pbbam →
1.3.0+dfsg-2 →
armhf → 2020-09-13 06:04:49
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| pbbam 1.3.0+dfsg-2 (armhf) Sun, 13 Sep 2020 05:54:16 +0000 |
+==============================================================================+
Package: pbbam
Version: 1.3.0+dfsg-2
Source Version: 1.3.0+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-c034c2c1-e252-4689-a054-60c9a4c8b28f' 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 [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.8 MB in 9s (2880 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pbbam' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/pbbam.git
Please use:
git clone https://salsa.debian.org/med-team/pbbam.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 7785 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main pbbam 1.3.0+dfsg-2 (dsc) [2320 B]
Get:2 http://172.17.0.1/private bullseye-staging/main pbbam 1.3.0+dfsg-2 (tar) [7774 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main pbbam 1.3.0+dfsg-2 (diff) [8804 B]
Fetched 7785 kB in 1s (6205 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pbbam-s8ODEO/pbbam-1.3.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pbbam-s8ODEO' 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-W3Aydp/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-W3Aydp/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-W3Aydp/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (9542 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:
bsdextrautils libpam-cap netbase sensible-utils
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 17 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-W3Aydp/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 (66.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12498 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 (= 13), 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 (= 13), 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-W3Aydp/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-W3Aydp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ Sources [593 B]
Get:5 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ Packages [662 B]
Fetched 2588 B in 0s (11.4 kB/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 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 libboost1.71-dev libbrotli1 libcroco3
libcurl3-gnutls libcurl4 libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgtest-dev
libhts-dev libhts3 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14
libpbcopper-dev libpbcopper1.3.0 libpipeline1 libprocps8 libpsl5
libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0
librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1 libsub-override-perl
libtool libuchardet0 libuv1 libxml2 m4 man-db meson mime-support ninja-build
pkg-config po-debconf procps python3 python3-cram python3-minimal
python3-pkg-resources python3.8 python3.8-minimal samtools zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff lrzip libboost-doc libboost1.71-doc
libboost-atomic1.71-dev libboost-chrono1.71-dev libboost-container1.71-dev
libboost-context1.71-dev libboost-contract1.71-dev
libboost-coroutine1.71-dev libboost-date-time1.71-dev
libboost-exception1.71-dev libboost-fiber1.71-dev
libboost-filesystem1.71-dev libboost-graph1.71-dev
libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev
libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev
libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev
libboost-program-options1.71-dev libboost-python1.71-dev
libboost-random1.71-dev libboost-regex1.71-dev
libboost-serialization1.71-dev libboost-stacktrace1.71-dev
libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev
libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev
libboost1.71-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user
liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk
python3-venv python3-setuptools python3.8-venv python3.8-doc binfmt-support
cwltool
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
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev 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 libboost1.71-dev libbrotli1 libcroco3
libcurl3-gnutls libcurl4 libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgtest-dev
libhts-dev libhts3 libicu67 libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14
libpbcopper-dev libpbcopper1.3.0 libpipeline1 libprocps8 libpsl5
libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0
librtmp1 libsigsegv2 libssh2-1 libssl-dev libssl1.1 libsub-override-perl
libtool libuchardet0 libuv1 libxml2 m4 man-db meson mime-support ninja-build
pkg-config po-debconf procps python3 python3-cram python3-minimal
python3-pkg-resources python3.8 python3.8-minimal samtools
sbuild-build-depends-pbbam-dummy zlib1g-dev
0 upgraded, 83 newly installed, 0 to remove and 17 not upgraded.
Need to get 49.0 MB/50.2 MB of archives.
After this operation, 284 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-W3Aydp/apt_archive ./ sbuild-build-depends-pbbam-dummy 0.invalid.0 [948 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.5-2 [752 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.5-2 [1628 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.2-3 [37.6 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.5-2 [1677 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.5-2 [420 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.2-3 [20.8 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.2-3 [63.7 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2-1 [79.5 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.16-5 [59.8 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.16-5 [238 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.16.3-3+rpi1 [1628 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6 [578 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2 [259 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-10+b3 [62.0 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10+b3 [112 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10+b3 [318 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10+b3 [135 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-3 [63.0 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.72.0-1 [300 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp1 armhf 1.7.4-3.1 [65.8 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.4.0-1 [133 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.38.0-3 [115 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.16.3-3+rpi1 [2653 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf d-shlibs all 0.94 [17.7 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.180-1 [162 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.4-1 [1159 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf dh-exec armhf 0.23.2+b3 [25.7 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf googletest all 1.10.0-3 [626 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-6+b1 [9099 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.71.0.3+b3 [4620 B]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.72.0-1 [297 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libgtest-dev armhf 1.10.0-3 [218 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-5 [321 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.10.2-5 [4796 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libpbcopper1.3.0 armhf 1.3.0+dfsg-3 [277 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libpbcopper-dev armhf 1.3.0+dfsg-3 [149 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1g-1 [1573 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf ninja-build armhf 1.10.1-1 [92.5 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 46.1.3-1 [183 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf meson all 0.55.2-1 [416 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf python3-cram all 0.7-4 [17.3 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf samtools armhf 1.10-4 [477 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12498 files and directories currently installed.)
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Not building database; man-db/auto-update is not 'true'.
