unanimity →
3.3.0+dfsg-2.1 →
armhf → 2019-03-16 23:25:43
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| unanimity 3.3.0+dfsg-2.1 (armhf) Sat, 16 Mar 2019 23:11:45 +0000 |
+==============================================================================+
Package: unanimity
Version: 3.3.0+dfsg-2.1
Source Version: 3.3.0+dfsg-2.1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-1e872048-7c8c-4dc5-8edb-185824ae8b7d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 MB]
Fetched 24.4 MB in 10s (2412 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: 'unanimity' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/unanimity.git
Please use:
git clone https://salsa.debian.org/med-team/unanimity.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 3612 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main unanimity 3.3.0+dfsg-2.1 (dsc) [2292 B]
Get:2 http://172.17.0.1/private buster-staging/main unanimity 3.3.0+dfsg-2.1 (tar) [3601 kB]
Get:3 http://172.17.0.1/private buster-staging/main unanimity 3.3.0+dfsg-2.1 (diff) [9244 B]
Fetched 3612 kB in 1s (4988 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/unanimity-mv5RVl/unanimity-3.3.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/unanimity-mv5RVl' 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-ve77DH/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-ve77DH/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ve77DH/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-ve77DH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (10.8 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 46 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15903 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 (>= 12~), dh-python, cmake, swig, python-setuptools, python-all-dev, python-numpy, libboost-dev, libhts-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libpbcopper-dev, libseqan2-dev, pandoc
Filtered Build-Depends: debhelper (>= 12~), dh-python, cmake, swig, python-setuptools, python-all-dev, python-numpy, libboost-dev, libhts-dev, libpbbam-dev (>= 0.18.0+dfsg-1~), libpbcopper-dev, libseqan2-dev, pandoc
dpkg-deb: building package 'sbuild-build-depends-unanimity-dummy' in '/<<BUILDDIR>>/resolver-ve77DH/apt_archive/sbuild-build-depends-unanimity-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-unanimity-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-ve77DH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ Sources [579 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ Packages [664 B]
Fetched 2576 B in 0s (13.4 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install unanimity build dependencies (apt-based resolver)
---------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales
libgpg-error-l10n libnss-systemd libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
cpp-8 debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file
g++-8 gcc-8 gcc-8-base gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libarchive13 libasan5 libatomic1 libblas3 libboost-dev
libboost1.67-dev libbsd0 libcc1-0 libcroco3 libcurl3-gnutls libcurl4
libdeflate0 libelf1 libexpat1-dev libfile-stripnondeterminism-perl
libgcc-8-dev libgcc1 libgfortran5 libglib2.0-0 libgomp1 libhts-dev libhts2
libicu63 libjsoncpp1 liblapack3 liblua5.1-0 liblzma-dev libmagic-mgc
libmagic1 libmpdec2 libnghttp2-14 libpbbam-dev libpbbam0.19.0
libpbcopper-dev libpipeline1 libpsl5 libpython-all-dev libpython-dev
libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib librhash0 librtmp1 libseqan2-dev
libsigsegv2 libssh2-1 libssl-dev libssl1.1 libstdc++-8-dev libstdc++6
libtool libubsan1 libuchardet0 libuv1 libxml2 libyaml-0-2 m4 man-db
mime-support pandoc pandoc-data po-debconf python python-all python-all-dev
python-dev python-minimal python-numpy python-pkg-resources
python-setuptools python2 python2-dev python2-minimal python2.7
python2.7-dev python2.7-minimal python3 python3-distutils python3-lib2to3
python3-minimal python3.7 python3.7-minimal swig swig3.0 zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation cmake-doc ninja-build gcc-8-locales dh-make gcc-8-doc
libstdc++6-8-dbg libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan5-dbg liblsan0-dbg libtsan0-dbg libubsan1-dbg libmpx2-dbg
libquadmath0-dbg gettext-doc libasprintf-dev libgettextpo-dev groff lrzip
libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
liblzma-doc libssl-doc libstdc++-8-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc
texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php ruby
r-base-core libjs-mathjax node-katex libmail-box-perl python-doc python-tk
gfortran python-pytest python-numpy-dbg python-numpy-doc
python-setuptools-doc python2-doc python2.7-doc binfmt-support python3-doc
python3-tk python3-venv python3.7-venv python3.7-doc swig-doc swig-examples
swig3.0-examples swig3.0-doc
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs publicsuffix libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cmake cmake-data
debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13
libblas3 libboost-dev libboost1.67-dev libbsd0 libcroco3 libcurl3-gnutls
libcurl4 libdeflate0 libelf1 libexpat1-dev libfile-stripnondeterminism-perl
libgfortran5 libglib2.0-0 libhts-dev libhts2 libicu63 libjsoncpp1 liblapack3
liblua5.1-0 liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14
libpbbam-dev libpbbam0.19.0 libpbcopper-dev libpipeline1 libpsl5
libpython-all-dev libpython-dev libpython-stdlib libpython2-dev
libpython2-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal
libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib librhash0 librtmp1 libseqan2-dev libsigsegv2 libssh2-1
libssl-dev libtool libuchardet0 libuv1 libxml2 libyaml-0-2 m4 man-db
mime-support pandoc pandoc-data po-debconf python python-all python-all-dev
python-dev python-minimal python-numpy python-pkg-resources
python-setuptools python2 python2-dev python2-minimal python2.7
python2.7-dev python2.7-minimal python3 python3-distutils python3-lib2to3
python3-minimal python3.7 python3.7-minimal
sbuild-build-depends-unanimity-dummy swig swig3.0 zlib1g-dev
The following packages will be upgraded:
cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0 libgcc-8-dev
libgcc1 libgomp1 libssl1.1 libstdc++-8-dev libstdc++6 libubsan1
14 upgraded, 101 newly installed, 0 to remove and 32 not upgraded.
