pbbam →
1.0.6+dfsg-2 →
armhf → 2020-02-04 19:03:19
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| pbbam 1.0.6+dfsg-2 (armhf) Tue, 04 Feb 2020 16:58:18 +0000 |
+==============================================================================+
Package: pbbam
Version: 1.0.6+dfsg-2
Source Version: 1.0.6+dfsg-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-ebc5c705-9ac8-4cbd-a815-4eede30c4e55' 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 [12.7 MB]
Fetched 24.2 MB in 41s (590 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 7766 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main pbbam 1.0.6+dfsg-2 (dsc) [2320 B]
Get:2 http://172.17.0.1/private bullseye-staging/main pbbam 1.0.6+dfsg-2 (tar) [7755 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main pbbam 1.0.6+dfsg-2 (diff) [8500 B]
Fetched 7766 kB in 2s (5006 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbbam-EgUd6F/pbbam-1.0.6+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbbam-EgUd6F' 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-TMQfFP/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-TMQfFP/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-TMQfFP/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-TMQfFP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-TMQfFP/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-TMQfFP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-TMQfFP/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-TMQfFP/apt_archive ./ Packages [434 B]
Fetched 2110 B in 2s (1156 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 0 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-TMQfFP/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 ... 12256 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, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>= 1.3.0), python3-cram, libgtest-dev, samtools
Filtered Build-Depends: debhelper-compat (= 12), dh-exec, d-shlibs, meson, pkg-config, cmake, libboost-dev, zlib1g-dev, libssl-dev, libhts-dev, libpbcopper-dev (>= 1.3.0), python3-cram, libgtest-dev, samtools
dpkg-deb: building package 'sbuild-build-depends-pbbam-dummy' in '/<<BUILDDIR>>/resolver-TMQfFP/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-TMQfFP/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-TMQfFP/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-TMQfFP/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-TMQfFP/apt_archive ./ Sources [592 B]
Get:5 copy:/<<BUILDDIR>>/resolver-TMQfFP/apt_archive ./ Packages [661 B]
Fetched 2586 B in 2s (1382 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 cmake cmake-data
d-shlibs debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file
gettext gettext-base googletest groff-base intltool-debian
libarchive-zip-perl libarchive13 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 libhts3 libicu63 libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1
libmpdec2 libncurses6 libnghttp2-14 libpbcopper-dev libpbcopper1.3.0
libpipeline1 libprocps7 libpsl5 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl-dev
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libuv1 libxml2
m4 man-db meson mime-support ninja-build pkg-config po-debconf procps
python3 python3-cram python3-minimal python3.7 python3.7-minimal samtools
sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev
groff lrzip libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-contract1.67-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 python3.7-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 psmisc cwltool
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
d-shlibs debhelper dh-autoreconf dh-exec dh-strip-nondeterminism dwz file
gettext gettext-base googletest groff-base intltool-debian
libarchive-zip-perl libarchive13 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 libhts3 libicu63 libjsoncpp1 libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1
libmpdec2 libncurses6 libnghttp2-14 libpbcopper-dev libpbcopper1.3.0
libpipeline1 libprocps7 libpsl5 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librhash0 librtmp1 libsigsegv2 libssh2-1 libssl-dev
libssl1.1 libsub-override-perl libtinfo5 libtool libuchardet0 libuv1 libxml2
m4 man-db meson mime-support ninja-build pkg-config po-debconf procps
python3 python3-cram python3-minimal python3.7 python3.7-minimal samtools
sbuild-build-depends-pbbam-dummy sensible-utils zlib1g-dev
0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded.
Need to get 48.8 MB of archives.
After this operation, 277 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-TMQfFP/apt_archive ./ sbuild-build-depends-pbbam-dummy 0.invalid.0 [952 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 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [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 3.7.6-1+b1 [585 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 3.7.6-1+b1 [1525 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-3 [36.8 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 3.7.6-1+b1 [1669 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.6-1+b1 [351 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-3 [20.2 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-3 [62.1 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libprocps7 armhf 2:3.3.15-2 [58.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.15-2 [235 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.15.4-1+rpi1 [1580 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.0-1+b1 [292 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6 [261 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.67.0-2 [284 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3.1 [65.8 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.3.9-1 [133 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.33.1-3 [112 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.15.4-1+rpi1 [2540 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf d-shlibs all 0.88 [17.4 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.9 [183 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1+rpi1 [1137 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.9 [994 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf dh-exec armhf 0.23.2+b2 [25.7 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf googletest all 1.10.0-2 [626 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-17 [8389 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b11 [4464 B]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.5-1 [78.0 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libgtest-dev armhf 1.10.0-2 [218 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-2 [327 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.10.2-2 [4784 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libpbcopper1.3.0 armhf 1.3.0+dfsg-3 [277 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libpbcopper-dev armhf 1.3.0+dfsg-3 [149 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1d-2 [1570 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf ninja-build armhf 1.10.0-1 [90.4 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf meson all 0.52.1-1 [358 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf python3-cram all 0.7-4 [17.3 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.9-7+rpi1 [401 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libbsd0:armhf.
(Reading database ... 12256 files and directories currently installed.)
Preparing to unpack .../00-libbsd0_0.10.0-1_armhf.deb ...
Unpacking libbsd0:armhf (0.10.0-1) ...
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Unpacking bsdmainutils (11.1.2) ...
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Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
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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) ...
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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
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Setting up python3 (3.7.5-3) ...
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Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up python3-cram (0.7-4) ...
Setting up cmake (3.15.4-1+rpi1) ...
