pbbam →
0.23.0+dfsg-1 →
armhf → 2019-11-27 02:13:58
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| pbbam 0.23.0+dfsg-1 (armhf) Wed, 27 Nov 2019 01:20:13 +0000 |
+==============================================================================+
Package: pbbam
Version: 0.23.0+dfsg-1
Source Version: 0.23.0+dfsg-1
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-476c2ca3-dcfa-497f-a0e8-b60f400d90c2' 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 [12.9 MB]
Fetched 24.4 MB in 31s (779 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: 'pbbam' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/pbbam.git
Please use:
git clone https://salsa.debian.org/med-team/pbbam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 7785 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main pbbam 0.23.0+dfsg-1 (dsc) [2273 B]
Get:2 http://172.17.0.1/private bullseye-staging/main pbbam 0.23.0+dfsg-1 (tar) [7775 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main pbbam 0.23.0+dfsg-1 (diff) [7796 B]
Fetched 7785 kB in 1s (7169 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbbam-sV8QLK/pbbam-0.23.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbbam-sV8QLK' 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-RIvqGV/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-RIvqGV/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-RIvqGV/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2247 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 31 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-RIvqGV/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 ... 12227 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), dh-exec, d-shlibs, meson, pkg-config, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libgtest-dev, python3-cram, samtools
Filtered Build-Depends: debhelper-compat (= 12), dh-exec, d-shlibs, meson, pkg-config, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libgtest-dev, python3-cram, samtools
dpkg-deb: building package 'sbuild-build-depends-pbbam-dummy' in '/<<BUILDDIR>>/resolver-RIvqGV/apt_archive/sbuild-build-depends-pbbam-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pbbam-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-RIvqGV/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ Sources [571 B]
Get:5 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ Packages [642 B]
Fetched 2546 B in 1s (3259 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pbbam build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base intltool-debian libarchive-zip-perl libboost-dev
libboost1.67-dev libbrotli1 libbsd0 libcroco3 libcurl3-gnutls
libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgtest-dev
libhts-dev libhts2 libicu63 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db meson
mime-support ninja-build pkg-config po-debconf python3 python3-cram
python3-minimal python3-pkg-resources python3.7 python3.7-minimal samtools
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
krb5-doc krb5-user liblzma-doc libssl-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3-setuptools
python3.7-venv python3.7-doc binfmt-support
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 python cwltool
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
googletest groff-base intltool-debian libarchive-zip-perl libboost-dev
libboost1.67-dev libbrotli1 libbsd0 libcroco3 libcurl3-gnutls
libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgtest-dev
libhts-dev libhts2 libicu63 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libncurses6
libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db meson
mime-support ninja-build pkg-config po-debconf python3 python3-cram
python3-minimal python3-pkg-resources python3.7 python3.7-minimal samtools
sbuild-build-depends-pbbam-dummy sensible-utils zlib1g-dev
0 upgraded, 77 newly installed, 0 to remove and 31 not upgraded.
Need to get 42.8 MB of archives.
After this operation, 250 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-RIvqGV/apt_archive ./ sbuild-build-depends-pbbam-dummy 0.invalid.0 [928 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+20191019-1 [316 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 2.9.0-1 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.5-2 [584 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.5-2 [1527 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-1 [36.6 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.5-2 [1668 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.5-2 [347 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-1 [20.1 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-1 [61.5 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf d-shlibs all 0.88 [17.4 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.1 [173 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-2 [136 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.2-3 [1137 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.1 [997 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf dh-exec armhf 0.23.2 [25.3 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf googletest armhf 1.9.0.20190831-1 [622 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b3 [4464 B]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-5 [257 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1 [73.9 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.66.0-1+b1 [295 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.3-3 [76.4 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libgtest-dev armhf 1.9.0.20190831-1 [208 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libhts2 armhf 1.9-11 [255 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.9-11 [4286 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1d-2 [1570 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf ninja-build armhf 1.9.0-3 [79.6 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 41.2.0-1 [154 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf meson all 0.52.0-2 [357 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf python3-cram all 0.7-3 [17.1 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.9-5 [397 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 42.8 MB in 4s (10.2 MB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 12227 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+20191019-1_armhf.deb ...
Unpacking libtinfo5:armhf (6.1+20191019-1) ...
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_2.9.0-1_armhf.deb ...
Unpacking man-db (2.9.0-1) ...
Selecting previously unselected package libssl1.1:armhf.
Preparing to unpack .../07-libssl1.1_1.1.1d-2_armhf.deb ...
Unpacking libssl1.1:armhf (1.1.1d-2) ...
Selecting previously unselected package libpython3.7-minimal:armhf.
Preparing to unpack .../08-libpython3.7-minimal_3.7.5-2_armhf.deb ...
Unpacking libpython3.7-minimal:armhf (3.7.5-2) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../09-libexpat1_2.2.9-1_armhf.deb ...
Unpacking libexpat1:armhf (2.2.9-1) ...
Selecting previously unselected package python3.7-minimal.
Preparing to unpack .../10-python3.7-minimal_3.7.5-2_armhf.deb ...
Unpacking python3.7-minimal (3.7.5-2) ...
Setting up libssl1.1:armhf (1.1.1d-2) ...
Setting up libpython3.7-minimal:armhf (3.7.5-2) ...
Setting up libexpat1:armhf (2.2.9-1) ...
Setting up python3.7-minimal (3.7.5-2) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13146 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.7.5-1_armhf.deb ...
Unpacking python3-minimal (3.7.5-1) ...
Selecting previously unselected package mime-support.
Preparing to unpack .../1-mime-support_3.64_all.deb ...
Unpacking mime-support (3.64) ...
Selecting previously unselected package libmpdec2:armhf.
Preparing to unpack .../2-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 .../3-libpython3.7-stdlib_3.7.5-2_armhf.deb ...
Unpacking libpython3.7-stdlib:armhf (3.7.5-2) ...
Selecting previously unselected package python3.7.
Preparing to unpack .../4-python3.7_3.7.5-2_armhf.deb ...
Unpacking python3.7 (3.7.5-2) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../5-libpython3-stdlib_3.7.5-1_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.7.5-1) ...
Setting up python3-minimal (3.7.5-1) ...
Selecting previously unselected package python3.
(Reading database ... 13584 files and directories currently installed.)
Preparing to unpack .../00-python3_3.7.5-1_armhf.deb ...
Unpacking python3 (3.7.5-1) ...
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%3a5.37-6_armhf.deb ...
Unpacking libmagic-mgc (1:5.37-6) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../03-libmagic1_1%3a5.37-6_armhf.deb ...
Unpacking libmagic1:armhf (1:5.37-6) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.37-6_armhf.deb ...
Unpacking file (1:5.37-6) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.19.8.1-10_armhf.deb ...
Unpacking gettext-base (0.19.8.1-10) ...
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_1.4.18-4_armhf.deb ...
Unpacking m4 (1.4.18-4) ...
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_0.19.8.1-10_all.deb ...
Unpacking autopoint (0.19.8.1-10) ...
Selecting previously unselected package d-shlibs.
Preparing to unpack .../12-d-shlibs_0.88_all.deb ...
Unpacking d-shlibs (0.88) ...
Selecting previously unselected package libtool.
Preparing to unpack .../13-libtool_2.4.6-11_all.deb ...
Unpacking libtool (2.4.6-11) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../14-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_12.7.1_all.deb ...
Unpacking libdebhelper-perl (12.7.1) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../16-libarchive-zip-perl_1.67-1_all.deb ...
Unpacking libarchive-zip-perl (1.67-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../17-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 .../18-libfile-stripnondeterminism-perl_1.6.3-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.6.3-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../19-dh-strip-nondeterminism_1.6.3-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.6.3-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../20-libelf1_0.176-1.1_armhf.deb ...
Unpacking libelf1:armhf (0.176-1.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../21-dwz_0.13-2_armhf.deb ...
Unpacking dwz (0.13-2) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../22-libglib2.0-0_2.62.2-3_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.62.2-3) ...
Selecting previously unselected package libicu63:armhf.
Preparing to unpack .../23-libicu63_63.2-2_armhf.deb ...