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Processing triggers for libc-bin (2.31-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-5+rpi1 gcc-10_10.2.0-5+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-7 binutils_2.35-2+rpi1 binutils-arm-linux-gnueabihf_2.35-2+rpi1 binutils-common_2.35-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 cmake_3.16.3-3+rpi1 cmake-data_3.16.3-3+rpi1 coreutils_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.2.0-5+rpi1 d-shlibs_0.94 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-exec_0.23.2+b3 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.1.0-1+rpi1 g++-10_10.2.0-5+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.2.0-5+rpi1 gcc-10-base_10.2.0-5+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 googletest_1.10.0-3 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_10.2.0-5+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-5+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.35-2+rpi1 libblkid1_2.36-3 libboost-dev_1.71.0.3+b3 libboost-iostreams1.71.0_1.71.0-6+b1 libboost1.71-dev_1.71.0-6+b1 libbrotli1_1.0.9-2 libbz2-1.0_1.0.8-4 libc-bin_2.31-3+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.43-1 libcap2-bin_1:2.43-1 libcc1-0_10.2.0-5+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35-2+rpi1 libctf0_2.35-2+rpi1 libcurl3-gnutls_7.72.0-1 libcurl4_7.72.0-1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2 libdeflate0_1.6-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.180-1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-5+rpi1 libgcc-s1_10.2.0-5+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.2.0-5+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libgtest-dev_1.10.0-3 libhogweed6_3.6-2 libhts-dev_1.10.2-5 libhts3_1.10.2-5 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjsoncpp1_1.7.4-3.1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 libldap-2.4-2_2.4.51+dfsg-1 libldap-common_2.4.51+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0~rc1-1 libmpfr6_4.1.0-3 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnpth0_1.6-2 libp11-kit0_0.23.21-2 libpam-cap_1:2.43-1 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_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libprocps8_2:3.3.16-5 libpsl5_0.21.0-1.1 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.5-2 libpython3.8-stdlib_3.8.5-2 libreadline8_8.0-4 librhash0_1.4.0-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1g-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-5+rpi1 libstdc++6_10.2.0-5+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.2-1+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.2.0-5+rpi1 libuchardet0_0.0.7-1 libudev1_246.2-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libuv1_1.38.0-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 meson_0.55.2-1 mime-support_3.64 mount_2.36-3 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 ninja-build_1.10.1-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 procps_2:3.3.16-5 python3_3.8.2-3 python3-cram_0.7-4 python3-minimal_3.8.2-3 python3-pkg-resources_46.1.3-1 python3.8_3.8.5-2 python3.8-minimal_3.8.5-2 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 samtools_1.10-4 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_2.96-4 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.vO0ZniEB/trustedkeys.kbx': General error
gpgv: Signature made Fri Sep 11 11:34:31 2020 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_1.3.0+dfsg-2.dsc
dpkg-source: info: extracting pbbam in /<<BUILDDIR>>/pbbam-1.3.0+dfsg
dpkg-source: info: unpacking pbbam_1.3.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking pbbam_1.3.0+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 disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-c034c2c1-e252-4689-a054-60c9a4c8b28f
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pbbam
dpkg-buildpackage: info: source version 1.3.0+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --buildsystem=meson
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/pbbam-1.3.0+dfsg'
dh_auto_clean
find -name "*.deb.t" -delete
rm -f -r /<<BUILDDIR>>/pbbam-1.3.0+dfsg/gendata
make[1]: Leaving directory '/<<BUILDDIR>>/pbbam-1.3.0+dfsg'
dh_autoreconf_clean -O--buildsystem=meson
dh_clean -O--buildsystem=meson
debian/rules binary-arch
dh binary-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: 0.55.2
Source dir: /<<BUILDDIR>>/pbbam-1.3.0+dfsg
Build dir: /<<BUILDDIR>>/pbbam-1.3.0+dfsg/obj-arm-linux-gnueabihf
Build type: native build
Project name: PacBioBAM
Project version: 1.3.0
Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'
Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now'
Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2'
Using 'CXXFLAGS' from environment with value: '-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security'
Using 'LDFLAGS' from environment with value: '-Wl,-z,relro -Wl,-z,now'
Using 'CPPFLAGS' from environment with value: '-Wdate-time -D_FORTIFY_SOURCE=2'
C++ compiler for the host machine: c++ (gcc 10.2.0 "c++ (Raspbian 10.2.0-5+rpi1) 10.2.0")
C++ linker for the host machine: c++ ld.bfd 2.35
Host machine cpu family: arm
Host machine cpu: armv8l
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
Found pkg-config: /usr/bin/pkg-config (0.29.2)
Run-time dependency Boost found: YES 1.71.0 (/usr/include)
Run-time dependency zlib found: YES 1.2.11
Run-time dependency htslib found: YES 1.10.2-5
Run-time dependency pbcopper found: YES 1.3.0
Configuring PbbamVersion.cpp using configuration
Program python3 found: YES
Program tools/check-formatting found: YES
Program cram3 found: YES
WARNING: Project targeting '>= 0.46.0' but tried to use feature introduced in '0.53.0': Fallback without variable name.
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
Configuring pbbamify.t using configuration
Build targets in project: 9
WARNING: Project specifies a minimum meson_version '>= 0.46.0' but uses features which were added in newer versions:
* 0.53.0: {'Fallback without variable name'}
Option buildtype is: plain [default: release]
Found ninja-1.10.1 at /usr/bin/ninja
dh_auto_build -a -O--buildsystem=meson
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v
[1/218] /usr/bin/meson --internal vcstagger ../src/PbbamGitHash.cpp.in src/PbbamGitHash.cpp 1.3.0 /<<BUILDDIR>>/pbbam-1.3.0+dfsg/src @PBBAM_GIT_SHA1@ '(.*)' /<<BUILDDIR>>/pbbam-1.3.0+dfsg/src/git describe --always '--dirty=*'