Need to get 131 MB/131 MB of archives.
After this operation, 490 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ve77DH/apt_archive ./ sbuild-build-depends-unanimity-dummy 0.invalid.0 [952 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-2 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.3.0-2+rpi1 [37.9 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.3.0-2+rpi1 [190 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.3.0-2+rpi1 [36.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.3.0-2+rpi1 [64.3 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.3.0-2+rpi1 [8108 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.3.0-2+rpi1 [317 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.3.0-2+rpi1 [103 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.3.0-2+rpi1 [7480 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.3.0-2+rpi1 [1545 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.3.0-2+rpi1 [595 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.3.0-2+rpi1 [7234 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.3.0-2+rpi1 [6805 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.3.0-2+rpi1 [325 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libpython2.7-minimal armhf 2.7.16~rc1-1 [394 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python2.7-minimal armhf 2.7.16~rc1-1 [1090 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf python2-minimal armhf 2.7.15-4 [41.4 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python-minimal armhf 2.7.15-4 [21.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.62 [37.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libssl1.1 armhf 1.1.1b-1 [1258 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libpython2.7-stdlib armhf 2.7.16~rc1-1 [1844 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf python2.7 armhf 2.7.16~rc1-1 [304 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpython2-stdlib armhf 2.7.15-4 [20.8 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libpython-stdlib armhf 2.7.15-4 [20.8 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf python2 armhf 2.7.15-4 [41.6 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf python armhf 2.7.15-4 [22.8 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libpython3.7-minimal armhf 3.7.2-3 [582 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf python3.7-minimal armhf 3.7.2-3 [1463 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.7.2-1 [36.6 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libpython3.7-stdlib armhf 3.7.2-3 [1663 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf python3.7 armhf 3.7.2-3 [323 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.7.2-1 [20.0 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.7.2-1 [61.5 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-4 [242 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-4 [110 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-4 [65.3 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf cmake-data all 3.13.4-1 [1476 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libarchive13 armhf 3.3.3-4 [270 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.36.0-2 [73.6 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.64.0-1 [292 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf librhash0 armhf 1.3.8-1 [132 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libuv1 armhf 1.24.1-1 [96.7 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf cmake armhf 3.13.4-1 [2559 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.1-1 [19.7 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.1-1 [13.0 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.176-1 [158 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.3-1 [1077 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf debhelper all 12.1.1 [1016 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.7.2-3 [76.7 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.7.2-3 [142 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf dh-python all 3.20180927 [95.8 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.3.0-2+rpi1 [206 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-2 [103 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.67.0.1+b1 [4140 B]
Get:83 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.64.0-1 [291 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libdeflate0 armhf 1.2-1 [48.4 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libexpat1-dev armhf 2.2.6-1 [127 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.9-10 [254 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.9-10 [4284 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-2 [1493 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf liblua5.1-0 armhf 5.1.5-8.1 [83.3 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libpbbam0.19.0 armhf 0.19.0+dfsg-4+rpi1 [455 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.1b-1 [1560 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libpbbam-dev armhf 0.19.0+dfsg-4+rpi1 [93.4 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libpbcopper-dev armhf 0.4.1+dfsg-2 [295 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libpython2.7 armhf 2.7.16~rc1-1 [872 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libpython2.7-dev armhf 2.7.16~rc1-1 [30.8 MB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libpython2-dev armhf 2.7.15-4 [20.9 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libpython-dev armhf 2.7.15-4 [20.9 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libpython-all-dev armhf 2.7.15-4 [1060 B]
Get:101 http://172.17.0.1/private buster-staging/main armhf libseqan2-dev all 2.4.0+dfsg-11 [1220 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libyaml-0-2 armhf 0.2.1-1 [38.8 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf pandoc-data all 2.2.1-3 [329 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf pandoc armhf 2.2.1-3+b2 [17.5 MB]
Get:105 http://172.17.0.1/private buster-staging/main armhf python-all armhf 2.7.15-4 [1044 B]
Get:106 http://172.17.0.1/private buster-staging/main armhf python2.7-dev armhf 2.7.16~rc1-1 [290 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf python2-dev armhf 2.7.15-4 [1212 B]
Get:108 http://172.17.0.1/private buster-staging/main armhf python-dev armhf 2.7.15-4 [1188 B]
Get:109 http://172.17.0.1/private buster-staging/main armhf python-all-dev armhf 2.7.15-4 [1064 B]
Get:110 http://172.17.0.1/private buster-staging/main armhf python-pkg-resources all 40.8.0-1 [182 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf python-numpy armhf 1:1.16.1-1 [1855 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf python-setuptools all 40.8.0-1 [382 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf swig3.0 armhf 3.0.12-2 [1221 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf swig armhf 3.0.12-2 [310 kB]
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
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Setting up python (2.7.15-4) ...