Unpacking libicu63:armhf (63.2-2) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../24-libxml2_2.9.4+dfsg1-8_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-8) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../25-libcroco3_0.6.13-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.13-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.19.8.1-10_armhf.deb ...
Unpacking gettext (0.19.8.1-10) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-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 .../28-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_12.7.1_all.deb ...
Unpacking debhelper (12.7.1) ...
Selecting previously unselected package dh-exec.
Preparing to unpack .../30-dh-exec_0.23.2_armhf.deb ...
Unpacking dh-exec (0.23.2) ...
Selecting previously unselected package googletest:armhf.
Preparing to unpack .../31-googletest_1.9.0.20190831-1_armhf.deb ...
Unpacking googletest:armhf (1.9.0.20190831-1) ...
Selecting previously unselected package libboost1.67-dev:armhf.
Preparing to unpack .../32-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 .../33-libboost-dev_1.67.0.2+b3_armhf.deb ...
Unpacking libboost-dev:armhf (1.67.0.2+b3) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../34-libbrotli1_1.0.7-5_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.7-5) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../35-libkeyutils1_1.6-6_armhf.deb ...
Unpacking libkeyutils1:armhf (1.6-6) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../36-libkrb5support0_1.17-6+b1_armhf.deb ...
Unpacking libkrb5support0:armhf (1.17-6+b1) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../37-libk5crypto3_1.17-6+b1_armhf.deb ...
Unpacking libk5crypto3:armhf (1.17-6+b1) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../38-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 .../39-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 .../40-libnghttp2-14_1.40.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.40.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../41-libpsl5_0.20.2-2_armhf.deb ...
Unpacking libpsl5:armhf (0.20.2-2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../42-librtmp1_2.4+20151223.gitfa8646d.1-2+b1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../43-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 .../44-libcurl3-gnutls_7.66.0-1+b1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.66.0-1+b1) ...
Selecting previously unselected package libdeflate0.
Preparing to unpack .../45-libdeflate0_1.3-3_armhf.deb ...
Unpacking libdeflate0 (1.3-3) ...
Selecting previously unselected package libgtest-dev:armhf.
Preparing to unpack .../46-libgtest-dev_1.9.0.20190831-1_armhf.deb ...
Unpacking libgtest-dev:armhf (1.9.0.20190831-1) ...
Selecting previously unselected package libhts2:armhf.
Preparing to unpack .../47-libhts2_1.9-11_armhf.deb ...
Unpacking libhts2:armhf (1.9-11) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../48-liblzma-dev_5.2.4-1_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.4-1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../49-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../50-libhts-dev_1.9-11_armhf.deb ...
Unpacking libhts-dev:armhf (1.9-11) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../51-libncurses6_6.1+20191019-1_armhf.deb ...
Unpacking libncurses6:armhf (6.1+20191019-1) ...
Selecting previously unselected package libssl-dev:armhf.
Preparing to unpack .../52-libssl-dev_1.1.1d-2_armhf.deb ...
Unpacking libssl-dev:armhf (1.1.1d-2) ...
Selecting previously unselected package ninja-build.
Preparing to unpack .../53-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 .../54-python3-pkg-resources_41.2.0-1_all.deb ...
Unpacking python3-pkg-resources (41.2.0-1) ...
Selecting previously unselected package meson.
Preparing to unpack .../55-meson_0.52.0-2_all.deb ...
Unpacking meson (0.52.0-2) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../56-pkg-config_0.29-6_armhf.deb ...
Unpacking pkg-config (0.29-6) ...
Selecting previously unselected package python3-cram.
Preparing to unpack .../57-python3-cram_0.7-3_all.deb ...
Unpacking python3-cram (0.7-3) ...
Selecting previously unselected package samtools.
Preparing to unpack .../58-samtools_1.9-5_armhf.deb ...
Unpacking samtools (1.9-5) ...
Selecting previously unselected package sbuild-build-depends-pbbam-dummy.
Preparing to unpack .../59-sbuild-build-depends-pbbam-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-pbbam-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 (3.64) ...
Setting up libmagic-mgc (1:5.37-6) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.2-3) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (12.7.1) ...
Setting up libbrotli1:armhf (1.0.7-5) ...
Setting up libnghttp2-14:armhf (1.40.0-1) ...
Setting up libmagic1:armhf (1:5.37-6) ...
Setting up libdeflate0 (1.3-3) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.37-6) ...
Setting up googletest:armhf (1.9.0.20190831-1) ...
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 autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.1+20191019-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libssl-dev:armhf (1.1.1d-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up pkg-config (0.29-6) ...
Setting up d-shlibs (0.88) ...
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+b3) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
Setting up libpython3.7-stdlib:armhf (3.7.5-2) ...
Setting up libgtest-dev:armhf (1.9.0.20190831-1) ...
Setting up libtool (2.4.6-11) ...
Setting up m4 (1.4.18-4) ...
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 autoconf (2.69-11) ...
Setting up dh-strip-nondeterminism (1.6.3-1) ...
Setting up dwz (0.13-2) ...
Setting up groff-base (1.22.4-3) ...
Setting up libpython3-stdlib:armhf (3.7.5-1) ...
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 (3.7.5-2) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libcurl3-gnutls:armhf (7.66.0-1+b1) ...
Setting up python3 (3.7.5-1) ...
Setting up man-db (2.9.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up python3-cram (0.7-3) ...
Setting up python3-pkg-resources (41.2.0-1) ...
Setting up libhts2:armhf (1.9-11) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.9-11) ...
Setting up meson (0.52.0-2) ...
Setting up samtools (1.9-5) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.7.1) ...
Setting up dh-exec (0.23.2) ...
Setting up sbuild-build-depends-pbbam-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-17+rpi1 gcc-9_9.2.1-17+rpi1 libc6-dev_2.29-2+rpi1 libstdc++-9-dev_9.2.1-17+rpi1 libstdc++6_9.2.1-17+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-2+rpi1 binutils-arm-linux-gnueabihf_2.33.1-2+rpi1 binutils-common_2.33.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3+rpi1 cpp-9_9.2.1-17+rpi1 d-shlibs_0.88 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1 debianutils_4.9 dh-autoreconf_19 dh-exec_0.23.2 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-2 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3+rpi1 g++-9_9.2.1-17+rpi1 gcc_4:9.2.1-3+rpi1 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+b3 gcc-9_9.2.1-17+rpi1 gcc-9-base_9.2.1-17+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 googletest_1.9.0.20190831-1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-17+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-17+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.33.1-2+rpi1 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b3 libboost1.67-dev_1.67.0-13 libbrotli1_1.0.7-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-2+rpi1 libc-dev-bin_2.29-2+rpi1 libc6_2.29-2+rpi1 libc6-dev_2.29-2+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-17+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcurl3-gnutls_7.66.0-1+b1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdeflate0_1.3-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-17+rpi1 libgcc1_1:9.2.1-17+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-4 libgomp1_9.2.1-17+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libgtest-dev_1.9.0.20190831-1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.9-11 libhts2_1.9-11 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl19_0.20-2 libisl21_0.21-2 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_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.32-5 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.1-2 libpsl5_0.20.2-2 libpython3-stdlib_3.7.5-1 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.1-2+rpi1 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1d-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-17+rpi1 libstdc++6_9.2.1-17+rpi1 libsub-override-perl_0.09-2 libsystemd0_242-7+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-17+rpi1 libuchardet0_0.0.6-3 libudev1_242-7+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.3+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17 meson_0.52.0-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.6 ninja-build_1.9.0-3 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkg-config_0.29-6 po-debconf_1.0.21 python3_3.7.5-1 python3-cram_0.7-3 python3-minimal_3.7.5-1 python3-pkg-resources_41.2.0-1 python3.7_3.7.5-2 python3.7-minimal_3.7.5-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 samtools_1.9-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pbbam-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 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 Mon Aug 5 04:30:36 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 ./pbbam_0.23.0+dfsg-1.dsc
dpkg-source: info: extracting pbbam in /<<BUILDDIR>>/pbbam-0.23.0+dfsg
dpkg-source: info: unpacking pbbam_0.23.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking pbbam_0.23.0+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_gtest_depcheck.patch
dpkg-source: info: applying use_debian_packaged_python3-cram.patch
dpkg-source: info: applying python3.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-476c2ca3-dcfa-497f-a0e8-b60f400d90c2
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbbam
dpkg-buildpackage: info: source version 0.23.0+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem=meson
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/pbbam-0.23.0+dfsg'
dh_auto_clean
find -name "*.deb.t" -delete
rm -f -r /<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata
make[1]: Leaving directory '/<<BUILDDIR>>/pbbam-0.23.0+dfsg'
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
dh_auto_configure -a -O--buildsystem=meson
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/arm-linux-gnueabihf
The Meson build system
Version: 0.52.0
Source dir: /<<BUILDDIR>>/pbbam-0.23.0+dfsg
Build dir: /<<BUILDDIR>>/pbbam-0.23.0+dfsg/obj-arm-linux-gnueabihf
Build type: native build
Project name: PacBioBAM
Project version: 0.23.0
Appending CXXFLAGS from environment: '-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'
Appending LDFLAGS from environment: ['-Wl,-z,relro', '-Wl,-z,now']
Appending CPPFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2'
Appending CXXFLAGS from environment: '-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'
Appending LDFLAGS from environment: ['-Wl,-z,relro', '-Wl,-z,now']
Appending CPPFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2'
C++ compiler for the host machine: c++ (gcc 9.2.1 "c++ (Raspbian 9.2.1-17+rpi1) 9.2.1 20191102")
C++ linker for the host machine: GNU ld.bfd 2.33.1
Host machine cpu family: arm
Host machine cpu: armv7l
Compiler for C++ supports arguments -Wduplicated-cond: YES
Compiler for C++ supports arguments -Wduplicated-branches: YES
Compiler for C++ supports arguments -Wlogical-op: YES
Compiler for C++ supports arguments -Wrestrict: YES
Compiler for C++ supports arguments -Wnull-dereference: YES
Compiler for C++ supports arguments -Wuseless-cast: YES
Compiler for C++ supports arguments -Wdouble-promotion: YES
Compiler for C++ supports arguments -Wshadow: YES
Compiler for C++ supports arguments -Wformat=1: 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 zlib found: YES 1.2.11
Run-time dependency htslib found: YES 1.9
Program python3 found: YES (/usr/bin/python3)
Program tools/check-formatting found: YES (/<<BUILDDIR>>/pbbam-0.23.0+dfsg/tools/check-formatting)
Program cram3 found: YES (/usr/bin/cram3)
Run-time dependency GTest found: YES (prebuilt)
Configuring group.fofn using configuration
Configuring PbbamTestData.h using configuration
Configuring synthetic_movie_all.subreadset.xml using configuration
Configuring Bam2SamVersion.h using configuration
Configuring bam2sam.t using configuration
Configuring PbIndexVersion.h using configuration
Configuring PbIndexDumpVersion.h using configuration
Configuring pbindexdump_json.t using configuration
Configuring pbindexdump_cpp.t using configuration
Configuring PbMergeVersion.h using configuration
Configuring pbmerge_pacbio_ordering.t using configuration
Configuring pbmerge_aligned_ordering.t using configuration
Configuring pbmerge_mixed_ordering.t using configuration
Configuring pbmerge_dataset.t using configuration
Configuring pbmerge_fofn.t using configuration
Configuring PbBamifyVersion.h using configuration
Program samtools found: YES (/usr/bin/samtools)
Configuring pbbamify.t using configuration
Build targets in project: 8
Option buildtype is: plain [default: release]
Found ninja-1.9.0 at /usr/bin/ninja
dh_auto_build -a -O--buildsystem=meson
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v
[1/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Accuracy.cpp.o' -MF 'src/25a6634@@pbbam@sha/Accuracy.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Accuracy.cpp.o' -c ../src/Accuracy.cpp
[2/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o' -c ../src/BaiIndexedBamReader.cpp
[3/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamFile.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamFile.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamFile.cpp.o' -c ../src/BamFile.cpp
[4/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' -MF 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' -c ../src/AlignmentPrinter.cpp
[5/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamReader.cpp.o' -c ../src/BamReader.cpp
[6/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamFileMerger.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamFileMerger.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamFileMerger.cpp.o' -c ../src/BamFileMerger.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../include/pbbam/CompositeBamReader.h:24,
from ../src/BamFileMerger.cpp:21:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[7/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamHeader.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamHeader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamHeader.cpp.o' -c ../src/BamHeader.cpp
[8/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o' -c ../src/BamRecordBuilder.cpp
[9/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o' -c ../src/BamRecordImpl.cpp
[10/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecordView.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordView.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordView.cpp.o' -c ../src/BamRecordView.cpp
[11/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o' -c ../src/BamRecordTags.cpp
[12/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamRecord.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamRecord.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamRecord.cpp.o' -c ../src/BamRecord.cpp
[13/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamWriter.cpp.o' -c ../src/BamWriter.cpp
[14/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Cigar.cpp.o' -MF 'src/25a6634@@pbbam@sha/Cigar.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Cigar.cpp.o' -c ../src/Cigar.cpp
[15/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BamTagCodec.cpp.o' -MF 'src/25a6634@@pbbam@sha/BamTagCodec.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BamTagCodec.cpp.o' -c ../src/BamTagCodec.cpp
[16/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/CigarOperation.cpp.o' -MF 'src/25a6634@@pbbam@sha/CigarOperation.cpp.o.d' -o 'src/25a6634@@pbbam@sha/CigarOperation.cpp.o' -c ../src/CigarOperation.cpp
[17/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ChemistryTable.cpp.o' -MF 'src/25a6634@@pbbam@sha/ChemistryTable.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ChemistryTable.cpp.o' -c ../src/ChemistryTable.cpp
[18/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/CompositeFastaReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/CompositeFastaReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/CompositeFastaReader.cpp.o' -c ../src/CompositeFastaReader.cpp
[19/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Config.cpp.o' -MF 'src/25a6634@@pbbam@sha/Config.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Config.cpp.o' -c ../src/Config.cpp
[20/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Compare.cpp.o' -MF 'src/25a6634@@pbbam@sha/Compare.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Compare.cpp.o' -c ../src/Compare.cpp
[21/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/BarcodeQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/BarcodeQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BarcodeQuery.cpp.o' -c ../src/BarcodeQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../include/pbbam/CompositeBamReader.h:24,
from ../src/BarcodeQuery.cpp:13:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[22/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o' -c ../src/DataSetElement.cpp
[23/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o' -c ../src/DataSetIO.cpp
[24/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSet.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSet.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSet.cpp.o' -c ../src/DataSet.cpp
[25/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o' -c ../src/DataSetXsd.cpp
[26/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o' -c ../src/DataSetBaseTypes.cpp
[27/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastaCache.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastaCache.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastaCache.cpp.o' -c ../src/FastaCache.cpp
[28/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastaReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastaReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastaReader.cpp.o' -c ../src/FastaReader.cpp
[29/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o' -c ../src/EntireFileQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../include/pbbam/CompositeBamReader.h:24,
from ../src/EntireFileQuery.cpp:11:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[30/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastaSequence.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastaSequence.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastaSequence.cpp.o' -c ../src/FastaSequence.cpp
[31/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o' -c ../src/FastaSequenceQuery.cpp
[32/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastqSequence.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastqSequence.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastqSequence.cpp.o' -c ../src/FastqSequence.cpp
[33/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastqReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastqReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastqReader.cpp.o' -c ../src/FastqReader.cpp
[34/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o' -MF 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o.d' -o 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o' -c ../src/DataSetTypes.cpp
[35/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FileProducer.cpp.o' -MF 'src/25a6634@@pbbam@sha/FileProducer.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FileProducer.cpp.o' -c ../src/FileProducer.cpp
[36/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastaWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastaWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastaWriter.cpp.o' -c ../src/FastaWriter.cpp