[2/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/meson-generated_.._PbbamGitHash.cpp.o -MF src/libpbbam.so.1.3.0.p/meson-generated_.._PbbamGitHash.cpp.o.d -o src/libpbbam.so.1.3.0.p/meson-generated_.._PbbamGitHash.cpp.o -c src/PbbamGitHash.cpp
[3/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/AlignmentPrinter.cpp.o -MF src/libpbbam.so.1.3.0.p/AlignmentPrinter.cpp.o.d -o src/libpbbam.so.1.3.0.p/AlignmentPrinter.cpp.o -c ../src/AlignmentPrinter.cpp
[4/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamFile.cpp.o -MF src/libpbbam.so.1.3.0.p/BamFile.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamFile.cpp.o -c ../src/BamFile.cpp
[5/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BaiIndexCache.cpp.o -MF src/libpbbam.so.1.3.0.p/BaiIndexCache.cpp.o.d -o src/libpbbam.so.1.3.0.p/BaiIndexCache.cpp.o -c ../src/BaiIndexCache.cpp
[6/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BaiIndexedBamReader.cpp.o -MF src/libpbbam.so.1.3.0.p/BaiIndexedBamReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/BaiIndexedBamReader.cpp.o -c ../src/BaiIndexedBamReader.cpp
[7/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamReader.cpp.o -MF src/libpbbam.so.1.3.0.p/BamReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamReader.cpp.o -c ../src/BamReader.cpp
[8/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamFileMerger.cpp.o -MF src/libpbbam.so.1.3.0.p/BamFileMerger.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamFileMerger.cpp.o -c ../src/BamFileMerger.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:28,
from ../src/BamFileMerger.cpp:18:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[9/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamRecordBuilder.cpp.o -MF src/libpbbam.so.1.3.0.p/BamRecordBuilder.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamRecordBuilder.cpp.o -c ../src/BamRecordBuilder.cpp
[10/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamHeader.cpp.o -MF src/libpbbam.so.1.3.0.p/BamHeader.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamHeader.cpp.o -c ../src/BamHeader.cpp
[11/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamRecordTags.cpp.o -MF src/libpbbam.so.1.3.0.p/BamRecordTags.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamRecordTags.cpp.o -c ../src/BamRecordTags.cpp
[12/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamRecordImpl.cpp.o -MF src/libpbbam.so.1.3.0.p/BamRecordImpl.cpp.o.d -o src/libpbbam.so.1.3.0.p/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:92:18: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
92 | 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:236:14: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
236 | bam_copy1(result.d_.get(), rawData.get());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[13/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamRecord.cpp.o -MF src/libpbbam.so.1.3.0.p/BamRecord.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamRecord.cpp.o -c ../src/BamRecord.cpp
[14/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamRecordView.cpp.o -MF src/libpbbam.so.1.3.0.p/BamRecordView.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamRecordView.cpp.o -c ../src/BamRecordView.cpp
[15/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BgzipFastaWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/BgzipFastaWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/BgzipFastaWriter.cpp.o -c ../src/BgzipFastaWriter.cpp
[16/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/BamWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamWriter.cpp.o -c ../src/BamWriter.cpp
[17/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BgzipFastqWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/BgzipFastqWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/BgzipFastqWriter.cpp.o -c ../src/BgzipFastqWriter.cpp
[18/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BamTagCodec.cpp.o -MF src/libpbbam.so.1.3.0.p/BamTagCodec.cpp.o.d -o src/libpbbam.so.1.3.0.p/BamTagCodec.cpp.o -c ../src/BamTagCodec.cpp
[19/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ChemistryTable.cpp.o -MF src/libpbbam.so.1.3.0.p/ChemistryTable.cpp.o.d -o src/libpbbam.so.1.3.0.p/ChemistryTable.cpp.o -c ../src/ChemistryTable.cpp
[20/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/BgzipWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/BgzipWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/BgzipWriter.cpp.o -c ../src/BgzipWriter.cpp
[21/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/Compare.cpp.o -MF src/libpbbam.so.1.3.0.p/Compare.cpp.o.d -o src/libpbbam.so.1.3.0.p/Compare.cpp.o -c ../src/Compare.cpp
[22/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/Config.cpp.o -MF src/libpbbam.so.1.3.0.p/Config.cpp.o.d -o src/libpbbam.so.1.3.0.p/Config.cpp.o -c ../src/Config.cpp
[23/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/CompositeFastaReader.cpp.o -MF src/libpbbam.so.1.3.0.p/CompositeFastaReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/CompositeFastaReader.cpp.o -c ../src/CompositeFastaReader.cpp
[24/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/CompositeBamReader.cpp.o -MF src/libpbbam.so.1.3.0.p/CompositeBamReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/CompositeBamReader.cpp.o -c ../src/CompositeBamReader.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:28,
from ../src/CompositeBamReader.cpp:12:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[25/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/CollectionMetadata.cpp.o -MF src/libpbbam.so.1.3.0.p/CollectionMetadata.cpp.o.d -o src/libpbbam.so.1.3.0.p/CollectionMetadata.cpp.o -c ../src/CollectionMetadata.cpp
[26/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/DataSetElement.cpp.o -MF src/libpbbam.so.1.3.0.p/DataSetElement.cpp.o.d -o src/libpbbam.so.1.3.0.p/DataSetElement.cpp.o -c ../src/DataSetElement.cpp
[27/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/DataSetIO.cpp.o -MF src/libpbbam.so.1.3.0.p/DataSetIO.cpp.o.d -o src/libpbbam.so.1.3.0.p/DataSetIO.cpp.o -c ../src/DataSetIO.cpp
[28/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/DataSetBaseTypes.cpp.o -MF src/libpbbam.so.1.3.0.p/DataSetBaseTypes.cpp.o.d -o src/libpbbam.so.1.3.0.p/DataSetBaseTypes.cpp.o -c ../src/DataSetBaseTypes.cpp
[29/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/DataSet.cpp.o -MF src/libpbbam.so.1.3.0.p/DataSet.cpp.o.d -o src/libpbbam.so.1.3.0.p/DataSet.cpp.o -c ../src/DataSet.cpp