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Setting up meson (0.52.1-1) ...
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Processing triggers for libc-bin (2.29-7+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_2.33.90.20200122-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-25+rpi1 gcc-9_9.2.1-25+rpi1 libc6-dev_2.29-7+rpi1 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.90.20200122-2+rpi1 binutils-arm-linux-gnueabihf_2.33.90.20200122-2+rpi1 binutils-common_2.33.90.20200122-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 cmake_3.15.4-1+rpi1 cmake-data_3.15.4-1+rpi1 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-25+rpi1 d-shlibs_0.88 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debianutils_4.9.1 dh-autoreconf_19 dh-exec_0.23.2+b2 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dirmngr_2.2.19-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-25+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-3+b1 gcc-8-base_8.3.0-26+rpi1 gcc-9_9.2.1-25+rpi1 gcc-9-base_9.2.1-25+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 googletest_1.10.0-2 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.3-1 groff-base_1.22.4-4 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 libarchive13_3.4.0-1+b1 libasan5_9.2.1-25+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-25+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.90.20200122-2+rpi1 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b11 libboost1.67-dev_1.67.0-17 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-7+rpi1 libc-dev-bin_2.29-7+rpi1 libc6_2.29-7+rpi1 libc6-dev_2.29-7+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-25+rpi1 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libctf-nobfd0_2.33.90.20200122-2+rpi1 libctf0_2.33.90.20200122-2+rpi1 libcurl3-gnutls_7.67.0-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.9 libdeflate0_1.5-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libgcc-9-dev_9.2.1-25+rpi1 libgcc1_1:9.2.1-25+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-1+rpi1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-25+rpi1 libgpg-error0_1.36-7 libgssapi-krb5-2_1.17-6+b1 libgtest-dev_1.10.0-2 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-2 libhts3_1.10.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libjsoncpp1_1.7.4-3.1 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 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 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+b2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2+b1 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 libpbcopper-dev_1.3.0+dfsg-3 libpbcopper1.3.0_1.3.0+dfsg-3 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1+b1 libpython3.7-stdlib_3.7.6-1+b1 libreadline8_8.0-3 librhash0_1.3.9-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.0+really3.30.1+fossil191229-1 libss2_1.45.5-2 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1d-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-25+rpi1 libstdc++6_9.2.1-25+rpi1 libsub-override-perl_0.09-2 libsystemd0_244.1-1+rpi1 libtasn1-6_4.15.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-25+rpi1 libuchardet0_0.0.6-3 libudev1_244.1-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libuv1_1.33.1-3 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-1 meson_0.52.1-1 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 ninja-build_1.10.0-1 passwd_1:4.8-1 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 procps_2:3.3.15-2 python3_3.7.5-3 python3-cram_0.7-4 python3-minimal_3.7.5-3 python3.7_3.7.6-1+b1 python3.7-minimal_3.7.6-1+b1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 samtools_1.9-7+rpi1 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+nmu1 sysvinit-utils_2.96-2.1 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 Sat Dec 21 12:36:00 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_1.0.6+dfsg-2.dsc
dpkg-source: info: extracting pbbam in /<<BUILDDIR>>/pbbam-1.0.6+dfsg
dpkg-source: info: unpacking pbbam_1.0.6+dfsg.orig.tar.xz
dpkg-source: info: unpacking pbbam_1.0.6+dfsg-2.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
dpkg-source: info: applying results_with_latest_samtools.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-ebc5c705-9ac8-4cbd-a815-4eede30c4e55
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbbam
dpkg-buildpackage: info: source version 1.0.6+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem=meson
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/pbbam-1.0.6+dfsg'
dh_auto_clean
find -name "*.deb.t" -delete
rm -f -r /<<BUILDDIR>>/pbbam-1.0.6+dfsg/gendata
make[1]: Leaving directory '/<<BUILDDIR>>/pbbam-1.0.6+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: 0.52.1
Source dir: /<<BUILDDIR>>/pbbam-1.0.6+dfsg
Build dir: /<<BUILDDIR>>/pbbam-1.0.6+dfsg/obj-arm-linux-gnueabihf
Build type: native build
Project name: PacBioBAM
Project version: 1.0.6
Appending CXXFLAGS from environment: '-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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-1.0.6+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 9.2.1-25+rpi1) 9.2.1 20200123")
C++ linker for the host machine: GNU ld.bfd 2.33.90.20200122
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 1.10.2
Run-time dependency pbcopper found: YES 1.3.0
Program python3 found: YES (/usr/bin/python3)
Program tools/check-formatting found: YES (/<<BUILDDIR>>/pbbam-1.0.6+dfsg/tools/check-formatting)
Program cram3 found: YES (/usr/bin/cram3)
Run-time dependency GTest found: YES 1.10.0
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-1.10.0 at /usr/bin/ninja
dh_auto_build -a -O--buildsystem=meson
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v
[1/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[2/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/BaiIndexCache.cpp.o' -MF 'src/25a6634@@pbbam@sha/BaiIndexCache.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BaiIndexCache.cpp.o' -c ../src/BaiIndexCache.cpp
[3/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[4/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[5/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[6/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:27,
from ../src/BamFileMerger.cpp:21:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[7/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[8/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[9/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
../src/BamRecordImpl.cpp: In member function ‘PacBio::BAM::BamRecordImpl& PacBio::BAM::BamRecordImpl::operator=(const PacBio::BAM::BamRecordImpl&)’:
../src/BamRecordImpl.cpp:90:18: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’, declared with attribute warn_unused_result [-Wunused-result]
90 | bam_copy1(d_.get(), other.d_.get());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
../src/BamRecordImpl.cpp: In static member function ‘static PacBio::BAM::BamRecordImpl PacBio::BAM::BamRecordImpl::FromRawData(const std::shared_ptr<bam1_t>&)’:
../src/BamRecordImpl.cpp:234:14: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’, declared with attribute warn_unused_result [-Wunused-result]
234 | bam_copy1(result.d_.get(), rawData.get());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[10/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[11/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[12/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[13/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[14/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/BgzipFastaWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/BgzipFastaWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BgzipFastaWriter.cpp.o' -c ../src/BgzipFastaWriter.cpp