[37/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Frames.cpp.o' -MF 'src/25a6634@@pbbam@sha/Frames.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Frames.cpp.o' -c ../src/Frames.cpp
[38/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FastqWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/FastqWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FastqWriter.cpp.o' -c ../src/FastqWriter.cpp
[39/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FofnReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/FofnReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FofnReader.cpp.o' -c ../src/FofnReader.cpp
[40/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/FileUtils.cpp.o' -MF 'src/25a6634@@pbbam@sha/FileUtils.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FileUtils.cpp.o' -c ../src/FileUtils.cpp
[41/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/GenomicInterval.cpp.o' -MF 'src/25a6634@@pbbam@sha/GenomicInterval.cpp.o.d' -o 'src/25a6634@@pbbam@sha/GenomicInterval.cpp.o' -c ../src/GenomicInterval.cpp
[42/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/IRecordWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/IRecordWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IRecordWriter.cpp.o' -c ../src/IRecordWriter.cpp
[43/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/MD5.cpp.o' -MF 'src/25a6634@@pbbam@sha/MD5.cpp.o.d' -o 'src/25a6634@@pbbam@sha/MD5.cpp.o' -c ../src/MD5.cpp
[44/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o' -c ../src/IndexedFastaReader.cpp
[45/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o' -MF 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o.d' -o 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o' -c ../src/MemoryUtils.cpp
[46/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' -c ../src/GenomicIntervalQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../include/pbbam/CompositeBamReader.h:24,
from ../src/GenomicIntervalQuery.cpp:11:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[47/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiFile.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiFile.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiFile.cpp.o' -c ../src/PbiFile.cpp
[48/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' -c ../src/IndexedBamWriter.cpp
../src/IndexedBamWriter.cpp: In member function ‘std::vector<PacBio::BAM::internal::GzIndexEntry> PacBio::BAM::internal::PbiBuilder2::LoadGzi()’:
../src/IndexedBamWriter.cpp:585:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
585 | fread(&entry.vAddress, sizeof(entry.vAddress), 1, gziFile.get());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/IndexedBamWriter.cpp:586:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
586 | fread(&entry.uAddress, sizeof(entry.uAddress), 1, gziFile.get());
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/BamHeader.h:15,
from ../include/pbbam/BamWriter.h:14,
from ../include/pbbam/IndexedBamWriter.h:13,
from ../src/IndexedBamWriter.cpp:7:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long unsigned int, std::allocator<long long unsigned int> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int, std::allocator<long long unsigned int> > >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from ../include/pbbam/BamHeader.h:15,
from ../include/pbbam/BamWriter.h:14,
from ../include/pbbam/IndexedBamWriter.h:13,
from ../src/IndexedBamWriter.cpp:7:
/usr/include/c++/9/bits/stl_vector.h: In member function ‘void PacBio::BAM::internal::PbiBuilder2::AddBasicData(const PacBio::BAM::BamRecord&, int64_t)’:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int, std::allocator<long long unsigned int> > >’ changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/BamHeader.h:15,
from ../include/pbbam/BamWriter.h:14,
from ../include/pbbam/IndexedBamWriter.h:13,
from ../src/IndexedBamWriter.cpp:7:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PacBio::BAM::internal::GzIndexEntry}; _Tp = PacBio::BAM::internal::GzIndexEntry; _Alloc = std::allocator<PacBio::BAM::internal::GzIndexEntry>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::BAM::internal::GzIndexEntry>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PacBio::BAM::internal::PbiFieldBlock2}; _Tp = PacBio::BAM::internal::PbiFieldBlock2; _Alloc = std::allocator<PacBio::BAM::internal::PbiFieldBlock2>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::BAM::internal::PbiFieldBlock2>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::PbiFieldBlock2*, std::vector<PacBio::BAM::internal::PbiFieldBlock2> >’} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::BAM::internal::PbiFieldBlock2>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::PbiFieldBlock2*, std::vector<PacBio::BAM::internal::PbiFieldBlock2> >’} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PacBio::BAM::internal::PbiFieldBlock2}; _Tp = PacBio::BAM::internal::PbiFieldBlock2; _Alloc = std::allocator<PacBio::BAM::internal::PbiFieldBlock2>]’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::PbiFieldBlock2*, std::vector<PacBio::BAM::internal::PbiFieldBlock2> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/boost/core/swap.hpp:25,
from /usr/include/boost/optional/optional.hpp:31,
from /usr/include/boost/optional.hpp:15,
from ../include/pbbam/ReadGroupInfo.h:16,
from ../include/pbbam/BamHeader.h:19,
from ../include/pbbam/BamWriter.h:14,
from ../include/pbbam/IndexedBamWriter.h:13,
from ../src/IndexedBamWriter.cpp:7:
/usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<PacBio::BAM::internal::PbiBuilder2::WriteVirtualOffsets()::<lambda(const PacBio::BAM::internal::GzIndexEntry&, const PacBio::BAM::internal::GzIndexEntry&)> >]’:
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<PacBio::BAM::internal::PbiBuilder2::WriteVirtualOffsets()::<lambda(const PacBio::BAM::internal::GzIndexEntry&, const PacBio::BAM::internal::GzIndexEntry&)> >]’:
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from /usr/include/boost/core/swap.hpp:25,
from /usr/include/boost/optional/optional.hpp:31,
from /usr/include/boost/optional.hpp:15,
from ../include/pbbam/ReadGroupInfo.h:16,
from ../include/pbbam/BamHeader.h:19,
from ../include/pbbam/BamWriter.h:14,
from ../include/pbbam/IndexedBamWriter.h:13,
from ../src/IndexedBamWriter.cpp:7:
/usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >; _Distance = int; _Tp = PacBio::BAM::internal::GzIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<PacBio::BAM::internal::PbiBuilder2::WriteVirtualOffsets()::<lambda(const PacBio::BAM::internal::GzIndexEntry&, const PacBio::BAM::internal::GzIndexEntry&)> >]’:
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/boost/core/swap.hpp:25,
from /usr/include/boost/optional/optional.hpp:31,
from /usr/include/boost/optional.hpp:15,
from ../include/pbbam/ReadGroupInfo.h:16,
from ../include/pbbam/BamHeader.h:19,
from ../include/pbbam/BamWriter.h:14,
from ../include/pbbam/IndexedBamWriter.h:13,
from ../src/IndexedBamWriter.cpp:7:
/usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<PacBio::BAM::internal::PbiBuilder2::WriteVirtualOffsets()::<lambda(const PacBio::BAM::internal::GzIndexEntry&, const PacBio::BAM::internal::GzIndexEntry&)> >]’:
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/BamHeader.h:15,
from ../include/pbbam/BamWriter.h:14,
from ../include/pbbam/IndexedBamWriter.h:13,
from ../src/IndexedBamWriter.cpp:7:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void PacBio::BAM::internal::PbiBuilder2::WriteFromTempFile()’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/boost/core/swap.hpp:25,
from /usr/include/boost/optional/optional.hpp:31,
from /usr/include/boost/optional.hpp:15,
from ../include/pbbam/ReadGroupInfo.h:16,
from ../include/pbbam/BamHeader.h:19,
from ../include/pbbam/BamWriter.h:14,
from ../include/pbbam/IndexedBamWriter.h:13,
from ../src/IndexedBamWriter.cpp:7:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::GzIndexEntry*, std::vector<PacBio::BAM::internal::GzIndexEntry> >’ changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[49/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o' -c ../src/PbiBuilder.cpp
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/BamHeader.h:15,
from ../src/MemoryUtils.h:12,
from ../src/PbiBuilder.cpp:26:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long unsigned int, std::allocator<long long unsigned int> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int, std::allocator<long long unsigned int> > >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PacBio::BAM::internal::PbiFieldBlock}; _Tp = PacBio::BAM::internal::PbiFieldBlock; _Alloc = std::allocator<PacBio::BAM::internal::PbiFieldBlock>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::BAM::internal::PbiFieldBlock>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::PbiFieldBlock*, std::vector<PacBio::BAM::internal::PbiFieldBlock> >’} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PacBio::BAM::internal::PbiFieldBlock}; _Tp = PacBio::BAM::internal::PbiFieldBlock; _Alloc = std::allocator<PacBio::BAM::internal::PbiFieldBlock>]’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::internal::PbiFieldBlock*, std::vector<PacBio::BAM::internal::PbiFieldBlock> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from ../include/pbbam/BamHeader.h:15,
from ../src/MemoryUtils.h:12,
from ../src/PbiBuilder.cpp:26:
/usr/include/c++/9/bits/stl_vector.h: In member function ‘void PacBio::BAM::PbiBuilder::AddRecord(const PacBio::BAM::BamRecord&, int64_t)’:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int, std::allocator<long long unsigned int> > >’ changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
[50/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o' -c ../src/PbiFilterQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiFilterQuery.h:12,