[30/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/DataSetXsd.cpp.o -MF src/libpbbam.so.1.3.0.p/DataSetXsd.cpp.o.d -o src/libpbbam.so.1.3.0.p/DataSetXsd.cpp.o -c ../src/DataSetXsd.cpp
[31/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FaiZmwChunker.cpp.o -MF src/libpbbam.so.1.3.0.p/FaiZmwChunker.cpp.o.d -o src/libpbbam.so.1.3.0.p/FaiZmwChunker.cpp.o -c ../src/FaiZmwChunker.cpp
In file included from /usr/include/c++/10/vector:72,
from ../src/FaiZmwChunker.h:13,
from ../src/FaiZmwChunker.cpp:9:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::BAM::FaiZmwChunk>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[32/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FaiIndex.cpp.o -MF src/libpbbam.so.1.3.0.p/FaiIndex.cpp.o.d -o src/libpbbam.so.1.3.0.p/FaiIndex.cpp.o -c ../src/FaiIndex.cpp
[33/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/EntireFileQuery.cpp.o -MF src/libpbbam.so.1.3.0.p/EntireFileQuery.cpp.o.d -o src/libpbbam.so.1.3.0.p/EntireFileQuery.cpp.o -c ../src/EntireFileQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:28,
from ../src/EntireFileQuery.cpp:11:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[34/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FastaCache.cpp.o -MF src/libpbbam.so.1.3.0.p/FastaCache.cpp.o.d -o src/libpbbam.so.1.3.0.p/FastaCache.cpp.o -c ../src/FastaCache.cpp
[35/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FastaReader.cpp.o -MF src/libpbbam.so.1.3.0.p/FastaReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/FastaReader.cpp.o -c ../src/FastaReader.cpp
[36/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FastaSequence.cpp.o -MF src/libpbbam.so.1.3.0.p/FastaSequence.cpp.o.d -o src/libpbbam.so.1.3.0.p/FastaSequence.cpp.o -c ../src/FastaSequence.cpp
[37/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/DataSetTypes.cpp.o -MF src/libpbbam.so.1.3.0.p/DataSetTypes.cpp.o.d -o src/libpbbam.so.1.3.0.p/DataSetTypes.cpp.o -c ../src/DataSetTypes.cpp
[38/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FastqSequence.cpp.o -MF src/libpbbam.so.1.3.0.p/FastqSequence.cpp.o.d -o src/libpbbam.so.1.3.0.p/FastqSequence.cpp.o -c ../src/FastqSequence.cpp
[39/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FastaWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/FastaWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/FastaWriter.cpp.o -c ../src/FastaWriter.cpp
[40/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FastaSequenceQuery.cpp.o -MF src/libpbbam.so.1.3.0.p/FastaSequenceQuery.cpp.o.d -o src/libpbbam.so.1.3.0.p/FastaSequenceQuery.cpp.o -c ../src/FastaSequenceQuery.cpp
[41/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FileProducer.cpp.o -MF src/libpbbam.so.1.3.0.p/FileProducer.cpp.o.d -o src/libpbbam.so.1.3.0.p/FileProducer.cpp.o -c ../src/FileProducer.cpp
[42/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FastqReader.cpp.o -MF src/libpbbam.so.1.3.0.p/FastqReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/FastqReader.cpp.o -c ../src/FastqReader.cpp
[43/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FofnReader.cpp.o -MF src/libpbbam.so.1.3.0.p/FofnReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/FofnReader.cpp.o -c ../src/FofnReader.cpp
[44/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FastqWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/FastqWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/FastqWriter.cpp.o -c ../src/FastqWriter.cpp
[45/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FileUtils.cpp.o -MF src/libpbbam.so.1.3.0.p/FileUtils.cpp.o.d -o src/libpbbam.so.1.3.0.p/FileUtils.cpp.o -c ../src/FileUtils.cpp
[46/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/IFastaWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/IFastaWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/IFastaWriter.cpp.o -c ../src/IFastaWriter.cpp
[47/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/IFastqWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/IFastqWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/IFastqWriter.cpp.o -c ../src/IFastqWriter.cpp
[48/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/FormatUtils.cpp.o -MF src/libpbbam.so.1.3.0.p/FormatUtils.cpp.o.d -o src/libpbbam.so.1.3.0.p/FormatUtils.cpp.o -c ../src/FormatUtils.cpp
[49/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/IndexedFastaReader.cpp.o -MF src/libpbbam.so.1.3.0.p/IndexedFastaReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/IndexedFastaReader.cpp.o -c ../src/IndexedFastaReader.cpp
[50/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/GenomicIntervalQuery.cpp.o -MF src/libpbbam.so.1.3.0.p/GenomicIntervalQuery.cpp.o.d -o src/libpbbam.so.1.3.0.p/GenomicIntervalQuery.cpp.o -c ../src/GenomicIntervalQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:28,
from ../src/GenomicIntervalQuery.cpp:11:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[51/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/IndexedFastqBgzfReader.cpp.o -MF src/libpbbam.so.1.3.0.p/IndexedFastqBgzfReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/IndexedFastqBgzfReader.cpp.o -c ../src/IndexedFastqBgzfReader.cpp
[52/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/IndexedFastqTextReader.cpp.o -MF src/libpbbam.so.1.3.0.p/IndexedFastqTextReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/IndexedFastqTextReader.cpp.o -c ../src/IndexedFastqTextReader.cpp
[53/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/IRecordWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/IRecordWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/IRecordWriter.cpp.o -c ../src/IRecordWriter.cpp
[54/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/IndexedFastqReaderImpl.cpp.o -MF src/libpbbam.so.1.3.0.p/IndexedFastqReaderImpl.cpp.o.d -o src/libpbbam.so.1.3.0.p/IndexedFastqReaderImpl.cpp.o -c ../src/IndexedFastqReaderImpl.cpp
[55/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/MD5.cpp.o -MF src/libpbbam.so.1.3.0.p/MD5.cpp.o.d -o src/libpbbam.so.1.3.0.p/MD5.cpp.o -c ../src/MD5.cpp
[56/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/IndexedFastqReader.cpp.o -MF src/libpbbam.so.1.3.0.p/IndexedFastqReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/IndexedFastqReader.cpp.o -c ../src/IndexedFastqReader.cpp
[57/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/IndexedBamWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/IndexedBamWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/IndexedBamWriter.cpp.o -c ../src/IndexedBamWriter.cpp
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/core/swap.hpp:27,