[15/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[16/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/BgzipFastqWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/BgzipFastqWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BgzipFastqWriter.cpp.o' -c ../src/BgzipFastqWriter.cpp
[17/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/BgzipWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/BgzipWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/BgzipWriter.cpp.o' -c ../src/BgzipWriter.cpp
[18/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[19/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:27,
from ../src/BarcodeQuery.cpp:13:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[20/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[21/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[22/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[23/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[24/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[25/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[26/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[27/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[28/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/FaiIndex.cpp.o' -MF 'src/25a6634@@pbbam@sha/FaiIndex.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FaiIndex.cpp.o' -c ../src/FaiIndex.cpp
[29/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:27,
from ../src/EntireFileQuery.cpp:11:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[30/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/FaiZmwChunker.cpp.o' -MF 'src/25a6634@@pbbam@sha/FaiZmwChunker.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FaiZmwChunker.cpp.o' -c ../src/FaiZmwChunker.cpp
In file included from /usr/include/c++/9/vector:72,
from ../src/FaiZmwChunker.h:13,
from ../src/FaiZmwChunker.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 = {PacBio::BAM::FaiZmwChunk}; _Tp = PacBio::BAM::FaiZmwChunk; _Alloc = std::allocator<PacBio::BAM::FaiZmwChunk>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::BAM::FaiZmwChunk>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::BAM::FaiZmwChunk*, std::vector<PacBio::BAM::FaiZmwChunk> >’} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {PacBio::BAM::FaiZmwChunk}; _Tp = PacBio::BAM::FaiZmwChunk; _Alloc = std::allocator<PacBio::BAM::FaiZmwChunk>]’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::BAM::FaiZmwChunk*, std::vector<PacBio::BAM::FaiZmwChunk> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
[31/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[32/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[33/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[34/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[35/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[36/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[37/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[38/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[39/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[40/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[41/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[42/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/IFastaWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/IFastaWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IFastaWriter.cpp.o' -c ../src/IFastaWriter.cpp
[43/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[44/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/IFastqWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/IFastqWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IFastqWriter.cpp.o' -c ../src/IFastqWriter.cpp
[45/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/FormatUtils.cpp.o' -MF 'src/25a6634@@pbbam@sha/FormatUtils.cpp.o.d' -o 'src/25a6634@@pbbam@sha/FormatUtils.cpp.o' -c ../src/FormatUtils.cpp
[46/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[47/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:27,
from ../src/GenomicIntervalQuery.cpp:11:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[48/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/IndexedFastqBgzfReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/IndexedFastqBgzfReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IndexedFastqBgzfReader.cpp.o' -c ../src/IndexedFastqBgzfReader.cpp
[49/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/IndexedFastqReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/IndexedFastqReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IndexedFastqReader.cpp.o' -c ../src/IndexedFastqReader.cpp
[50/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/IndexedFastqTextReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/IndexedFastqTextReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IndexedFastqTextReader.cpp.o' -c ../src/IndexedFastqTextReader.cpp
[51/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[52/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/IndexedFastqReaderImpl.cpp.o' -MF 'src/25a6634@@pbbam@sha/IndexedFastqReaderImpl.cpp.o.d' -o 'src/25a6634@@pbbam@sha/IndexedFastqReaderImpl.cpp.o' -c ../src/IndexedFastqReaderImpl.cpp
[53/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[54/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/BamHeader.h:17,
from ../include/pbbam/BamWriter.h:18,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.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 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:17,
from ../include/pbbam/BamWriter.h:18,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/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:17,
from ../include/pbbam/BamWriter.h:18,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.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 = {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 ‘std::vector<PacBio::BAM::internal::GzIndexEntry> PacBio::BAM::internal::PbiBuilder2::LoadGzi()’:
/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)...);
| ^~~~~~~~~~~~~~~~~
/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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/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:18,
from ../include/pbbam/BamHeader.h:20,
from ../include/pbbam/BamWriter.h:18,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/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:18,
from ../include/pbbam/BamHeader.h:20,
from ../include/pbbam/BamWriter.h:18,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/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:18,
from ../include/pbbam/BamHeader.h:20,
from ../include/pbbam/BamWriter.h:18,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function ‘void PacBio::BAM::internal::PbiBuilder2::WriteFromTempFile()’:
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[55/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/ccs_CCSPbiBuilder.cpp.o' -MF 'src/25a6634@@pbbam@sha/ccs_CCSPbiBuilder.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ccs_CCSPbiBuilder.cpp.o' -c ../src/ccs/CCSPbiBuilder.cpp
In file included from /usr/include/c++/9/vector:72,
from ../include/pbbam/Frames.h:14,
from ../include/pbbam/ccs/CCSRecord.h:9,
from ../include/pbbam/ccs/CCSPbiBuilder.h:11,
from ../src/ccs/CCSPbiBuilder.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 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::CCS::internal::PbiFieldBlock}; _Tp = PacBio::CCS::internal::PbiFieldBlock; _Alloc = std::allocator<PacBio::CCS::internal::PbiFieldBlock>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::CCS::internal::PbiFieldBlock>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::CCS::internal::PbiFieldBlock*, std::vector<PacBio::CCS::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::CCS::internal::PbiFieldBlock}; _Tp = PacBio::CCS::internal::PbiFieldBlock; _Alloc = std::allocator<PacBio::CCS::internal::PbiFieldBlock>]’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::CCS::internal::PbiFieldBlock*, std::vector<PacBio::CCS::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/Frames.h:14,