from ../src/PbiFilterQuery.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[51/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o' -c ../src/PbiIndexedBamReader.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../src/PbiIndexedBamReader.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[52/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o' -c ../src/PbiFilterTypes.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../src/PbiFilterTypes.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[53/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o' -c ../src/PbiIndexIO.cpp
[54/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o' -c ../src/PbiRawData.cpp
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/PbiRawData.h:14,
from ../src/PbiRawData.cpp:9:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from ../include/pbbam/PbiRawData.h:14,
from ../src/PbiRawData.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function ‘void PacBio::BAM::PbiRawBasicData::AddRecord(const PacBio::BAM::BamRecord&, int64_t)’:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
../src/PbiRawData.cpp:247:1: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’} changed in GCC 7.1
247 | }
| ^
[55/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/QualityValue.cpp.o' -MF 'src/25a6634@@pbbam@sha/QualityValue.cpp.o.d' -o 'src/25a6634@@pbbam@sha/QualityValue.cpp.o' -c ../src/QualityValue.cpp
[56/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o' -MF 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o' -c ../src/PbiFilter.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../src/PbiFilter.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[57/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o' -MF 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o' -c ../src/ProgramInfo.cpp
[58/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/QualityValues.cpp.o' -MF 'src/25a6634@@pbbam@sha/QualityValues.cpp.o.d' -o 'src/25a6634@@pbbam@sha/QualityValues.cpp.o' -c ../src/QualityValues.cpp
[59/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/RecordType.cpp.o' -MF 'src/25a6634@@pbbam@sha/RecordType.cpp.o.d' -o 'src/25a6634@@pbbam@sha/RecordType.cpp.o' -c ../src/RecordType.cpp
[60/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o' -c ../src/QNameQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../include/pbbam/CompositeBamReader.h:24,
from ../src/QNameQuery.cpp:15:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[61/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/SamWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/SamWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/SamWriter.cpp.o' -c ../src/SamWriter.cpp
[62/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o' -c ../src/ReadAccuracyQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../include/pbbam/CompositeBamReader.h:24,
from ../src/ReadAccuracyQuery.cpp:11:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[63/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/StringUtilities.cpp.o' -MF 'src/25a6634@@pbbam@sha/StringUtilities.cpp.o.d' -o 'src/25a6634@@pbbam@sha/StringUtilities.cpp.o' -c ../src/StringUtilities.cpp
[64/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o' -MF 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o.d' -o 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o' -c ../src/SequenceInfo.cpp
[65/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o' -MF 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o.d' -o 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o' -c ../src/SamTagCodec.cpp
[66/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/TagCollection.cpp.o' -MF 'src/25a6634@@pbbam@sha/TagCollection.cpp.o.d' -o 'src/25a6634@@pbbam@sha/TagCollection.cpp.o' -c ../src/TagCollection.cpp
[67/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o' -c ../src/SubreadLengthQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../include/pbbam/CompositeBamReader.h:24,
from ../src/SubreadLengthQuery.cpp:13:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[68/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o' -MF 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o' -c ../src/ReadGroupInfo.cpp
[69/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o' -MF 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o' -c ../src/ValidationErrors.cpp
[70/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ValidationException.cpp.o' -MF 'src/25a6634@@pbbam@sha/ValidationException.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ValidationException.cpp.o' -c ../src/ValidationException.cpp
[71/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Version.cpp.o' -MF 'src/25a6634@@pbbam@sha/Version.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Version.cpp.o' -c ../src/Version.cpp
[72/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Validator.cpp.o' -MF 'src/25a6634@@pbbam@sha/Validator.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Validator.cpp.o' -c ../src/Validator.cpp
[73/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o' -c ../src/VirtualZmwReader.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../src/VirtualZmwReader.h:16,
from ../src/VirtualZmwReader.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[74/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o' -c ../src/VirtualZmwCompositeReader.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../src/VirtualZmwReader.h:16,
from ../src/VirtualZmwCompositeReader.h:16,
from ../src/VirtualZmwCompositeReader.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[75/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/VirtualRegion.cpp.o' -MF 'src/25a6634@@pbbam@sha/VirtualRegion.cpp.o.d' -o 'src/25a6634@@pbbam@sha/VirtualRegion.cpp.o' -c ../src/VirtualRegion.cpp
[76/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o' -MF 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o.d' -o 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o' -c ../src/VirtualRegionTypeMap.cpp
[77/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o' -MF 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o.d' -o 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o' -c ../src/VirtualZmwBamRecord.cpp
[78/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o' -c ../src/XmlWriter.cpp
[79/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/Tag.cpp.o' -MF 'src/25a6634@@pbbam@sha/Tag.cpp.o.d' -o 'src/25a6634@@pbbam@sha/Tag.cpp.o' -c ../src/Tag.cpp
[80/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/XmlReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/XmlReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/XmlReader.cpp.o' -c ../src/XmlReader.cpp
[81/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o' -MF 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o.d' -o 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o' -c ../src/WhitelistedZmwReadStitcher.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../src/VirtualZmwReader.h:16,
from ../src/WhitelistedZmwReadStitcher.cpp:14:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[82/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o' -c ../src/ZmwTypeMap.cpp
[83/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfFile.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfFile.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfFile.cpp.o' -c ../src/vcf/VcfFile.cpp
[84/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o' -c ../src/ZmwReadStitcher.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../src/VirtualZmwReader.h:16,
from ../src/ZmwReadStitcher.cpp:16:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[85/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o' -c ../src/ZmwGroupQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../include/pbbam/CompositeBamReader.h:24,
from ../src/ZmwGroupQuery.cpp:17:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[86/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o' -c ../src/vcf/VcfHeader.cpp
[87/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o' -c ../src/ZmwQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiIndexedBamReader.h:14,
from ../include/pbbam/CompositeBamReader.h:24,
from ../src/ZmwQuery.cpp:13:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[88/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o' -c ../src/vcf/VcfFormat.cpp
[89/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfHeaderTypes.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfHeaderTypes.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfHeaderTypes.cpp.o' -c ../src/vcf/VcfHeaderTypes.cpp
[90/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o' -c ../src/vcf/VcfReader.cpp
[91/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o' -c ../src/vcf/VcfWriter.cpp
[92/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o' -c ../src/vcf/VcfQuery.cpp
[93/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o' -c ../src/vcf/VcfSort.cpp
[94/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o' -MF 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o.d' -o 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o' -c ../src/vcf/VcfVariant.cpp
[95/179] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o' -MF 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o.d' -o 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o' -c ../src/pugixml/pugixml.cpp
[96/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o' -c ../tests/src/test_BamRecordImplTags.cpp
[97/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o' -c ../tests/src/test_AlignmentPrinter.cpp
[98/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o' -c ../tests/src/test_BamRecordBuilder.cpp
[99/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o' -c ../tests/src/test_BamRecordImplCore.cpp