from /usr/include/boost/optional/optional.hpp:31,
from /usr/include/boost/optional.hpp:15,
from ../include/pbbam/ReadGroupInfo.h:19,
from ../include/pbbam/BamHeader.h:21,
from ../include/pbbam/BamWriter.h:19,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: 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
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/core/swap.hpp:27,
from /usr/include/boost/optional/optional.hpp:31,
from /usr/include/boost/optional.hpp:15,
from ../include/pbbam/ReadGroupInfo.h:19,
from ../include/pbbam/BamHeader.h:21,
from ../include/pbbam/BamWriter.h:19,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: 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
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/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++/10/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++/10/vector:72,
from ../include/pbbam/BamHeader.h:18,
from ../include/pbbam/BamWriter.h:19,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/usr/include/c++/10/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++/10/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’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/pbbam/BamHeader.h:18,
from ../include/pbbam/BamWriter.h:19,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void PacBio::BAM::internal::PbiBuilder2::AddBasicData(const PacBio::BAM::BamRecord&, int64_t)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/pbbam/BamHeader.h:18,
from ../include/pbbam/BamWriter.h:19,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::BAM::internal::GzIndexEntry>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘std::vector<PacBio::BAM::internal::GzIndexEntry> PacBio::BAM::internal::PbiBuilder2::LoadGzi()’:
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::BAM::internal::PbiFieldBlock2>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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++/10/algorithm:62,
from /usr/include/boost/core/swap.hpp:27,
from /usr/include/boost/optional/optional.hpp:31,
from /usr/include/boost/optional.hpp:15,
from ../include/pbbam/ReadGroupInfo.h:19,
from ../include/pbbam/BamHeader.h:21,
from ../include/pbbam/BamWriter.h:19,
from ../include/pbbam/IndexedBamWriter.h:15,
from ../src/IndexedBamWriter.cpp:9:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _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++/10/bits/stl_algo.h:1662:5: 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
1662 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: 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++/10/bits/stl_algo.h:1662:5: 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++/10/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++/10/bits/stl_algo.h:1945:5: 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
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: 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++/10/bits/stl_algo.h:1959:25: 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
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: 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
1937 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In member function ‘void PacBio::BAM::internal::PbiBuilder2::WriteVirtualOffsets()’:
/usr/include/c++/10/bits/stl_algo.h:1974:25: 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
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: 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
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: 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
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[58/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/KSeqReader.cpp.o -MF src/libpbbam.so.1.3.0.p/KSeqReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/KSeqReader.cpp.o -c ../src/KSeqReader.cpp
[59/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/MemoryUtils.cpp.o -MF src/libpbbam.so.1.3.0.p/MemoryUtils.cpp.o.d -o src/libpbbam.so.1.3.0.p/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:33:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
33 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../src/MemoryUtils.h:14,
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:33:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
33 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../src/MemoryUtils.h:14,
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:33:14: warning: ‘sam_hdr_t::cigar_tab’ is deprecated: Use bam_cigar_table[] instead [-Wdeprecated-declarations]
33 | rawData->cigar_tab = nullptr;
| ^~~~~~~~~
In file included from ../src/MemoryUtils.h:14,
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");
| ^~~~~~~~~
[60/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/PbiFile.cpp.o -MF src/libpbbam.so.1.3.0.p/PbiFile.cpp.o.d -o src/libpbbam.so.1.3.0.p/PbiFile.cpp.o -c ../src/PbiFile.cpp
[61/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/PbiBuilder.cpp.o -MF src/libpbbam.so.1.3.0.p/PbiBuilder.cpp.o.d -o src/libpbbam.so.1.3.0.p/PbiBuilder.cpp.o -c ../src/PbiBuilder.cpp
In file included from /usr/include/c++/10/vector:72,
from ../include/pbbam/BamRecord.h:18,
from ../src/PbiBuilder.cpp:30:
/usr/include/c++/10/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++/10/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’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/pbbam/BamRecord.h:18,
from ../src/PbiBuilder.cpp:30:
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void PacBio::BAM::PbiBuilder::PbiBuilderPrivate::AddBasicData(const PacBio::BAM::BamRecord&, int64_t)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/pbbam/BamRecord.h:18,
from ../src/PbiBuilder.cpp:30:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::BAM::internal::PbiFieldBlock>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[62/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/PbiFilterQuery.cpp.o -MF src/libpbbam.so.1.3.0.p/PbiFilterQuery.cpp.o.d -o src/libpbbam.so.1.3.0.p/PbiFilterQuery.cpp.o -c ../src/PbiFilterQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
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:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[63/218] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -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/pbbam_test.p/src_test_BedWriter.cpp.o -MF tests/pbbam_test.p/src_test_BedWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BedWriter.cpp.o -c ../tests/src/test_BedWriter.cpp