from ../include/pbbam/ccs/CCSRecord.h:9,
from ../include/pbbam/ccs/CCSPbiBuilder.h:11,
from ../src/ccs/CCSPbiBuilder.cpp:9:
/usr/include/c++/9/bits/stl_vector.h: In member function ‘void PacBio::CCS::CCSPbiBuilder::AddRecord(const PacBio::CCS::CCSRecord&)’:
/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);
| ^~~~~~~~~~~~~~~~~
[56/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/KSeqReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/KSeqReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/KSeqReader.cpp.o' -c ../src/KSeqReader.cpp
[57/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
../src/MemoryUtils.cpp: In static member function ‘static std::shared_ptr<sam_hdr_t> PacBio::BAM::BamHeaderMemory::MakeRawHeader(const PacBio::BAM::BamHeader&)’:
../src/MemoryUtils.cpp:32:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
32 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../src/MemoryUtils.h:13,
from ../src/MemoryUtils.cpp:5:
/usr/include/htslib/sam.h:74:19: note: declared here
74 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
| ^~~~~~~~~
../src/MemoryUtils.cpp:32:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
32 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../src/MemoryUtils.h:13,
from ../src/MemoryUtils.cpp:5:
/usr/include/htslib/sam.h:74:19: note: declared here
74 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
| ^~~~~~~~~
../src/MemoryUtils.cpp:32:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
32 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../src/MemoryUtils.h:13,
from ../src/MemoryUtils.cpp:5:
/usr/include/htslib/sam.h:74:19: note: declared here
74 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
| ^~~~~~~~~
[58/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[59/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:17,
from ../src/MemoryUtils.h:16,
from ../src/PbiBuilder.cpp:28:
/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:17,
from ../src/MemoryUtils.h:16,
from ../src/PbiBuilder.cpp:28:
/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);
| ^~~~~~~~~~~~~~~~~
[60/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiFilterQuery.h:14,
from ../src/PbiFilterQuery.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[61/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../src/PbiIndexedBamReader.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[62/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../src/PbiFilterTypes.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[63/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:16,
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:16,
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);
| ^~~~~~~~~~~~~~~~~
[64/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[65/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../src/PbiFilter.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[66/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[67/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[68/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:27,
from ../src/QNameQuery.cpp:15:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[69/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[70/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:27,
from ../src/ReadAccuracyQuery.cpp:11:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[71/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[72/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[73/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[74/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[75/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[76/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:27,
from ../src/SubreadLengthQuery.cpp:13:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[77/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/TextFileReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/TextFileReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/TextFileReader.cpp.o' -c ../src/TextFileReader.cpp
[78/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[79/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/TextFileWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/TextFileWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/TextFileWriter.cpp.o' -c ../src/TextFileWriter.cpp
[80/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[81/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[82/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[83/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../src/VirtualZmwCompositeReader.h:18,
from ../src/VirtualZmwCompositeReader.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[84/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[85/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[86/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[87/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[88/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[89/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../src/VirtualZmwReader.h:17,
from ../src/VirtualZmwReader.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[90/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/ZmwChunkedFastaReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwChunkedFastaReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwChunkedFastaReader.cpp.o' -c ../src/ZmwChunkedFastaReader.cpp
[91/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[92/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/ZmwChunkedFastxReaderImpl.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwChunkedFastxReaderImpl.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwChunkedFastxReaderImpl.cpp.o' -c ../src/ZmwChunkedFastxReaderImpl.cpp
[93/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/ZmwChunkedFastqReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwChunkedFastqReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwChunkedFastqReader.cpp.o' -c ../src/ZmwChunkedFastqReader.cpp
[94/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../src/VirtualZmwReader.h:17,
from ../src/WhitelistedZmwReadStitcher.cpp:14:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[95/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/ZmwChunkedFastxTextReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwChunkedFastxTextReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwChunkedFastxTextReader.cpp.o' -c ../src/ZmwChunkedFastxTextReader.cpp
[96/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/ZmwChunkedFastxBgzfReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/ZmwChunkedFastxBgzfReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ZmwChunkedFastxBgzfReader.cpp.o' -c ../src/ZmwChunkedFastxBgzfReader.cpp
[97/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[98/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../src/VirtualZmwReader.h:17,
from ../src/ZmwReadStitcher.cpp:16:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[99/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/bed_BedReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/bed_BedReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/bed_BedReader.cpp.o' -c ../src/bed/BedReader.cpp
[100/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/bed_BedWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/bed_BedWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/bed_BedWriter.cpp.o' -c ../src/bed/BedWriter.cpp
[101/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:27,