[100/179] c++ -o src/libpbbam.so.0.23.0 'src/25a6634@@pbbam@sha/Accuracy.cpp.o' 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' 'src/25a6634@@pbbam@sha/BaiIndexedBamReader.cpp.o' 'src/25a6634@@pbbam@sha/BamFile.cpp.o' 'src/25a6634@@pbbam@sha/BamFileMerger.cpp.o' 'src/25a6634@@pbbam@sha/BamHeader.cpp.o' 'src/25a6634@@pbbam@sha/BamReader.cpp.o' 'src/25a6634@@pbbam@sha/BamRecord.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordBuilder.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordImpl.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordTags.cpp.o' 'src/25a6634@@pbbam@sha/BamRecordView.cpp.o' 'src/25a6634@@pbbam@sha/BamTagCodec.cpp.o' 'src/25a6634@@pbbam@sha/BamWriter.cpp.o' 'src/25a6634@@pbbam@sha/BarcodeQuery.cpp.o' 'src/25a6634@@pbbam@sha/ChemistryTable.cpp.o' 'src/25a6634@@pbbam@sha/Cigar.cpp.o' 'src/25a6634@@pbbam@sha/CigarOperation.cpp.o' 'src/25a6634@@pbbam@sha/Compare.cpp.o' 'src/25a6634@@pbbam@sha/CompositeFastaReader.cpp.o' 'src/25a6634@@pbbam@sha/Config.cpp.o' 'src/25a6634@@pbbam@sha/DataSet.cpp.o' 'src/25a6634@@pbbam@sha/DataSetBaseTypes.cpp.o' 'src/25a6634@@pbbam@sha/DataSetElement.cpp.o' 'src/25a6634@@pbbam@sha/DataSetIO.cpp.o' 'src/25a6634@@pbbam@sha/DataSetTypes.cpp.o' 'src/25a6634@@pbbam@sha/DataSetXsd.cpp.o' 'src/25a6634@@pbbam@sha/EntireFileQuery.cpp.o' 'src/25a6634@@pbbam@sha/FastaCache.cpp.o' 'src/25a6634@@pbbam@sha/FastaReader.cpp.o' 'src/25a6634@@pbbam@sha/FastaSequence.cpp.o' 'src/25a6634@@pbbam@sha/FastaSequenceQuery.cpp.o' 'src/25a6634@@pbbam@sha/FastaWriter.cpp.o' 'src/25a6634@@pbbam@sha/FastqReader.cpp.o' 'src/25a6634@@pbbam@sha/FastqSequence.cpp.o' 'src/25a6634@@pbbam@sha/FastqWriter.cpp.o' 'src/25a6634@@pbbam@sha/FileProducer.cpp.o' 'src/25a6634@@pbbam@sha/FileUtils.cpp.o' 'src/25a6634@@pbbam@sha/FofnReader.cpp.o' 'src/25a6634@@pbbam@sha/Frames.cpp.o' 'src/25a6634@@pbbam@sha/GenomicInterval.cpp.o' 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o' 'src/25a6634@@pbbam@sha/IRecordWriter.cpp.o' 'src/25a6634@@pbbam@sha/MD5.cpp.o' 'src/25a6634@@pbbam@sha/MemoryUtils.cpp.o' 'src/25a6634@@pbbam@sha/PbiBuilder.cpp.o' 'src/25a6634@@pbbam@sha/PbiFile.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilter.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilterQuery.cpp.o' 'src/25a6634@@pbbam@sha/PbiFilterTypes.cpp.o' 'src/25a6634@@pbbam@sha/PbiIndexedBamReader.cpp.o' 'src/25a6634@@pbbam@sha/PbiIndexIO.cpp.o' 'src/25a6634@@pbbam@sha/PbiRawData.cpp.o' 'src/25a6634@@pbbam@sha/ProgramInfo.cpp.o' 'src/25a6634@@pbbam@sha/QNameQuery.cpp.o' 'src/25a6634@@pbbam@sha/QualityValue.cpp.o' 'src/25a6634@@pbbam@sha/QualityValues.cpp.o' 'src/25a6634@@pbbam@sha/ReadAccuracyQuery.cpp.o' 'src/25a6634@@pbbam@sha/ReadGroupInfo.cpp.o' 'src/25a6634@@pbbam@sha/RecordType.cpp.o' 'src/25a6634@@pbbam@sha/SamTagCodec.cpp.o' 'src/25a6634@@pbbam@sha/SamWriter.cpp.o' 'src/25a6634@@pbbam@sha/SequenceInfo.cpp.o' 'src/25a6634@@pbbam@sha/StringUtilities.cpp.o' 'src/25a6634@@pbbam@sha/SubreadLengthQuery.cpp.o' 'src/25a6634@@pbbam@sha/Tag.cpp.o' 'src/25a6634@@pbbam@sha/TagCollection.cpp.o' 'src/25a6634@@pbbam@sha/Validator.cpp.o' 'src/25a6634@@pbbam@sha/ValidationErrors.cpp.o' 'src/25a6634@@pbbam@sha/ValidationException.cpp.o' 'src/25a6634@@pbbam@sha/Version.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwBamRecord.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwCompositeReader.cpp.o' 'src/25a6634@@pbbam@sha/VirtualZmwReader.cpp.o' 'src/25a6634@@pbbam@sha/VirtualRegion.cpp.o' 'src/25a6634@@pbbam@sha/VirtualRegionTypeMap.cpp.o' 'src/25a6634@@pbbam@sha/XmlReader.cpp.o' 'src/25a6634@@pbbam@sha/XmlWriter.cpp.o' 'src/25a6634@@pbbam@sha/WhitelistedZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam@sha/ZmwGroupQuery.cpp.o' 'src/25a6634@@pbbam@sha/ZmwReadStitcher.cpp.o' 'src/25a6634@@pbbam@sha/ZmwQuery.cpp.o' 'src/25a6634@@pbbam@sha/ZmwTypeMap.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfFile.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfFormat.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfHeader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfHeaderTypes.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfQuery.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfReader.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfSort.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfVariant.cpp.o' 'src/25a6634@@pbbam@sha/vcf_VcfWriter.cpp.o' 'src/25a6634@@pbbam@sha/pugixml_pugixml.cpp.o' -Wl,--as-needed -Wl,--no-undefined -shared -fPIC -Wl,--start-group -Wl,-soname,libpbbam.so.0.23.0 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhts.so -Wl,--end-group
[101/179] /usr/bin/meson --internal symbolextractor src/libpbbam.so.0.23.0 'src/25a6634@@pbbam@sha/libpbbam.so.0.23.0.symbols'
[102/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o' -c ../tests/src/test_Accuracy.cpp
[103/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o' -c ../tests/src/test_BamFile.cpp
[104/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecord.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecord.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecord.cpp.o' -c ../tests/src/test_BamRecord.cpp
[105/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamHeader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamHeader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamHeader.cpp.o' -c ../tests/src/test_BamHeader.cpp
[106/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' -c ../tests/src/test_BamWriter.cpp
[107/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o' -c ../tests/src/test_BarcodeQuery.cpp
[108/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o' -c ../tests/src/test_Cigar.cpp
[109/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' -c ../tests/src/test_BamRecordClipping.cpp
[110/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' -c ../tests/src/test_BamRecordMapping.cpp
[111/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o' -c ../tests/src/test_DataSetCore.cpp
[112/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o' -c ../tests/src/test_DataSetQuery.cpp
[113/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetXsd.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetXsd.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetXsd.cpp.o' -c ../tests/src/test_DataSetXsd.cpp
[114/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_EndToEnd.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_EndToEnd.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_EndToEnd.cpp.o' -c ../tests/src/test_EndToEnd.cpp
[115/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o' -c ../tests/src/test_Compare.cpp
[116/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_DataSetIO.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_DataSetIO.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_DataSetIO.cpp.o' -c ../tests/src/test_DataSetIO.cpp
[117/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' -c ../tests/src/test_BamRecordImplVariableData.cpp
[118/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o' -c ../tests/src/test_EntireFileQuery.cpp
[119/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o' -c ../tests/src/test_Fasta.cpp
[120/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o' -c ../tests/src/test_Frames.cpp
[121/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Fastq.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Fastq.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Fastq.cpp.o' -c ../tests/src/test_Fastq.cpp
[122/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_FileUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FileUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FileUtils.cpp.o' -c ../tests/src/test_FileUtils.cpp
[123/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervals.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervals.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervals.cpp.o' -c ../tests/src/test_GenomicIntervals.cpp
[124/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o' -c ../tests/src/test_IndexedBamWriter.cpp
[125/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervalQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervalQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervalQuery.cpp.o' -c ../tests/src/test_GenomicIntervalQuery.cpp
[126/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o' -c ../tests/src/test_IndexedFastaReader.cpp
[127/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o' -c ../tests/src/test_LongCigar.cpp
[128/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o' -c ../tests/src/test_Intervals.cpp
[129/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o' -c ../tests/src/test_QNameQuery.cpp
[130/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o' -c ../tests/src/test_PacBioIndex.cpp
In file included from /usr/include/c++/9/vector:72,
from /usr/include/gtest/gtest.h:60,
from ../tests/src/test_PacBioIndex.cpp:8:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/gtest/gtest.h:60,
from ../tests/src/test_PacBioIndex.cpp:8:
/usr/include/c++/9/bits/stl_vector.h: In member function ‘virtual void PacBioIndexTest_CreateOnTheFly_Test::TestBody()’:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
[131/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o' -c ../tests/src/test_QualityValues.cpp
[132/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o' -c ../tests/src/test_Pulse2BaseCache.cpp
[133/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o' -c ../tests/src/test_ReadAccuracyQuery.cpp
[134/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o' -c ../tests/src/test_ReadGroupInfo.cpp
[135/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o' -c ../tests/src/test_SamWriter.cpp
[136/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o' -c ../tests/src/test_PbiFilterQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../include/pbbam/PbiFilterQuery.h:12,
from ../tests/src/test_PbiFilterQuery.cpp:14:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[137/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o' -c ../tests/src/test_SequenceUtils.cpp
[138/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o' -c ../tests/src/test_StringUtils.cpp
[139/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o' -c ../tests/src/test_SubreadLengthQuery.cpp
[140/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o' -c ../tests/src/test_TimeUtils.cpp
[141/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o' -c ../tests/src/test_VcfFile.cpp