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Setting up libstdc++-8-dev:armhf (8.3.0-2+rpi1) ...
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Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up intltool-debian (0.35.0+20060710.5) ...
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Setting up po-debconf (1.0.21) ...
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Setting up dh-autoreconf (19) ...
Setting up debhelper (12.1.1) ...
Setting up dh-strip-nondeterminism (1.1.1-1) ...
Setting up sbuild-build-depends-unanimity-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.5 g++-8_8.3.0-2+rpi1 gcc-8_8.3.0-2+rpi1 libc6-dev_2.28-7+rpi1 libstdc++-8-dev_8.3.0-2+rpi1 libstdc++6_8.3.0-2+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~rc3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.46 bash_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20190110 cmake_3.13.4-1 cmake-data_3.13.4-1 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.3.0-2+rpi1 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12.1.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-python_3.20180927 dh-strip-nondeterminism_1.1.1-1 diffutils_1:3.7-2 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-2 dpkg_1.19.5 dpkg-dev_1.19.5 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 g++_4:8.2.0-2+rpi1 g++-8_8.3.0-2+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.3.0-2+rpi1 gcc-8-base_8.3.0-2+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 inetutils-ping_2:1.9.4-7 init-system-helpers_1.56+nmu1 initramfs-tools_0.133 initramfs-tools-core_0.133 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.6-1+rpi1 kmod_26-1 krb5-locales_1.17-1 libacl1_2.2.52-5 libapparmor1_2.13.2-7 libapt-pkg5.0_1.8.0~rc3 libarchive-zip-perl_1.64-1 libarchive13_3.3.3-4 libargon2-1_0~20171227-0.2 libasan5_8.3.0-2+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-2+rpi1 libattr1_1:2.4.47-4 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblas3_3.8.0-2 libblkid1_2.33.1-0.1 libboost-dev_1.67.0.1+b1 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9 libc-bin_2.28-7+rpi1 libc-dev-bin_2.28-7+rpi1 libc6_2.28-7+rpi1 libc6-dev_2.28-7+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-2 libcc1-0_8.3.0-2+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.1.0-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.64.0-1 libcurl4_7.64.0-1 libdb5.3_5.3.28+dfsg1-0.3 libdbus-1-3_1.12.12-1 libdebconfclient0_0.247 libdeflate0_1.2-1 libdevmapper1.02.1_2:1.02.155-2 libdpkg-perl_1.19.5 libdrm-common_2.4.97-1+rpi1 libdrm2_2.4.97-1+rpi1 libelf1_0.176-1 libexpat1_2.2.6-1 libexpat1-dev_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.1-1 libgcc-8-dev_8.3.0-2+rpi1 libgcc1_1:8.3.0-2+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-3 libgdbm3_1.8.3-14 libgdbm6_1.18.1-3 libgfortran5_8.3.0-2+rpi1 libglib2.0-0_2.58.3-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.6-2 libgomp1_8.3.0-2+rpi1 libgpg-error-l10n_1.35-1 libgpg-error0_1.35-1 libgssapi-krb5-2_1.17-1 libhogweed4_3.4.1-1 libhts-dev_1.9-10 libhts2_1.9-10 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1+ds-2 libjsoncpp1_1.7.4-3 libk5crypto3_1.17-1 libkeyutils1_1.6-2 libklibc_2.0.6-1+rpi1 libkmod2_26-1 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 liblapack3_3.8.0-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblua5.1-0_5.1.5-8.1 liblz4-1_1.8.3-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses5_6.1+20181013-2 libncurses6_6.1+20181013-2 libncursesw5_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnghttp2-14_1.36.0-2 libnpth0_1.6-1 libnss-systemd_241-1+rpi1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam-systemd_241-1+rpi1 libpam0g_1.3.1-5 libpbbam-dev_0.19.0+dfsg-4+rpi1 libpbbam0.19.0_0.19.0+dfsg-4+rpi1 libpbcopper-dev_0.4.1+dfsg-2 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-4 libpipeline1_1.5.1-2 libplymouth4_0.9.4-1 libpng16-16_1.6.36-5 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libpython-all-dev_2.7.15-4 libpython-dev_2.7.15-4 libpython-stdlib_2.7.15-4 libpython2-dev_2.7.15-4 libpython2-stdlib_2.7.15-4 libpython2.7_2.7.16~rc1-1 libpython2.7-dev_2.7.16~rc1-1 libpython2.7-minimal_2.7.16~rc1-1 libpython2.7-stdlib_2.7.16~rc1-1 libpython3-stdlib_3.7.2-1 libpython3.7-minimal_3.7.2-3 libpython3.7-stdlib_3.7.2-3 libreadline7_7.0-5 librhash0_1.3.8-1 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libseqan2-dev_2.4.0+dfsg-11 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-2 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl-dev_1.1.1b-1 libssl1.1_1.1.1b-1 libstdc++-8-dev_8.3.0-2+rpi1 libstdc++6_8.3.0-2+rpi1 libsystemd0_241-1+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.3.0-2+rpi1 libuchardet0_0.0.6-3 libudev1_241-1+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1 libuv1_1.24.1-1 libxml2_2.9.4+dfsg1-7+b1 