[64/218] c++ -Itests/pbbam_test.p -Itests -I../tests -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST_ALL_NO_LIB -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/pbbam_test.p/src_test_BamWriter.cpp.o -MF tests/pbbam_test.p/src_test_BamWriter.cpp.o.d -o tests/pbbam_test.p/src_test_BamWriter.cpp.o -c ../tests/src/test_BamWriter.cpp
[65/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/PbiFilterTypes.cpp.o -MF src/libpbbam.so.1.3.0.p/PbiFilterTypes.cpp.o.d -o src/libpbbam.so.1.3.0.p/PbiFilterTypes.cpp.o -c ../src/PbiFilterTypes.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../src/PbiFilterTypes.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[66/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/PbiIndexedBamReader.cpp.o -MF src/libpbbam.so.1.3.0.p/PbiIndexedBamReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/PbiIndexedBamReader.cpp.o -c ../src/PbiIndexedBamReader.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
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:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[67/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/PbiFilter.cpp.o -MF src/libpbbam.so.1.3.0.p/PbiFilter.cpp.o.d -o src/libpbbam.so.1.3.0.p/PbiFilter.cpp.o -c ../src/PbiFilter.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
from ../src/PbiFilter.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[68/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ProgramInfo.cpp.o -MF src/libpbbam.so.1.3.0.p/ProgramInfo.cpp.o.d -o src/libpbbam.so.1.3.0.p/ProgramInfo.cpp.o -c ../src/ProgramInfo.cpp
[69/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/PbiRawData.cpp.o -MF src/libpbbam.so.1.3.0.p/PbiRawData.cpp.o.d -o src/libpbbam.so.1.3.0.p/PbiRawData.cpp.o -c ../src/PbiRawData.cpp
In file included from /usr/include/c++/10/vector:72,
from ../include/pbbam/PbiRawData.h:17,
from ../src/PbiRawData.cpp:9:
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/pbbam/PbiRawData.h:17,
from ../src/PbiRawData.cpp:9:
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void PacBio::BAM::PbiRawBasicData::AddRecord(const PacBio::BAM::BamRecord&, int64_t)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[70/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/RecordType.cpp.o -MF src/libpbbam.so.1.3.0.p/RecordType.cpp.o.d -o src/libpbbam.so.1.3.0.p/RecordType.cpp.o -c ../src/RecordType.cpp
[71/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/PbiIndexIO.cpp.o -MF src/libpbbam.so.1.3.0.p/PbiIndexIO.cpp.o.d -o src/libpbbam.so.1.3.0.p/PbiIndexIO.cpp.o -c ../src/PbiIndexIO.cpp
In file included from /usr/include/c++/10/vector:72,
from ../src/PbiIndexIO.h:15,
from ../src/PbiIndexIO.cpp:5:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator<long long int>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function ‘static void PacBio::BAM::PbiIndexIO::LoadFromDataSet(PacBio::BAM::PbiRawData&, const PacBio::BAM::DataSet&)’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/PbiIndexIO.cpp:195:1: note: parameter passing for argument of type ‘std::vector<long long int>::iterator’ changed in GCC 7.1
195 | }
| ^
[72/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/RunMetadata.cpp.o -MF src/libpbbam.so.1.3.0.p/RunMetadata.cpp.o.d -o src/libpbbam.so.1.3.0.p/RunMetadata.cpp.o -c ../src/RunMetadata.cpp
[73/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/SamWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/SamWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/SamWriter.cpp.o -c ../src/SamWriter.cpp
[74/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/RunMetadataParser.cpp.o -MF src/libpbbam.so.1.3.0.p/RunMetadataParser.cpp.o.d -o src/libpbbam.so.1.3.0.p/RunMetadataParser.cpp.o -c ../src/RunMetadataParser.cpp
[75/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/StringUtilities.cpp.o -MF src/libpbbam.so.1.3.0.p/StringUtilities.cpp.o.d -o src/libpbbam.so.1.3.0.p/StringUtilities.cpp.o -c ../src/StringUtilities.cpp
[76/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/SamTagCodec.cpp.o -MF src/libpbbam.so.1.3.0.p/SamTagCodec.cpp.o.d -o src/libpbbam.so.1.3.0.p/SamTagCodec.cpp.o -c ../src/SamTagCodec.cpp
[77/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ReadGroupInfo.cpp.o -MF src/libpbbam.so.1.3.0.p/ReadGroupInfo.cpp.o.d -o src/libpbbam.so.1.3.0.p/ReadGroupInfo.cpp.o -c ../src/ReadGroupInfo.cpp
[78/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/SequenceInfo.cpp.o -MF src/libpbbam.so.1.3.0.p/SequenceInfo.cpp.o.d -o src/libpbbam.so.1.3.0.p/SequenceInfo.cpp.o -c ../src/SequenceInfo.cpp
[79/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/TagCollection.cpp.o -MF src/libpbbam.so.1.3.0.p/TagCollection.cpp.o.d -o src/libpbbam.so.1.3.0.p/TagCollection.cpp.o -c ../src/TagCollection.cpp
[80/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/TextFileReader.cpp.o -MF src/libpbbam.so.1.3.0.p/TextFileReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/TextFileReader.cpp.o -c ../src/TextFileReader.cpp
[81/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/TextFileWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/TextFileWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/TextFileWriter.cpp.o -c ../src/TextFileWriter.cpp
[82/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ValidationErrors.cpp.o -MF src/libpbbam.so.1.3.0.p/ValidationErrors.cpp.o.d -o src/libpbbam.so.1.3.0.p/ValidationErrors.cpp.o -c ../src/ValidationErrors.cpp
[83/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ValidationException.cpp.o -MF src/libpbbam.so.1.3.0.p/ValidationException.cpp.o.d -o src/libpbbam.so.1.3.0.p/ValidationException.cpp.o -c ../src/ValidationException.cpp
[84/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/Version.cpp.o -MF src/libpbbam.so.1.3.0.p/Version.cpp.o.d -o src/libpbbam.so.1.3.0.p/Version.cpp.o -c ../src/Version.cpp
[85/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/Validator.cpp.o -MF src/libpbbam.so.1.3.0.p/Validator.cpp.o.d -o src/libpbbam.so.1.3.0.p/Validator.cpp.o -c ../src/Validator.cpp
[86/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/Tag.cpp.o -MF src/libpbbam.so.1.3.0.p/Tag.cpp.o.d -o src/libpbbam.so.1.3.0.p/Tag.cpp.o -c ../src/Tag.cpp
[87/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/VirtualRegion.cpp.o -MF src/libpbbam.so.1.3.0.p/VirtualRegion.cpp.o.d -o src/libpbbam.so.1.3.0.p/VirtualRegion.cpp.o -c ../src/VirtualRegion.cpp