[142/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o' -c ../tests/src/test_PbiFilter.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../tests/src/test_PbiFilter.cpp:14:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[143/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o' -c ../tests/src/test_Validator.cpp
[144/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o' -c ../tests/src/test_VcfReader.cpp
[145/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o' -c ../tests/src/test_VcfHeader.cpp
[146/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o' -c ../tests/src/test_VcfFormat.cpp
[147/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o' -c ../tests/src/test_VcfSort.cpp
[148/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o' -c ../tests/src/test_VcfQuery.cpp
[149/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o' -c ../tests/src/test_VcfVariant.cpp
[150/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o' -c ../tests/src/test_Tags.cpp
[151/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o' -c ../tests/src/test_VcfWriter.cpp
[152/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o' -c ../tests/src/test_ZmwQuery.cpp
[153/179] /usr/bin/python3 ../tests/scripts/generate_data.py /<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests/data /<<BUILDDIR>>/pbbam-0.23.0+dfsg/obj-arm-linux-gnueabihf/tests
Generating test data in /<<BUILDDIR>>/pbbam-0.23.0+dfsg/obj-arm-linux-gnueabihf/tests
- Creating file: truncated.bam...done.
- Creating file: chunking_emptyfilters.subreadset.xml...done.
- Creating file: chunking_missingfilters.subreadset.xml...done.
- Creating file: normal.fa...done.
- Creating file: normal.fq...done.
- Creating symlink: aligned.bam...done.
- Creating symlink: aligned.bam.bai...done.
- Creating symlink: aligned.bam.pbi...done.
- Creating symlink: aligned2.bam...done.
- Creating symlink: aligned2.bam.bai...done.
- Creating symlink: aligned2.bam.pbi...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done.
- Creating symlink: missing_pbi.bam...done.
[154/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o' -c ../tests/src/test_Version.cpp
[155/179] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' -c ../tools/pbindex/src/main.cpp
[156/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o' -c ../tests/src/test_WhitelistedZmwReadStitcher.cpp
[157/179] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp
[158/179] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o' -c ../tools/bam2sam/src/Bam2Sam.cpp
[159/179] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' -c ../tools/bam2sam/src/main.cpp
[160/179] c++ -Itools/f9d35d4@@pbindex@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindex -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o' -c ../tools/pbindex/src/PbIndex.cpp
[161/179] c++ -o tools/pbindex 'tools/f9d35d4@@pbindex@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndex.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.23.0 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-0.23.0+dfsg/obj-arm-linux-gnueabihf/src
[162/179] c++ -Itools/f9d35d4@@bam2sam@exe -Itools -I../tools -Iinclude -I../include -I../tools/bam2sam -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp
[163/179] c++ -o tools/bam2sam 'tools/f9d35d4@@bam2sam@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2Sam.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group /usr/lib/arm-linux-gnueabihf/libhts.so -pthread /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group
[164/179] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' -c ../tools/pbindexdump/src/CppFormatter.cpp
[165/179] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o' -c ../tests/src/test_ZmwReadStitcher.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../tests/src/test_ZmwReadStitcher.cpp:11:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[166/179] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o' -c ../tools/pbindexdump/src/PbIndexDump.cpp
[167/179] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp
[168/179] c++ -o tests/pbbam_test 'tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_AlignmentPrinter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamFile.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamHeader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecord.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordBuilder.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordClipping.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplCore.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplTags.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordImplVariableData.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamRecordMapping.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BamWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BarcodeQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Cigar.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Compare.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetCore.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetIO.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_DataSetXsd.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_EndToEnd.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_EntireFileQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Fasta.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Fastq.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FileUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Frames.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervalQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_GenomicIntervals.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_IndexedBamWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastaReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Intervals.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_LongCigar.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_PacBioIndex.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_PbiFilterQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_QNameQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_QualityValues.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Pulse2BaseCache.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ReadAccuracyQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ReadGroupInfo.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_SamWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_SequenceUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_StringUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_SubreadLengthQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Tags.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_TimeUtils.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Validator.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfFile.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfFormat.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfHeader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfSort.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfVariant.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_VcfWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_Version.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_WhitelistedZmwReadStitcher.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ZmwReadStitcher.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_ZmwQuery.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.23.0 -lgtest -lgtest_main -pthread /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-0.23.0+dfsg/obj-arm-linux-gnueabihf/src
[169/179] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -c ../tools/pbindexdump/src/main.cpp
[170/179] c++ -Itools/f9d35d4@@pbindexdump@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbindexdump -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' -c ../tools/pbindexdump/src/JsonFormatter.cpp
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/PbiRawData.h:14,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, double, std::allocator>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from ../tools/pbindexdump/src/json.hpp:54,
from ../tools/pbindexdump/src/JsonFormatter.h:8,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from ../tools/pbindexdump/src/json.hpp:54,
from ../tools/pbindexdump/src/JsonFormatter.h:8,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/stl_map.h: In member function ‘nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::value_type& nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::operator[](const T (&)[n]) [with T = char; unsigned int n = 12; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function ‘nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::value_type& nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::operator[](const T (&)[n]) [with T = char; unsigned int n = 11; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function ‘nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::value_type& nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::operator[](const T (&)[n]) [with T = char; unsigned int n = 4; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function ‘nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::value_type& nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::operator[](const T (&)[n]) [with T = char; unsigned int n = 7; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function ‘nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::value_type& nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::operator[](const T (&)[n]) [with T = char; unsigned int n = 5; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function ‘nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::value_type& nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberFloatType, AllocatorType>::operator[](const T (&)[n]) [with T = char; unsigned int n = 10; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberFloatType = double; AllocatorType = std::allocator]’:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatRaw()’:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/PbiRawData.h:14,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void pbindexdump::JsonFormatter::FormatMetadata()’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from ../tools/pbindexdump/src/json.hpp:54,