libyaml-0-2_0.2.1-1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-2 mawk_1.3.3-17 mime-support_3.62 mount_2.33.1-0.1 multiarch-support_2.28-7+rpi1 nano_3.2-2 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 openssl_1.1.1a-1 pandoc_2.2.1-3+b2 pandoc-data_2.2.1-3 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-4 perl-base_5.28.1-4 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-4 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 python_2.7.15-4 python-all_2.7.15-4 python-all-dev_2.7.15-4 python-dev_2.7.15-4 python-minimal_2.7.15-4 python-numpy_1:1.16.1-1 python-pkg-resources_40.8.0-1 python-setuptools_40.8.0-1 python2_2.7.15-4 python2-dev_2.7.15-4 python2-minimal_2.7.15-4 python2.7_2.7.16~rc1-1 python2.7-dev_2.7.16~rc1-1 python2.7-minimal_2.7.16~rc1-1 python3_3.7.2-1 python3-distutils_3.7.2-3 python3-lib2to3_3.7.2-3 python3-minimal_3.7.2-1 python3.7_3.7.2-3 python3.7-minimal_3.7.2-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-unanimity-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 swig_3.0.12-2 swig3.0_3.0.12-2 systemd_241-1+rpi1 systemd-sysv_241-1+rpi1 sysvinit-utils_2.93-8 tar_1.30+dfsg-5 tzdata_2018i-1 udev_241-1+rpi1 util-linux_2.33.1-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Feb 6 07:18:37 2019 UTC
gpgv: using RSA key 3AFA757FAC6EA11D2FF45DF088D24287A2D898B1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./unanimity_3.3.0+dfsg-2.1.dsc
dpkg-source: info: extracting unanimity in /<<BUILDDIR>>/unanimity-3.3.0+dfsg
dpkg-source: info: unpacking unanimity_3.3.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking unanimity_3.3.0+dfsg-2.1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying add_missing_library_files
dpkg-source: info: applying git-version.patch
dpkg-source: info: applying no-static-linking.patch
dpkg-source: info: applying do_not_refer_to_non-existing_images.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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-1e872048-7c8c-4dc5-8edb-185824ae8b7d
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package unanimity
dpkg-buildpackage: info: source version 3.3.0+dfsg-2.1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean \
--package=unanimity \
--no-package=python-consensuscore2 \
--buildsystem=cmake \
--builddirectory=build
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg'
dh_auto_clean
rm -f config-main
rm -f doc/JULIET.html doc/PBCCS.html
make[1]: Leaving directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg'
dh_autoreconf_clean -O--package=unanimity -O--no-package=python-consensuscore2 -O--buildsystem=cmake -O--builddirectory=build
dh_clean -O--package=unanimity -O--no-package=python-consensuscore2 -O--buildsystem=cmake -O--builddirectory=build
dh clean \
--package=python-consensuscore2 \
--no-package=unanimity \
--with python2 \
--buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg'
dh_auto_clean
I: pybuild base:217: python2.7 setup.py clean
running clean
removing '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/.pybuild/cpython2_2.7_consensuscore2/build' (and everything under it)
'build/bdist.linux-armhf' does not exist -- can't clean it
'build/scripts-2.7' does not exist -- can't clean it
rm -f config-main
rm -f doc/JULIET.html doc/PBCCS.html
make[1]: Leaving directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg'
dh_autoreconf_clean -O--package=python-consensuscore2 -O--no-package=unanimity -O--buildsystem=pybuild
dh_clean -O--package=python-consensuscore2 -O--no-package=unanimity -O--buildsystem=pybuild
debian/rules build-arch
dh build-arch \
--package=unanimity \
--no-package=python-consensuscore2 \
--buildsystem=cmake \
--builddirectory=build
dh_update_autotools_config -a -O--package=unanimity -O--no-package=python-consensuscore2 -O--buildsystem=cmake -O--builddirectory=build
dh_autoreconf -a -O--package=unanimity -O--no-package=python-consensuscore2 -O--buildsystem=cmake -O--builddirectory=build
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg'
dh_auto_configure -- \
-DCMAKE_EXE_LINKER_FLAGS=-pthread \
-DUNY_build_tests=OFF \
-DPYTHON_SWIG=ON \
-DZLIB_INCLUDE_DIRS=/usr/include \
-DBoost_INCLUDE_DIRS=/usr/include \
-DPacBioBAM_INCLUDE_DIRS=/usr/include \
-DPacBioBAM_LIBRARIES=/usr/lib/arm-linux-gnueabihf/libpbbam.so \
-DSEQAN_INCLUDE_DIRS=/usr/include \
-Dpbcopper_INCLUDE_DIRS=/usr/include \
-Dpbcopper_LIBRARIES=/usr/lib/arm-linux-gnueabihf/libpbcopper.a
cd build && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DCMAKE_EXE_LINKER_FLAGS=-pthread -DUNY_build_tests=OFF -DPYTHON_SWIG=ON -DZLIB_INCLUDE_DIRS=/usr/include -DBoost_INCLUDE_DIRS=/usr/include -DPacBioBAM_INCLUDE_DIRS=/usr/include -DPacBioBAM_LIBRARIES=/usr/lib/arm-linux-gnueabihf/libpbbam.so -DSEQAN_INCLUDE_DIRS=/usr/include -Dpbcopper_INCLUDE_DIRS=/usr/include -Dpbcopper_LIBRARIES=/usr/lib/arm-linux-gnueabihf/libpbcopper.a ..