from ../src/ZmwGroupQuery.cpp:17:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[102/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:27,
from ../src/ZmwQuery.cpp:13:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[103/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_PbIndexDumpWorkflow.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDumpWorkflow.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDumpWorkflow.cpp.o' -c ../tools/pbindexdump/src/PbIndexDumpWorkflow.cpp
[104/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/ccs_CCSRecordFormat.cpp.o' -MF 'src/25a6634@@pbbam@sha/ccs_CCSRecordFormat.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ccs_CCSRecordFormat.cpp.o' -c ../src/ccs/CCSRecordFormat.cpp
[105/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/ccs_CCSRecordWriter.cpp.o' -MF 'src/25a6634@@pbbam@sha/ccs_CCSRecordWriter.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ccs_CCSRecordWriter.cpp.o' -c ../src/ccs/CCSRecordWriter.cpp
[106/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_PbIndexDumpSettings.cpp.o' -MF 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDumpSettings.cpp.o.d' -o 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDumpSettings.cpp.o' -c ../tools/pbindexdump/src/PbIndexDumpSettings.cpp
[107/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[108/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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/ccs_CCSRecordReader.cpp.o' -MF 'src/25a6634@@pbbam@sha/ccs_CCSRecordReader.cpp.o.d' -o 'src/25a6634@@pbbam@sha/ccs_CCSRecordReader.cpp.o' -c ../src/ccs/CCSRecordReader.cpp
[109/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[110/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[111/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[112/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[113/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[114/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[115/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[116/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[117/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
../tests/src/test_BamHeader.cpp: In member function ‘virtual void BamHeaderTest_ConvertToRawDataOk_Test::TestBody()’:
../tests/src/test_BamHeader.cpp:197:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
197 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../tests/src/test_BamHeader.cpp:9:
/usr/include/htslib/sam.h:74:19: note: declared here
74 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
| ^~~~~~~~~
../tests/src/test_BamHeader.cpp:197:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
197 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../tests/src/test_BamHeader.cpp:9:
/usr/include/htslib/sam.h:74:19: note: declared here
74 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
| ^~~~~~~~~
../tests/src/test_BamHeader.cpp:197:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
197 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../tests/src/test_BamHeader.cpp:9:
/usr/include/htslib/sam.h:74:19: note: declared here
74 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
| ^~~~~~~~~
../tests/src/test_BamHeader.cpp: In member function ‘virtual void BamHeaderTest_ExtractFromRawDataOk_Test::TestBody()’:
../tests/src/test_BamHeader.cpp:251:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
251 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../tests/src/test_BamHeader.cpp:9:
/usr/include/htslib/sam.h:74:19: note: declared here
74 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
| ^~~~~~~~~
../tests/src/test_BamHeader.cpp:251:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
251 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../tests/src/test_BamHeader.cpp:9:
/usr/include/htslib/sam.h:74:19: note: declared here
74 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
| ^~~~~~~~~
../tests/src/test_BamHeader.cpp:251:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
251 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../tests/src/test_BamHeader.cpp:9:
/usr/include/htslib/sam.h:74:19: note: declared here
74 | const int8_t *cigar_tab HTS_DEPRECATED("Use bam_cigar_table[] instead");
| ^~~~~~~~~
[118/216] c++ -Isrc/25a6634@@pbbam@sha -Isrc -I../src -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[119/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[120/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[121/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[122/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
../tests/src/test_BamRecordImplCore.cpp: In lambda function:
../tests/src/test_BamRecordImplCore.cpp:279:18: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’, declared with attribute warn_unused_result [-Wunused-result]
279 | bam_copy1(PacBio::BAM::BamRecordMemory::GetRawData(result).get(), rawData.get());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[123/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[124/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[125/216] c++ -o src/libpbbam.so.1.0.6 'src/25a6634@@pbbam@sha/AlignmentPrinter.cpp.o' 'src/25a6634@@pbbam@sha/BaiIndexCache.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/BgzipFastaWriter.cpp.o' 'src/25a6634@@pbbam@sha/BgzipFastqWriter.cpp.o' 'src/25a6634@@pbbam@sha/BgzipWriter.cpp.o' 'src/25a6634@@pbbam@sha/ChemistryTable.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/FaiIndex.cpp.o' 'src/25a6634@@pbbam@sha/FaiZmwChunker.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/FormatUtils.cpp.o' 'src/25a6634@@pbbam@sha/GenomicIntervalQuery.cpp.o' 'src/25a6634@@pbbam@sha/IFastaWriter.cpp.o' 'src/25a6634@@pbbam@sha/IFastqWriter.cpp.o' 'src/25a6634@@pbbam@sha/IndexedBamWriter.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastaReader.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastqBgzfReader.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastqReader.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastqTextReader.cpp.o' 'src/25a6634@@pbbam@sha/IndexedFastqReaderImpl.cpp.o' 'src/25a6634@@pbbam@sha/IRecordWriter.cpp.o' 'src/25a6634@@pbbam@sha/KSeqReader.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/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/TextFileReader.cpp.o' 'src/25a6634@@pbbam@sha/TextFileWriter.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/ZmwChunkedFastaReader.cpp.o' 'src/25a6634@@pbbam@sha/ZmwChunkedFastqReader.cpp.o' 'src/25a6634@@pbbam@sha/ZmwChunkedFastxBgzfReader.cpp.o' 'src/25a6634@@pbbam@sha/ZmwChunkedFastxReaderImpl.cpp.o' 'src/25a6634@@pbbam@sha/ZmwChunkedFastxTextReader.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/bed_BedReader.cpp.o' 'src/25a6634@@pbbam@sha/bed_BedWriter.cpp.o' 'src/25a6634@@pbbam@sha/ccs_CCSPbiBuilder.cpp.o' 'src/25a6634@@pbbam@sha/ccs_CCSRecordFormat.cpp.o' 'src/25a6634@@pbbam@sha/ccs_CCSRecordReader.cpp.o' 'src/25a6634@@pbbam@sha/ccs_CCSRecordWriter.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.1.0.6 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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 /usr/lib/arm-linux-gnueabihf/libpbcopper.so -Wl,--end-group
[126/216] /usr/bin/meson --internal symbolextractor src/libpbbam.so.1.0.6 'src/25a6634@@pbbam@sha/libpbbam.so.1.0.6.symbols'
[127/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[128/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[129/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_BedReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BedReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BedReader.cpp.o' -c ../tests/src/test_BedReader.cpp
[130/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_BgzipFastqWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BgzipFastqWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BgzipFastqWriter.cpp.o' -c ../tests/src/test_BgzipFastqWriter.cpp