from ../tools/pbindexdump/src/JsonFormatter.h:8,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatRecords()’:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/PbiRawData.h:14,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from ../tools/pbindexdump/src/json.hpp:54,
from ../tools/pbindexdump/src/JsonFormatter.h:8,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function ‘void pbindexdump::JsonFormatter::FormatReferences()’:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/PbiRawData.h:14,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from ../tools/pbindexdump/src/json.hpp:54,
from ../tools/pbindexdump/src/JsonFormatter.h:8,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
[171/179] c++ -o tools/pbindexdump 'tools/f9d35d4@@pbindexdump@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDump.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.23.0 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-0.23.0+dfsg/obj-arm-linux-gnueabihf/src
[172/179] c++ -Itools/f9d35d4@@pbmerge@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' -MF 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' -c ../tools/pbmerge/src/main.cpp
[173/179] c++ -Itools/f9d35d4@@pbmerge@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbmerge -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp
[174/179] c++ -o tools/pbmerge 'tools/f9d35d4@@pbmerge@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.23.0 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-0.23.0+dfsg/obj-arm-linux-gnueabihf/src
[175/179] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o' -c ../tools/common/OptionParser.cpp
[176/179] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' -c ../tools/pbbamify/src/main.cpp
[177/179] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o' -c ../tools/pbbamify/src/PbBamify.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:900,
from ../include/pbbam/PbiFilter.h:244,
from ../tools/pbbamify/src/PbBamify.cpp:8:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:437:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
437 | return static_cast<uint32_t>(seed);
| ^
[178/179] c++ -Itools/f9d35d4@@pbbamify@exe -Itools -I../tools -Iinclude -I../include -I../tools/pbbamify -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++11 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -c ../tools/pbbamify/src/QueryLookup.cpp
[179/179] c++ -o tools/pbbamify 'tools/f9d35d4@@pbbamify@exe/common_OptionParser.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamify.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-0.23.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.0.23.0 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-0.23.0+dfsg/obj-arm-linux-gnueabihf/src
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/pbbam-0.23.0+dfsg'
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
-e 's|@PacBioBAM_BinDir@/||g' \
-e 's|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$SAMTOOLS/samtools/g' \
tests/src/cram/pbmerge_pacbio_ordering.t.in > tests/src/cram/pbmerge_pacbio_ordering.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
-e 's|@PacBioBAM_BinDir@/||g' \
-e 's|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$SAMTOOLS/samtools/g' \
tests/src/cram/pbmerge_mixed_ordering.t.in > tests/src/cram/pbmerge_mixed_ordering.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
-e 's|@PacBioBAM_BinDir@/||g' \
-e 's|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$SAMTOOLS/samtools/g' \
tests/src/cram/pbmerge_aligned_ordering.t.in > tests/src/cram/pbmerge_aligned_ordering.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
-e 's|@PacBioBAM_BinDir@/||g' \
-e 's|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$SAMTOOLS/samtools/g' \
tests/src/cram/pbindexdump_json.t.in > tests/src/cram/pbindexdump_json.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
-e 's|@PacBioBAM_BinDir@/||g' \
-e 's|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$SAMTOOLS/samtools/g' \
tests/src/cram/pbindexdump_cpp.t.in > tests/src/cram/pbindexdump_cpp.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
-e 's|@PacBioBAM_BinDir@/||g' \
-e 's|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$SAMTOOLS/samtools/g' \
tests/src/cram/pbmerge_fofn.t.in > tests/src/cram/pbmerge_fofn.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
-e 's|@PacBioBAM_BinDir@/||g' \
-e 's|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$SAMTOOLS/samtools/g' \
tests/src/cram/pbbamify.t.in > tests/src/cram/pbbamify.deb.t
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
-e 's|@PacBioBAM_BinDir@/||g' \
-e 's|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|0.23.0+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$SAMTOOLS/samtools/g' \
tests/src/cram/pbmerge_dataset.t.in > tests/src/cram/pbmerge_dataset.deb.t
dh_auto_configure -O--buildsystem=meson
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/arm-linux-gnueabihf
Directory already configured.
Just run your build command (e.g. ninja) and Meson will regenerate as necessary.
If ninja fails, run "ninja reconfigure" or "meson --reconfigure"
to force Meson to regenerate.
If build failures persist, run "meson setup --wipe" to rebuild from scratch
using the same options as passed when configuring the build.
To change option values, run "meson configure" instead.
mkdir -p /<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata
python3 tests/scripts/generate_data.py /<<BUILDDIR>>/pbbam-0.23.0+dfsg/tests/data /<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata
Generating test data in /<<BUILDDIR>>/pbbam-0.23.0+dfsg/gendata
- Creating file: truncated.bam...done.
- Creating file: chunking_emptyfilters.subreadset.xml...done.
- Creating file: chunking_missingfilters.subreadset.xml...done.
- Creating file: normal.fa...done.
- Creating file: normal.fq...done.
- Creating symlink: aligned.bam...done.
- Creating symlink: aligned.bam.bai...done.
- Creating symlink: aligned.bam.pbi...done.
- Creating symlink: aligned2.bam...done.
- Creating symlink: aligned2.bam.bai...done.
- Creating symlink: aligned2.bam.pbi...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.1.subreads.bam.pbi...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam...done.
- Creating symlink: m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi...done.
- Creating symlink: missing_pbi.bam...done.
# Fix broken PATH
synthetic_movie_all_path=`find $PWD -name synthetic_movie_all.subreadset.xml` ; \
sed -i -e "s?.GENERATEDDATADIR/synthetic_movie_all.subreadset.xml?${synthetic_movie_all_path}?" tests/src/cram/pbbamify*
BINDIR=`dirname $(find $PWD -name pbmerge -type f -executable)`; \
LIBDIR=`find $PWD -name lib -type d`; \
PATH="$BINDIR:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" LD_LIBRARY_PATH="$LIBDIR:" \
cram3 -v --preserve-env tests/src/cram/pbmerge_pacbio_ordering.deb.t tests/src/cram/pbmerge_mixed_ordering.deb.t tests/src/cram/pbmerge_aligned_ordering.deb.t tests/src/cram/pbindexdump_json.deb.t tests/src/cram/pbindexdump_cpp.deb.t tests/src/cram/pbmerge_fofn.deb.t tests/src/cram/pbbamify.deb.t tests/src/cram/pbmerge_dataset.deb.t
tests/src/cram/pbmerge_pacbio_ordering.deb.t: passed
tests/src/cram/pbmerge_mixed_ordering.deb.t: passed
tests/src/cram/pbmerge_aligned_ordering.deb.t: failed
--- tests/src/cram/pbmerge_aligned_ordering.deb.t
+++ tests/src/cram/pbmerge_aligned_ordering.deb.t.err
@@ -122,6 +122,8 @@
Explicit Output Filename (also enables PBI):
$ $PBMERGE -o $MERGED_BAM $INPUT_1 $INPUT_2
+ ERROR: stoul
+ [1]
$ samtools view -H $MERGED_BAM
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@@ -131,26 +133,6 @@
@PG\tID:pbmerge-0.23.0\tPN:pbmerge\tVN:0.23.0 (esc)
$ samtools view $MERGED_BAM | cut -f 1,3,4 | head -n 20
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/49050/48_1132\tlambda_NEB3011\t1 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/387_1134\tlambda_NEB3011\t303 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/32328/0_344\tlambda_NEB3011\t676 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/9936_10187\tlambda_NEB3011\t2171 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/6469/10232_10394\tlambda_NEB3011\t2204 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7468_8906\tlambda_NEB3011\t3573 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/5557_7235\tlambda_NEB3011\t4507 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/13473/7285_8657\tlambda_NEB3011\t4508 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/426_1045\tlambda_NEB3011\t4593 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/30983/7064_7421\tlambda_NEB3011\t4670 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/19915/0_382\tlambda_NEB3011\t4843 (esc)
- m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/7247/7338_7831\tlambda_NEB3011\t4904 (esc)
$ [ -f $MERGED_BAM_PBI ] && echo "Found" || echo "Not found"
Found
tests/src/cram/pbindexdump_json.deb.t: passed
tests/src/cram/pbindexdump_cpp.deb.t: passed
tests/src/cram/pbmerge_fofn.deb.t: passed
tests/src/cram/pbbamify.deb.t: passed
tests/src/cram/pbmerge_dataset.deb.t: passed
# Ran 8 tests, 0 skipped, 1 failed.
make[1]: *** [debian/rules:22: override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/pbbam-0.23.0+dfsg'
make: *** [debian/rules:13: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-11-27T02:13:50Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 2555
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 599
Job: pbbam_0.23.0+dfsg-1
Machine Architecture: armhf
Package: pbbam
Package-Time: 3217
Source-Version: 0.23.0+dfsg-1
Space: 0
Status: failed
Version: 0.23.0+dfsg-1
--------------------------------------------------------------------------------
Finished at 2019-11-27T02:13:50Z
Build needed 00:00:00, 0k disc space