-- The CXX compiler identification is GNU 8.3.0
-- The C compiler identification is GNU 8.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS
-- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success
-- Found PythonInterp: /usr/bin/python (found version "2.7.16")
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LIBDIR
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
ZLIB_INCLUDE_DIRS
-- Build files have been written to: /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build
touch config-main
make[1]: Leaving directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg'
dh_auto_build -a -O--package=unanimity -O--no-package=python-consensuscore2 -O--buildsystem=cmake -O--builddirectory=build
cd build && make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
/usr/bin/cmake -S/<<BUILDDIR>>/unanimity-3.3.0+dfsg -B/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/CMakeFiles /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
make -f src/CMakeFiles/unanimity.dir/build.make src/CMakeFiles/unanimity.dir/depend
make -f src/CMakeFiles/cc2.dir/build.make src/CMakeFiles/cc2.dir/depend
make[3]: Entering directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/unanimity-3.3.0+dfsg /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src/CMakeFiles/unanimity.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/unanimity-3.3.0+dfsg /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src/CMakeFiles/cc2.dir/DependInfo.cmake --color=
Scanning dependencies of target unanimity
make[3]: Leaving directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
make -f src/CMakeFiles/unanimity.dir/build.make src/CMakeFiles/unanimity.dir/build
make[3]: Entering directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
Scanning dependencies of target cc2
make[3]: Leaving directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
make -f src/CMakeFiles/cc2.dir/build.make src/CMakeFiles/cc2.dir/build
[ 1%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Filters.cpp
[ 2%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/ConsensusModelFactory.cpp
make[3]: Entering directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
[ 3%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Consensus.cpp
[ 4%] Building CXX object src/CMakeFiles/cc2.dir/__/generated/UnanimityGitHash.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/__/generated/UnanimityGitHash.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated/UnanimityGitHash.cpp
[ 6%] Building CXX object src/CMakeFiles/cc2.dir/__/generated/UnanimityVersion.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/__/generated/UnanimityVersion.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated/UnanimityVersion.cpp
[ 7%] Building CXX object src/CMakeFiles/cc2.dir/__/generated/ModelInternalInitializer.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/__/generated/ModelInternalInitializer.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated/ModelInternalInitializer.cpp
[ 8%] Building CXX object src/CMakeFiles/cc2.dir/align/AffineAlignment.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/align/AffineAlignment.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/align/AffineAlignment.cpp
[ 9%] Building CXX object src/CMakeFiles/cc2.dir/align/AlignConfig.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/align/AlignConfig.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/align/AlignConfig.cpp
[ 11%] Building CXX object src/CMakeFiles/cc2.dir/align/BandedChainAlignment.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/align/BandedChainAlignment.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/align/BandedChainAlignment.cpp
[ 12%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/GenomicConsensus.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/align/BandedChainAlignment.h:10,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/align/BandedChainAlignment.cpp:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PacBio::Align::Seed&}; _Tp = PacBio::Align::Seed; _Alloc = std::allocator<PacBio::Align::Seed>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PacBio::Align::Seed>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::Align::Seed*, std::vector<PacBio::Align::Seed> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PacBio::Align::Seed>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::Align::Seed*, std::vector<PacBio::Align::Seed> >’} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/align/BandedChainAlignment.h:10,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/align/BandedChainAlignment.cpp:3:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘std::vector<PacBio::Align::Seed> PacBio::Align::Internal::BandedChainAlignerImpl::MergeSeeds(const std::vector<PacBio::Align::Seed>&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::Seed*, std::vector<PacBio::Align::Seed> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::Seed*, std::vector<PacBio::Align::Seed> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 13%] Building CXX object src/CMakeFiles/cc2.dir/align/LinearAlignment.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/align/LinearAlignment.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/align/LinearAlignment.cpp
[ 14%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/IPoaModel.cpp