[131/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_BedWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BedWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BedWriter.cpp.o' -c ../tests/src/test_BedWriter.cpp
[132/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_BgzipFastaWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BgzipFastaWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BgzipFastaWriter.cpp.o' -c ../tests/src/test_BgzipFastaWriter.cpp
[133/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_BgzipWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_BgzipWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_BgzipWriter.cpp.o' -c ../tests/src/test_BgzipWriter.cpp
[134/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_CCSPbiBuilder.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_CCSPbiBuilder.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_CCSPbiBuilder.cpp.o' -c ../tests/src/test_CCSPbiBuilder.cpp
[135/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_CCSRecordIO.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_CCSRecordIO.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_CCSRecordIO.cpp.o' -c ../tests/src/test_CCSRecordIO.cpp
[136/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[137/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[138/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[139/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[140/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[141/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[142/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_FaiIndex.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FaiIndex.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FaiIndex.cpp.o' -c ../tests/src/test_FaiIndex.cpp
[143/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_FaiZmwChunker.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FaiZmwChunker.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FaiZmwChunker.cpp.o' -c ../tests/src/test_FaiZmwChunker.cpp
[144/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[145/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[146/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[147/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_FastaSequenceQuery.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FastaSequenceQuery.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FastaSequenceQuery.cpp.o' -c ../tests/src/test_FastaSequenceQuery.cpp
[148/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_FastaReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FastaReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FastaReader.cpp.o' -c ../tests/src/test_FastaReader.cpp
[149/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_FastaSequence.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FastaSequence.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FastaSequence.cpp.o' -c ../tests/src/test_FastaSequence.cpp
[150/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_FastqSequence.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FastqSequence.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FastqSequence.cpp.o' -c ../tests/src/test_FastqSequence.cpp
[151/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_FastqWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FastqWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FastqWriter.cpp.o' -c ../tests/src/test_FastqWriter.cpp
[152/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_FastaWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FastaWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FastaWriter.cpp.o' -c ../tests/src/test_FastaWriter.cpp
[153/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_FastqReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_FastqReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_FastqReader.cpp.o' -c ../tests/src/test_FastqReader.cpp
[154/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[155/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[156/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[157/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[158/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[159/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[160/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_IndexedFastqReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastqReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_IndexedFastqReader.cpp.o' -c ../tests/src/test_IndexedFastqReader.cpp
[161/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[162/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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);
| ^~~~~~~~~~~~~~~~~
[163/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[164/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[165/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[166/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[167/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[168/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[169/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[170/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[171/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[172/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[173/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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:927,
from ../include/pbbam/PbiFilter.h:247,
from ../include/pbbam/PbiFilterQuery.h:14,
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:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[174/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[175/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[176/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_TextFileReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_TextFileReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_TextFileReader.cpp.o' -c ../tests/src/test_TextFileReader.cpp
[177/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[178/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[179/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_TextFileWriter.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_TextFileWriter.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_TextFileWriter.cpp.o' -c ../tests/src/test_TextFileWriter.cpp
[180/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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:927,
from ../include/pbbam/PbiFilter.h:247,
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:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[181/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[182/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[183/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[184/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[185/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[186/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[187/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[188/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[189/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[190/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[191/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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_ZmwChunkedFastxReader.cpp.o' -MF 'tests/59830eb@@pbbam_test@exe/src_test_ZmwChunkedFastxReader.cpp.o.d' -o 'tests/59830eb@@pbbam_test@exe/src_test_ZmwChunkedFastxReader.cpp.o' -c ../tests/src/test_ZmwChunkedFastxReader.cpp
[192/216] /usr/bin/python3 ../tests/scripts/generate_data.py /<<BUILDDIR>>/pbbam-1.0.6+dfsg/tests/data /<<BUILDDIR>>/pbbam-1.0.6+dfsg/obj-arm-linux-gnueabihf/tests
Generating test data in /<<BUILDDIR>>/pbbam-1.0.6+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.