[88/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/VirtualRegionTypeMap.cpp.o -MF src/libpbbam.so.1.3.0.p/VirtualRegionTypeMap.cpp.o.d -o src/libpbbam.so.1.3.0.p/VirtualRegionTypeMap.cpp.o -c ../src/VirtualRegionTypeMap.cpp
[89/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/VirtualZmwBamRecord.cpp.o -MF src/libpbbam.so.1.3.0.p/VirtualZmwBamRecord.cpp.o.d -o src/libpbbam.so.1.3.0.p/VirtualZmwBamRecord.cpp.o -c ../src/VirtualZmwBamRecord.cpp
[90/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/VirtualZmwCompositeReader.cpp.o -MF src/libpbbam.so.1.3.0.p/VirtualZmwCompositeReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/VirtualZmwCompositeReader.cpp.o -c ../src/VirtualZmwCompositeReader.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
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:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[91/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/VirtualZmwReader.cpp.o -MF src/libpbbam.so.1.3.0.p/VirtualZmwReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/VirtualZmwReader.cpp.o -c ../src/VirtualZmwReader.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
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:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[92/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/XmlWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/XmlWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/XmlWriter.cpp.o -c ../src/XmlWriter.cpp
[93/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ZmwChunkedFastaReader.cpp.o -MF src/libpbbam.so.1.3.0.p/ZmwChunkedFastaReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/ZmwChunkedFastaReader.cpp.o -c ../src/ZmwChunkedFastaReader.cpp
[94/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/XmlReader.cpp.o -MF src/libpbbam.so.1.3.0.p/XmlReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/XmlReader.cpp.o -c ../src/XmlReader.cpp
[95/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ZmwChunkedFastqReader.cpp.o -MF src/libpbbam.so.1.3.0.p/ZmwChunkedFastqReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/ZmwChunkedFastqReader.cpp.o -c ../src/ZmwChunkedFastqReader.cpp
[96/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/WhitelistedZmwReadStitcher.cpp.o -MF src/libpbbam.so.1.3.0.p/WhitelistedZmwReadStitcher.cpp.o.d -o src/libpbbam.so.1.3.0.p/WhitelistedZmwReadStitcher.cpp.o -c ../src/WhitelistedZmwReadStitcher.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../src/WhitelistedZmwReadStitcher.cpp:17:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[97/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ZmwChunkedFastxReaderImpl.cpp.o -MF src/libpbbam.so.1.3.0.p/ZmwChunkedFastxReaderImpl.cpp.o.d -o src/libpbbam.so.1.3.0.p/ZmwChunkedFastxReaderImpl.cpp.o -c ../src/ZmwChunkedFastxReaderImpl.cpp
[98/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ZmwChunkedFastxTextReader.cpp.o -MF src/libpbbam.so.1.3.0.p/ZmwChunkedFastxTextReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/ZmwChunkedFastxTextReader.cpp.o -c ../src/ZmwChunkedFastxTextReader.cpp
[99/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ZmwChunkedFastxBgzfReader.cpp.o -MF src/libpbbam.so.1.3.0.p/ZmwChunkedFastxBgzfReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/ZmwChunkedFastxBgzfReader.cpp.o -c ../src/ZmwChunkedFastxBgzfReader.cpp
[100/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ZmwTypeMap.cpp.o -MF src/libpbbam.so.1.3.0.p/ZmwTypeMap.cpp.o.d -o src/libpbbam.so.1.3.0.p/ZmwTypeMap.cpp.o -c ../src/ZmwTypeMap.cpp
[101/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ZmwReadStitcher.cpp.o -MF src/libpbbam.so.1.3.0.p/ZmwReadStitcher.cpp.o.d -o src/libpbbam.so.1.3.0.p/ZmwReadStitcher.cpp.o -c ../src/ZmwReadStitcher.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
from ../src/ZmwReadStitcher.cpp:17:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[102/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ZmwQuery.cpp.o -MF src/libpbbam.so.1.3.0.p/ZmwQuery.cpp.o.d -o src/libpbbam.so.1.3.0.p/ZmwQuery.cpp.o -c ../src/ZmwQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
from ../include/pbbam/PbiIndexedBamReader.h:17,
from ../include/pbbam/CompositeBamReader.h:28,
from ../src/ZmwQuery.cpp:13:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[103/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/bed_BedWriter.cpp.o -MF src/libpbbam.so.1.3.0.p/bed_BedWriter.cpp.o.d -o src/libpbbam.so.1.3.0.p/bed_BedWriter.cpp.o -c ../src/bed/BedWriter.cpp
[104/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/bed_BedReader.cpp.o -MF src/libpbbam.so.1.3.0.p/bed_BedReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/bed_BedReader.cpp.o -c ../src/bed/BedReader.cpp
[105/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ZmwGroupQuery.cpp.o -MF src/libpbbam.so.1.3.0.p/ZmwGroupQuery.cpp.o.d -o src/libpbbam.so.1.3.0.p/ZmwGroupQuery.cpp.o -c ../src/ZmwGroupQuery.cpp
In file included from ../include/pbbam/PbiFilterTypes.h:958,
from ../include/pbbam/PbiFilter.h:246,
from ../include/pbbam/ZmwGroupQuery.h:17,
from ../src/ZmwGroupQuery.cpp:9:
../include/pbbam/internal/PbiFilterTypes.inl: In function ‘uint32_t PacBio::BAM::BoostHashCombine(int32_t)’:
../include/pbbam/internal/PbiFilterTypes.inl:472:12: warning: useless cast to type ‘uint32_t’ {aka ‘unsigned int’} [-Wuseless-cast]
472 | return static_cast<uint32_t>(seed);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
[106/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ccs_CCSRecord.cpp.o -MF src/libpbbam.so.1.3.0.p/ccs_CCSRecord.cpp.o.d -o src/libpbbam.so.1.3.0.p/ccs_CCSRecord.cpp.o -c ../src/ccs/CCSRecord.cpp
FAILED: src/libpbbam.so.1.3.0.p/ccs_CCSRecord.cpp.o
c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ccs_CCSRecord.cpp.o -MF src/libpbbam.so.1.3.0.p/ccs_CCSRecord.cpp.o.d -o src/libpbbam.so.1.3.0.p/ccs_CCSRecord.cpp.o -c ../src/ccs/CCSRecord.cpp
../src/ccs/CCSRecord.cpp: In member function ‘PacBio::Data::Read PacBio::CCS::CCSRecord::ToRead(std::string, std::string) const’:
../src/ccs/CCSRecord.cpp:19:58: error: no matching function for call to ‘PacBio::Data::ReadId::ReadId(<brace-enclosed initializer list>)’
19 | Data::Interval{QueryStart, QueryEnd}},
| ^
In file included from /usr/include/pbcopper/data/Read.h:19,
from ../include/pbbam/ccs/CCSRecord.h:12,
from ../src/ccs/CCSRecord.cpp:9:
/usr/include/pbcopper/data/ReadId.h:29:5: note: candidate: ‘PacBio::Data::ReadId::ReadId(const std::shared_ptr<std::__cxx11::basic_string<char> >&, size_t, const PacBio::Data::Interval&)’