[ 16%] Building CXX object src/CMakeFiles/cc2.dir/align/PairwiseAlignment.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/align/PairwiseAlignment.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/align/PairwiseAlignment.cpp
[ 17%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Input.cpp
[ 18%] Building CXX object src/CMakeFiles/cc2.dir/matrix/BasicDenseMatrix.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/matrix/BasicDenseMatrix.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/matrix/BasicDenseMatrix.cpp
[ 19%] Building CXX object src/CMakeFiles/cc2.dir/matrix/ScaledMatrix.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/matrix/ScaledMatrix.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/matrix/ScaledMatrix.cpp
[ 20%] Building CXX object src/CMakeFiles/cc2.dir/matrix/SparseMatrix.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/matrix/SparseMatrix.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/matrix/SparseMatrix.cpp
[ 22%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Intervals.cpp
[ 23%] Building CXX object src/CMakeFiles/cc2.dir/models/MarginalModelForm.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -fPIC -std=c++14 -o CMakeFiles/cc2.dir/models/MarginalModelForm.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp
In file included from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:18:
/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/../Recursor.h: In member function ‘size_t PacBio::Consensus::Recursor<Derived>::FillAlphaBeta(const PacBio::Consensus::AbstractTemplate&, PacBio::Consensus::AbstractRecursor::M&, PacBio::Consensus::AbstractRecursor::M&, double) const’:
/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/../Recursor.h:711:91: error: no matching function for call to ‘max(long unsigned int, size_t)’
std::max(100ul, static_cast<size_t>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1)));
^
In file included from /usr/include/c++/8/memory:62,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:7:
/usr/include/c++/8/bits/stl_algobase.h:219:5: note: candidate: ‘template<class _Tp> constexpr const _Tp& std::max(const _Tp&, const _Tp&)’
max(const _Tp& __a, const _Tp& __b)
^~~
/usr/include/c++/8/bits/stl_algobase.h:219:5: note: template argument deduction/substitution failed:
In file included from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:18:
/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/../Recursor.h:711:91: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘size_t’ {aka ‘unsigned int’})
std::max(100ul, static_cast<size_t>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1)));
^
In file included from /usr/include/c++/8/memory:62,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:7:
/usr/include/c++/8/bits/stl_algobase.h:265:5: note: candidate: ‘template<class _Tp, class _Compare> constexpr const _Tp& std::max(const _Tp&, const _Tp&, _Compare)’
max(const _Tp& __a, const _Tp& __b, _Compare __comp)
^~~
/usr/include/c++/8/bits/stl_algobase.h:265:5: note: template argument deduction/substitution failed:
In file included from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:18:
/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/../Recursor.h:711:91: note: deduced conflicting types for parameter ‘const _Tp’ (‘long unsigned int’ and ‘size_t’ {aka ‘unsigned int’})
std::max(100ul, static_cast<size_t>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1)));
^
In file included from /usr/include/c++/8/algorithm:62,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/data/Read.h:5,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/consensus/ModelConfig.h:20,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:11:
/usr/include/c++/8/bits/stl_algo.h:3462:5: note: candidate: ‘template<class _Tp> constexpr _Tp std::max(std::initializer_list<_Tp>)’
max(initializer_list<_Tp> __l)
^~~
/usr/include/c++/8/bits/stl_algo.h:3462:5: note: template argument deduction/substitution failed:
In file included from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:18:
/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/../Recursor.h:711:91: note: mismatched types ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
std::max(100ul, static_cast<size_t>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1)));
^
In file included from /usr/include/c++/8/algorithm:62,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/data/Read.h:5,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/consensus/ModelConfig.h:20,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:11:
/usr/include/c++/8/bits/stl_algo.h:3468:5: note: candidate: ‘template<class _Tp, class _Compare> constexpr _Tp std::max(std::initializer_list<_Tp>, _Compare)’
max(initializer_list<_Tp> __l, _Compare __comp)
^~~
/usr/include/c++/8/bits/stl_algo.h:3468:5: note: template argument deduction/substitution failed:
In file included from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:18:
/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/models/../Recursor.h:711:91: note: mismatched types ‘std::initializer_list<_Tp>’ and ‘long unsigned int’
std::max(100ul, static_cast<size_t>(0.5 + REBANDING_THRESHOLD * (I + 1) * (J + 1)));
^
make[3]: *** [src/CMakeFiles/cc2.dir/build.make:209: src/CMakeFiles/cc2.dir/models/MarginalModelForm.cpp.o] Error 1
make[3]: Leaving directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
make[2]: *** [CMakeFiles/Makefile2:177: src/CMakeFiles/cc2.dir/all] Error 2
make[2]: *** Waiting for unfinished jobs....
