019-09-01 05:52 ./usr/lib/debug/.build-id/74/11258efd25fbf927776ae66bc1f6eb943d6f78.debug
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root     36060 2019-09-01 05:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/blasr.debug
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/share/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/share/doc/
lrwxrwxrwx root/root         0 2019-09-01 05:52 ./usr/share/doc/blasr-dbgsym -> blasr


blasr_5.3.3+dfsg-2_armhf.deb
----------------------------

 new Debian package, version 2.0.
 size 178280 bytes: control archive=1016 bytes.
     722 bytes,    14 lines      control              
     635 bytes,    10 lines      md5sums              
 Package: blasr
 Version: 5.3.3+dfsg-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 530
 Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libhdf5-cpp-103 (>= 1.10.1), libpbbam0.19.0 (>= 0.19.0+dfsg), libstdc++6 (>= 5.2), libpbseq
 Section: science
 Priority: optional
 Homepage: https://github.com/PacificBiosciences/blasr
 Description: mapping single-molecule sequencing reads
  Basic local alignment with successive refinement (BLASR) is a method
  for mapping single-molecule sequencing reads against a reference genome.
  Such reads are thousands of bases long, with divergence between them
  and the genome being dominated by insertion and deletion error.

drwxr-xr-x root/root         0 2019-09-01 05:52 ./
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/bin/
-rwxr-xr-x root/root    470292 2019-09-01 05:52 ./usr/bin/blasr
-rwxr-xr-x root/root     47040 2019-09-01 05:52 ./usr/bin/sawriter
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/share/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/share/doc/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/share/doc/blasr/
-rw-r--r-- root/root       373 2019-09-01 05:52 ./usr/share/doc/blasr/NEWS.Debian.gz
-rw-r--r-- root/root      1291 2019-03-11 18:23 ./usr/share/doc/blasr/README.md
-rw-r--r-- root/root        41 2019-09-01 05:52 ./usr/share/doc/blasr/TODO.Debian
-rw-r--r-- root/root      1509 2019-09-01 05:52 ./usr/share/doc/blasr/changelog.Debian.gz
-rw-r--r-- root/root      2081 2019-09-01 05:52 ./usr/share/doc/blasr/copyright
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/share/lintian/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/share/lintian/overrides/
-rw-r--r-- root/root        84 2019-09-01 05:52 ./usr/share/lintian/overrides/blasr
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/share/man/
drwxr-xr-x root/root         0 2019-09-01 05:52 ./usr/share/man/man1/
-rw-r--r-- root/root      1369 2019-09-01 05:52 ./usr/share/man/man1/blasr.1.gz
-rw-r--r-- root/root       872 2019-09-01 05:52 ./usr/share/man/man1/sawriter.1.gz


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 96092
Build-Time: 210
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 473
Job: blasr_5.3.3+dfsg-2
Machine Architecture: armhf
Package: blasr
Package-Time: 699
Source-Version: 5.3.3+dfsg-2
Space: 96092
Status: successful
Version: 5.3.3+dfsg-2
--------------------------------------------------------------------------------
Finished at 2019-09-06T05:09:42Z
Build needed 00:11:39, 96092k disk space