29 | ReadId(const std::shared_ptr<std::string>& movieName, size_t holeNumber,
| ^~~~~~
/usr/include/pbcopper/data/ReadId.h:29:48: note: no known conversion for argument 1 from ‘std::string’ {aka ‘std::__cxx11::basic_string<char>’} to ‘const std::shared_ptr<std::__cxx11::basic_string<char> >&’
29 | ReadId(const std::shared_ptr<std::string>& movieName, size_t holeNumber,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
/usr/include/pbcopper/data/ReadId.h:27:5: note: candidate: ‘PacBio::Data::ReadId::ReadId(const string&)’
27 | ReadId(const std::string& readName);
| ^~~~~~
/usr/include/pbcopper/data/ReadId.h:27:5: note: candidate expects 1 argument, 3 provided
/usr/include/pbcopper/data/ReadId.h:26:5: note: candidate: ‘PacBio::Data::ReadId::ReadId(const string&, size_t)’
26 | ReadId(const std::string& movieName, size_t holeNumber);
| ^~~~~~
/usr/include/pbcopper/data/ReadId.h:26:5: note: candidate expects 2 arguments, 3 provided
/usr/include/pbcopper/data/ReadId.h:25:5: note: candidate: ‘PacBio::Data::ReadId::ReadId(const std::shared_ptr<std::__cxx11::basic_string<char> >&, size_t)’
25 | ReadId(const std::shared_ptr<std::string>& movieName, size_t holeNumber);
| ^~~~~~
/usr/include/pbcopper/data/ReadId.h:25:5: note: candidate expects 2 arguments, 3 provided
/usr/include/pbcopper/data/ReadId.h:18:8: note: candidate: ‘PacBio::Data::ReadId::ReadId(const PacBio::Data::ReadId&)’
18 | struct ReadId
| ^~~~~~
/usr/include/pbcopper/data/ReadId.h:18:8: note: candidate expects 1 argument, 3 provided
/usr/include/pbcopper/data/ReadId.h:18:8: note: candidate: ‘PacBio::Data::ReadId::ReadId(PacBio::Data::ReadId&&)’
/usr/include/pbcopper/data/ReadId.h:18:8: note: candidate expects 1 argument, 3 provided
../src/ccs/CCSRecord.cpp:26:29: error: no matching function for call to ‘PacBio::Data::Read::Read(<brace-enclosed initializer list>)’
26 | std::move(chemistry)};
| ^
In file included from ../include/pbbam/ccs/CCSRecord.h:12,
from ../src/ccs/CCSRecord.cpp:9:
/usr/include/pbcopper/data/Read.h:33:5: note: candidate: ‘PacBio::Data::Read::Read(const string&, std::string, PacBio::Data::QualityValues, PacBio::Data::SNR, PacBio::Data::Position, PacBio::Data::Position, PacBio::Data::Frames, PacBio::Data::Frames)’
33 | Read(const std::string& name, std::string seq, QualityValues qualities, SNR snr,
| ^~~~
/usr/include/pbcopper/data/Read.h:33:5: note: conversion of argument 1 would be ill-formed:
/usr/include/pbcopper/data/Read.h:31:5: note: candidate: ‘PacBio::Data::Read::Read(const string&, std::string, PacBio::Data::QualityValues, PacBio::Data::SNR, PacBio::Data::Position, PacBio::Data::Position)’
31 | Read(const std::string& name, std::string seq, QualityValues qualities, SNR snr,
| ^~~~
/usr/include/pbcopper/data/Read.h:31:5: note: candidate expects 6 arguments, 8 provided
/usr/include/pbcopper/data/Read.h:30:5: note: candidate: ‘PacBio::Data::Read::Read(const string&, std::string, PacBio::Data::QualityValues, PacBio::Data::SNR)’
30 | Read(const std::string& name, std::string seq, QualityValues qualities, SNR snr);
| ^~~~
/usr/include/pbcopper/data/Read.h:30:5: note: candidate expects 4 arguments, 8 provided
/usr/include/pbcopper/data/Read.h:28:5: note: candidate: ‘PacBio::Data::Read::Read(PacBio::Data::ReadId, std::string, PacBio::Data::Frames, PacBio::Data::LocalContextFlags, PacBio::Data::Accuracy, PacBio::Data::SNR, std::string)’
28 | Read(Data::ReadId id, std::string seq, Frames pw, LocalContextFlags flags,
| ^~~~
/usr/include/pbcopper/data/Read.h:28:5: note: candidate expects 7 arguments, 8 provided
/usr/include/pbcopper/data/Read.h:26:8: note: candidate: ‘PacBio::Data::Read::Read(const PacBio::Data::Read&)’
26 | struct Read
| ^~~~
/usr/include/pbcopper/data/Read.h:26:8: note: candidate expects 1 argument, 8 provided
/usr/include/pbcopper/data/Read.h:26:8: note: candidate: ‘PacBio::Data::Read::Read(PacBio::Data::Read&&)’
/usr/include/pbcopper/data/Read.h:26:8: note: candidate expects 1 argument, 8 provided
[107/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ccs_CCSRecordFormat.cpp.o -MF src/libpbbam.so.1.3.0.p/ccs_CCSRecordFormat.cpp.o.d -o src/libpbbam.so.1.3.0.p/ccs_CCSRecordFormat.cpp.o -c ../src/ccs/CCSRecordFormat.cpp
[108/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ccs_CCSRecordReader.cpp.o -MF src/libpbbam.so.1.3.0.p/ccs_CCSRecordReader.cpp.o.d -o src/libpbbam.so.1.3.0.p/ccs_CCSRecordReader.cpp.o -c ../src/ccs/CCSRecordReader.cpp
[109/218] c++ -Isrc/libpbbam.so.1.3.0.p -Isrc -I../src -Iinclude -I../include -I/usr/include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/pbbam-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DBOOST_ALL_NO_LIB -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ src/libpbbam.so.1.3.0.p/ccs_CCSPbiBuilder.cpp.o -MF src/libpbbam.so.1.3.0.p/ccs_CCSPbiBuilder.cpp.o.d -o src/libpbbam.so.1.3.0.p/ccs_CCSPbiBuilder.cpp.o -c ../src/ccs/CCSPbiBuilder.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/pbcopper/data/Frames.h:10,
from ../include/pbbam/ccs/CCSRecord.h:9,
from ../include/pbbam/ccs/CCSPbiBuilder.h:11,
from ../src/ccs/CCSPbiBuilder.cpp:9:
/usr/include/c++/10/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++/10/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’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<PacBio::CCS::internal::PbiFieldBlock>::iterator’ changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/vector.tcc:121:21: 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++/10/vector:67,
from /usr/include/pbcopper/data/Frames.h:10,
from ../include/pbbam/ccs/CCSRecord.h:9,
from ../include/pbbam/ccs/CCSPbiBuilder.h:11,
from ../src/ccs/CCSPbiBuilder.cpp:9:
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void PacBio::CCS::CCSPbiBuilder::AddRecord(const PacBio::CCS::CCSRecord&)’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
ninja: build stopped: subcommand failed.
dh_auto_build: error: cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v returned exit code 1
make: *** [debian/rules:13: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-09-13T06:04:42Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 117864
Build-Time: 249
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 358
Job: pbbam_1.3.0+dfsg-2
Machine Architecture: armhf
Package: pbbam
Package-Time: 626
Source-Version: 1.3.0+dfsg-2
Space: 117864
Status: attempted
Version: 1.3.0+dfsg-2
--------------------------------------------------------------------------------
Finished at 2020-09-13T06:04:42Z
Build needed 00:10:26, 117864k disk space