[ 24%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Output.cpp
[ 25%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Settings.cpp
[ 27%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Sorting.cpp
[ 28%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Workflow.cpp
[ 29%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/arrow/ArrowModel.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/arrow/ArrowModel.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/arrow/ArrowModel.cpp
[ 30%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastaWriter.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastaWriter.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/io/FastaWriter.cpp
[ 32%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastqWriter.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastqWriter.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/io/FastqWriter.cpp
[ 33%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/GffWriter.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/GffWriter.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/io/GffWriter.cpp
[ 34%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/VcfWriter.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/VcfWriter.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/io/VcfWriter.cpp
In file included from /usr/include/c++/8/vector:69,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/IPoaModel.h:6,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/ArrowModel.h:5,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/arrow/ArrowModel.cpp:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PacBio::Data::Read, PacBio::Data::StrandType, unsigned int, unsigned int}; _Tp = PacBio::Data::MappedRead; _Alloc = std::allocator<PacBio::Data::MappedRead>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PacBio::Data::MappedRead>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::Data::MappedRead*, std::vector<PacBio::Data::MappedRead> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In static member function ‘static std::vector<PacBio::Data::MappedRead> PacBio::GenomicConsensus::experimental::Arrow::MakeMappedReads(const std::vector<PacBio::BAM::BamRecord>&, const PacBio::GenomicConsensus::experimental::ReferenceWindow&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Data::MappedRead*, std::vector<PacBio::Data::MappedRead> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[ 35%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/plurality/PluralityModel.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/plurality/PluralityModel.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/plurality/PluralityModel.cpp
[ 37%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/poa/PoaModel.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/poa/PoaModel.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/poa/PoaModel.cpp
[ 38%] Building CXX object src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/ChemistryMapping.cpp
[ 39%] Building CXX object src/CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/ChemistryTriple.cpp
[ 40%] Building CXX object src/CMakeFiles/unanimity.dir/Interval.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/Interval.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/Interval.cpp
[ 41%] Building CXX object src/CMakeFiles/unanimity.dir/ReadId.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/ReadId.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/ReadId.cpp
[ 43%] Building CXX object src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/SparsePoa.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SparsePoa.cpp
[ 44%] Building CXX object src/CMakeFiles/unanimity.dir/SubreadResultCounter.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/SubreadResultCounter.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SubreadResultCounter.cpp
[ 45%] Building CXX object src/CMakeFiles/unanimity.dir/Timer.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/Timer.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/Timer.cpp
[ 46%] Building CXX object src/CMakeFiles/unanimity.dir/Utility.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/Utility.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/Utility.cpp
[ 48%] Building CXX object src/CMakeFiles/unanimity.dir/ConsensusSettings.cpp.o
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/c++ -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/include -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/generated -I/<<BUILDDIR>>/unanimity-3.3.0+dfsg/src -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/unanimity-3.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -std=c++14 -o CMakeFiles/unanimity.dir/ConsensusSettings.cpp.o -c /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/ConsensusSettings.cpp
In file included from /usr/include/c++/8/map:60,
from /usr/include/pbcopper/json/internal/json.hpp:54,
from /usr/include/pbcopper/json/JSON.h:7,
from /usr/include/pbcopper/cli/Option.h:14,
from /usr/include/pbcopper/cli/Interface.h:11,
from /usr/include/pbcopper/cli/CLI.h:12,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/ccs/ConsensusSettings.h:9,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/ConsensusSettings.cpp:3:
/usr/include/c++/8/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >; _Compare = std::less<void>; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from /usr/include/pbcopper/json/internal/json.hpp:54,
from /usr/include/pbcopper/json/JSON.h:7,
from /usr/include/pbcopper/cli/Option.h:14,
from /usr/include/pbcopper/cli/Interface.h:11,
from /usr/include/pbcopper/cli/CLI.h:12,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/ccs/ConsensusSettings.h:9,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/ConsensusSettings.cpp:3:
/usr/include/c++/8/bits/stl_map.h: In member function ‘nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::value_type& nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::operator[](T*) [with T = const char; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’:
/usr/include/c++/8/bits/stl_map.h:518:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/algorithm:62,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SparsePoa.cpp:3:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const PacBio::Align::Seed&, const PacBio::Align::Seed&)>]’:
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const PacBio::Align::Seed&, const PacBio::Align::Seed&)>]’:
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const PacBio::Align::{anonymous}::SDPHit&, const PacBio::Align::{anonymous}::SDPHit&)>]’:
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SparsePoa.cpp:3:
/usr/include/c++/8/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >; _Distance = int; _Tp = PacBio::Align::{anonymous}::SDPHit; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const PacBio::Align::Seed&, const PacBio::Align::Seed&)>]’:
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >; _Distance = int; _Tp = PacBio::Align::{anonymous}::SDPHit; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const PacBio::Align::{anonymous}::SDPHit&, const PacBio::Align::{anonymous}::SDPHit&)>]’:
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
In file included from /usr/include/c++/8/map:60,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/ccs/SparseAlignment.h:5,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SparsePoa.cpp:14:
/usr/include/c++/8/bits/stl_tree.h: In member function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = PacBio::Align::{anonymous}::SDPHit; _Val = PacBio::Align::{anonymous}::SDPHit; _KeyOfValue = std::_Identity<PacBio::Align::{anonymous}::SDPHit>; _Compare = std::less<PacBio::Align::{anonymous}::SDPHit>; _Alloc = std::allocator<PacBio::Align::{anonymous}::SDPHit>]’:
/usr/include/c++/8/bits/stl_tree.h:2146:5: note: parameter passing for argument of type ‘std::_Rb_tree<PacBio::Align::{anonymous}::SDPHit, PacBio::Align::{anonymous}::SDPHit, std::_Identity<PacBio::Align::{anonymous}::SDPHit>, std::less<PacBio::Align::{anonymous}::SDPHit>, std::allocator<PacBio::Align::{anonymous}::SDPHit> >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<PacBio::Align::{anonymous}::SDPHit>’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SparsePoa.cpp:3:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const PacBio::Align::{anonymous}::SDPHit&, const PacBio::Align::{anonymous}::SDPHit&)>]’:
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const PacBio::Align::{anonymous}::SDPHit&, const PacBio::Align::{anonymous}::SDPHit&)>]’:
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const PacBio::Align::Seed&, const PacBio::Align::Seed&)>]’:
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘void PacBio::Align::{anonymous}::ChainSeedsImpl(std::priority_queue<PacBio::Align::{anonymous}::ChainHit, std::vector<PacBio::Align::{anonymous}::ChainHit>, PacBio::Align::{anonymous}::ChainHitCompare>*, std::vector<boost::optional<unsigned int> >*, std::vector<PacBio::Align::{anonymous}::SDPHit>*, std::vector<long int>&, size_t, const PacBio::Align::ChainSeedsConfig&)’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::{anonymous}::SDPHit*, std::vector<PacBio::Align::{anonymous}::SDPHit> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SparsePoa.cpp:7:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PacBio::Align::Seed&}; _Tp = PacBio::Align::Seed; _Alloc = std::allocator<PacBio::Align::Seed>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<PacBio::Align::Seed>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<PacBio::Align::Seed*, std::vector<PacBio::Align::Seed> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]’:
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SparsePoa.cpp:7:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void PacBio::QGram::internal::IndexImpl::Init()’:
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’ changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/pbcopper/qgram/Index.h:77,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/align/FindSeeds.h:11,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/align/SparseAlignment.h:16,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/include/pacbio/ccs/SparseAlignment.h:18,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SparsePoa.cpp:14:
/usr/include/pbcopper/qgram/internal/Index-inl.h:106:1: note: parameter passing for argument of type ‘std::vector<long long unsigned int>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >’} changed in GCC 7.1
}
^
In file included from /usr/include/c++/8/vector:64,
from /<<BUILDDIR>>/unanimity-3.3.0+dfsg/src/SparsePoa.cpp:7:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘virtual PacBio::Poa::detail::SdpAnchorVector PacBio::Poa::SdpRangeFinder::FindAnchors(const string&, const string&) const’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<PacBio::Align::Seed*, std::vector<PacBio::Align::Seed> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[ 49%] Linking CXX static library libunanimity.a
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/cmake -P CMakeFiles/unanimity.dir/cmake_clean_target.cmake
cd /<<BUILDDIR>>/unanimity-3.3.0+dfsg/build/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/unanimity.dir/link.txt --verbose=1
/usr/bin/ar qc libunanimity.a CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/arrow/ArrowModel.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastaWriter.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastqWriter.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/GffWriter.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/VcfWriter.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/plurality/PluralityModel.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/poa/PoaModel.cpp.o CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o CMakeFiles/unanimity.dir/Interval.cpp.o CMakeFiles/unanimity.dir/ReadId.cpp.o CMakeFiles/unanimity.dir/SparsePoa.cpp.o CMakeFiles/unanimity.dir/SubreadResultCounter.cpp.o CMakeFiles/unanimity.dir/Timer.cpp.o CMakeFiles/unanimity.dir/Utility.cpp.o CMakeFiles/unanimity.dir/ConsensusSettings.cpp.o
/usr/bin/ranlib libunanimity.a
make[3]: Leaving directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
[ 49%] Built target unanimity
make[2]: Leaving directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
make[1]: *** [Makefile:133: all] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/unanimity-3.3.0+dfsg/build'
dh_auto_build: cd build && make -j4 "INSTALL=install --strip-program=true" returned exit code 2
make: *** [debian/rules:28: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-03-16T23:25:41Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 123428
Build-Time: 164
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 651
Job: unanimity_3.3.0+dfsg-2.1
Machine Architecture: armhf
Package: unanimity
Package-Time: 836
Source-Version: 3.3.0+dfsg-2.1
Space: 123428
Status: attempted
Version: 3.3.0+dfsg-2.1
--------------------------------------------------------------------------------
Finished at 2019-03-16T23:25:41Z
Build needed 00:13:56, 123428k disk space