[193/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[194/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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:927,
from ../include/pbbam/PbiFilter.h:247,
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:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[195/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_Bam2SamWorkflow.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2SamWorkflow.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2SamWorkflow.cpp.o' -c ../tools/bam2sam/src/Bam2SamWorkflow.cpp
[196/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_PbIndexSettings.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndexSettings.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndexSettings.cpp.o' -c ../tools/pbindex/src/PbIndexSettings.cpp
[197/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[198/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_Bam2SamSettings.cpp.o' -MF 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2SamSettings.cpp.o.d' -o 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2SamSettings.cpp.o' -c ../tools/bam2sam/src/Bam2SamSettings.cpp
[199/216] c++ -o tools/bam2sam 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_main.cpp.o' 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2SamSettings.cpp.o' 'tools/f9d35d4@@bam2sam@exe/bam2sam_src_Bam2SamWorkflow.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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 /usr/lib/arm-linux-gnueabihf/libpbcopper.so -Wl,--end-group
[200/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_PbIndexWorkflow.cpp.o' -MF 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndexWorkflow.cpp.o.d' -o 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndexWorkflow.cpp.o' -c ../tools/pbindex/src/PbIndexWorkflow.cpp
[201/216] c++ -o tools/pbindex 'tools/f9d35d4@@pbindex@exe/pbindex_src_main.cpp.o' 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndexSettings.cpp.o' 'tools/f9d35d4@@pbindex@exe/pbindex_src_PbIndexWorkflow.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.0.6 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-1.0.6+dfsg/obj-arm-linux-gnueabihf/src
[202/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[203/216] c++ -Itests/59830eb@@pbbam_test@exe -Itests -I../tests -Iinclude -I../include -I/usr/lib/arm-linux-gnueabihf/pkgconfig/../../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group -lpthread -Wl,--end-group -DGTEST_HAS_PTHREAD=1 -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
[204/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[205/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[206/216] c++ -o tests/pbbam_test '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_BedReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BedWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BgzipFastaWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BgzipFastqWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_BgzipWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_CCSPbiBuilder.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_CCSRecordIO.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_FaiIndex.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FaiZmwChunker.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FastaReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FastaSequence.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FastaSequenceQuery.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FastaWriter.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FastqReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FastqSequence.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_FastqWriter.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_IndexedFastqReader.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_TextFileReader.cpp.o' 'tests/59830eb@@pbbam_test@exe/src_test_TextFileWriter.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_ZmwChunkedFastxReader.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-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.0.6 /usr/lib/gcc/arm-linux-gnueabihf/9/../../../arm-linux-gnueabihf/libgtest_main.a -lpthread /usr/lib/gcc/arm-linux-gnueabihf/9/../../../arm-linux-gnueabihf/libgtest.a /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-1.0.6+dfsg/obj-arm-linux-gnueabihf/src
[207/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_PbMergeSettings.cpp.o' -MF 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_PbMergeSettings.cpp.o.d' -o 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_PbMergeSettings.cpp.o' -c ../tools/pbmerge/src/PbMergeSettings.cpp
[208/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_PbMergeWorkflow.cpp.o' -MF 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_PbMergeWorkflow.cpp.o.d' -o 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_PbMergeWorkflow.cpp.o' -c ../tools/pbmerge/src/PbMergeWorkflow.cpp
[209/216] c++ -o tools/pbmerge 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_main.cpp.o' 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_PbMergeSettings.cpp.o' 'tools/f9d35d4@@pbmerge@exe/pbmerge_src_PbMergeWorkflow.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.0.6 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-1.0.6+dfsg/obj-arm-linux-gnueabihf/src
[210/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_PbBamifySettings.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamifySettings.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamifySettings.cpp.o' -c ../tools/pbbamify/src/PbBamifySettings.cpp
[211/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[212/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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 /usr/include/pbcopper/cli2/CLI.h:10,
from ../tools/pbindexdump/src/PbIndexDumpSettings.h:8,
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, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _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 /usr/include/boost/detail/container_fwd.hpp:94,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from /usr/include/pbcopper/cli2/OptionValue.h:10,
from /usr/include/pbcopper/cli2/Option.h:12,
from /usr/include/pbcopper/cli2/Interface.h:16,
from /usr/include/pbcopper/cli2/CLI.h:12,
from ../tools/pbindexdump/src/PbIndexDumpSettings.h:8,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
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<void>; _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<void>, 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 /usr/include/boost/detail/container_fwd.hpp:94,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from /usr/include/pbcopper/cli2/OptionValue.h:10,
from /usr/include/pbcopper/cli2/Option.h:12,
from /usr/include/pbcopper/cli2/Interface.h:16,
from /usr/include/pbcopper/cli2/CLI.h:12,
from ../tools/pbindexdump/src/PbIndexDumpSettings.h:8,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
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, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::value_type& nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::operator[](T*) [with T = const char; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’:
/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<void>, 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 function ‘void PacBio::PbIndexDump::{anonymous}::FormatRaw(const PacBio::BAM::PbiRawData&, PacBio::JSON::Json&)’:
/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<void>, 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<void>, 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<void>, 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<void>, 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<void>, 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 /usr/include/pbcopper/cli2/CLI.h:10,
from ../tools/pbindexdump/src/PbIndexDumpSettings.h:8,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/vector.tcc: In function ‘void PacBio::PbIndexDump::{anonymous}::FormatMetadata(const PacBio::BAM::PbiRawData&, PacBio::JSON::Json&)’:
/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 /usr/include/boost/detail/container_fwd.hpp:94,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from /usr/include/pbcopper/cli2/OptionValue.h:10,
from /usr/include/pbcopper/cli2/Option.h:12,
from /usr/include/pbcopper/cli2/Interface.h:16,
from /usr/include/pbcopper/cli2/CLI.h:12,
from ../tools/pbindexdump/src/PbIndexDumpSettings.h:8,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
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<void>, 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<void>, 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<void>, 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 function ‘void PacBio::PbIndexDump::{anonymous}::FormatRecords(const PacBio::BAM::PbiRawData&, PacBio::JSON::Json&)’:
/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<void>, 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<void>, 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<void>, 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<void>, 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<void>, 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<void>, 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<void>, 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<void>, 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<void>, 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<void>, 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 /usr/include/pbcopper/cli2/CLI.h:10,
from ../tools/pbindexdump/src/PbIndexDumpSettings.h:8,
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 /usr/include/boost/detail/container_fwd.hpp:94,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from /usr/include/pbcopper/cli2/OptionValue.h:10,
from /usr/include/pbcopper/cli2/Option.h:12,
from /usr/include/pbcopper/cli2/Interface.h:16,
from /usr/include/pbcopper/cli2/CLI.h:12,
from ../tools/pbindexdump/src/PbIndexDumpSettings.h:8,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
from ../tools/pbindexdump/src/JsonFormatter.cpp:3:
/usr/include/c++/9/bits/stl_map.h: In static member function ‘static void PacBio::PbIndexDump::JsonFormatter::Run(const PacBio::PbIndexDump::Settings&)’:
/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<void>, 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<void>, 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<void>, 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 /usr/include/pbcopper/cli2/CLI.h:10,
from ../tools/pbindexdump/src/PbIndexDumpSettings.h:8,
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 /usr/include/boost/detail/container_fwd.hpp:94,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from /usr/include/pbcopper/cli2/OptionValue.h:10,
from /usr/include/pbcopper/cli2/Option.h:12,
from /usr/include/pbcopper/cli2/Interface.h:16,
from /usr/include/pbcopper/cli2/CLI.h:12,
from ../tools/pbindexdump/src/PbIndexDumpSettings.h:8,
from ../tools/pbindexdump/src/JsonFormatter.h:6,
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<void>, 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,
[213/216] c++ -o tools/pbindexdump 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_CppFormatter.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_JsonFormatter.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDumpSettings.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_PbIndexDumpWorkflow.cpp.o' 'tools/f9d35d4@@pbindexdump@exe/pbindexdump_src_main.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.0.6 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-1.0.6+dfsg/obj-arm-linux-gnueabihf/src
[214/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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
[215/216] 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++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+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_PbBamifyWorkflow.cpp.o' -MF 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamifyWorkflow.cpp.o.d' -o 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamifyWorkflow.cpp.o' -c ../tools/pbbamify/src/PbBamifyWorkflow.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:927,
from ../include/pbbam/PbiFilter.h:247,
from ../tools/pbbamify/src/PbBamifyWorkflow.cpp:19:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:480:38: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
480 | return static_cast<uint32_t>(seed);
| ^
[216/216] c++ -o tools/pbbamify 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_main.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamifySettings.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_PbBamifyWorkflow.cpp.o' 'tools/f9d35d4@@pbbamify@exe/pbbamify_src_QueryLookup.cpp.o' -Wl,--as-needed -Wl,--no-undefined -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.0.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libpbbam.so.1.0.6 /usr/lib/arm-linux-gnueabihf/libhts.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libpbcopper.so -Wl,--end-group '-Wl,-rpath,$ORIGIN/../src' -Wl,-rpath-link,/<<BUILDDIR>>/pbbam-1.0.6+dfsg/obj-arm-linux-gnueabihf/src
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/pbbam-1.0.6+dfsg'
sed \
-e 's/$BAM2SAM/samtools view/g' \
-e 's/\-\-header\-only/-H/g' \
-e 's/\-\-no\-header//g' \
-e 's|@PacBioBAM_BinDir@/||g' \
-e 's|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-1.0.6+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|1.0.6+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-1.0.6+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$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-1.0.6+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|1.0.6+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-1.0.6+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|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-1.0.6+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|1.0.6+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-1.0.6+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$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-1.0.6+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|1.0.6+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-1.0.6+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|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-1.0.6+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|1.0.6+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-1.0.6+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$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-1.0.6+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|1.0.6+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-1.0.6+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|$TOOLS_BIN/||g' \
-e 's|@PacBioBAM_TestsDir@|/<<BUILDDIR>>/pbbam-1.0.6+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|1.0.6+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-1.0.6+dfsg/gendata|g' \
-e '/@PG/s|+dfsg||g' \
-e 's/$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-1.0.6+dfsg/tests|g' \
-e 's|@PacBioBAM_VERSION@|1.0.6+dfsg|g' \
-e 's|@GeneratedTestDataDir@|/<<BUILDDIR>>/pbbam-1.0.6+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-1.0.6+dfsg/gendata
python3 tests/scripts/generate_data.py /<<BUILDDIR>>/pbbam-1.0.6+dfsg/tests/data /<<BUILDDIR>>/pbbam-1.0.6+dfsg/gendata
Generating test data in /<<BUILDDIR>>/pbbam-1.0.6+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
+ pbmerge ERROR: stoul
+ [1]
$ samtools view -H $MERGED_BAM | grep -v 'CL:samtools view -H '
@HD\tVN:1.3.1\tSO:coordinate\tpb:3.0.1 (esc)
@@ -131,26 +133,6 @@
@PG\tID:pbmerge-1.0.6\tPN:pbmerge\tVN:1.0.6 (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-1.0.6+dfsg'
make: *** [debian/rules:13: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-02-04T19:02:48Z
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: 6553
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 829
Job: pbbam_1.0.6+dfsg-2
Machine Architecture: armhf
Package: pbbam
Package-Time: 7470
Source-Version: 1.0.6+dfsg-2
Space: 0
Status: failed
Version: 1.0.6+dfsg-2
--------------------------------------------------------------------------------
Finished at 2020-02-04T19:02:48Z
Build needed 00:00:00, 0k disc space