Build log for prime-phylo (1.0.11-4+b1) on armhf

prime-phylo → 1.0.11-4+b1 → armhf → 2016-10-02 23:47:16

sbuild (Debian sbuild) 0.70.0 (03 Aug 2016) on bm-wb-04

+==============================================================================+
| prime-phylo 1.0.11-4+b1 (armhf)              Sun, 02 Oct 2016 23:24:50 +0000 |
+==============================================================================+

Package: prime-phylo
Version: 1.0.11-4+b1
Source Version: 1.0.11-4
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-f1ecb379-4131-4a60-9d6d-c2b325aad8a2' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9321 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.3 MB]
Fetched 20.6 MB in 23s (886 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: 'prime-phylo' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/prime-phylo.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/prime-phylo.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 759 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main prime-phylo 1.0.11-4 (dsc) [2134 B]
Get:2 http://172.17.0.1/private stretch-staging/main prime-phylo 1.0.11-4 (tar) [751 kB]
Get:3 http://172.17.0.1/private stretch-staging/main prime-phylo 1.0.11-4 (diff) [5892 B]
Fetched 759 kB in 0s (7520 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/prime-phylo-oEaCzh/prime-phylo-1.0.11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/prime-phylo-oEaCzh' 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-rAikKq/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-rAikKq/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-rAikKq/gpg/trustdb.gpg: trustdb created
gpg: key 5B825F7B5086BFC4: 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 5B825F7B5086BFC4: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 5B825F7B5086BFC4: 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-rAikKq/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-rAikKq/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-rAikKq/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-rAikKq/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-rAikKq/apt_archive ./ Packages [431 B]
Fetched 2079 B in 0s (3357 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  dirmngr fuse2fs gnupg-l10n libffi6 libfuse2 libgnutls30 libhogweed4
  libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
  libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages
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 2 not upgraded.
Need to get 768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-rAikKq/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 768 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14070 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 (>= 9.0.0), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev
Filtered Build-Depends: debhelper (>= 9.0.0), gengetopt, cmake, libblas-dev, liblapack-dev, gfortran, bison, flex, libopenmpi-dev, libxml2-dev, libboost-dev, libboost-mpi-dev, libboost-serialization-dev, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-prime-phylo-dummy' in '/<<BUILDDIR>>/resolver-jhnu1A/apt_archive/sbuild-build-depends-prime-phylo-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-prime-phylo-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-jhnu1A/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-jhnu1A/gpg/trustdb.gpg: trustdb created
gpg: key 5B825F7B5086BFC4: 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 5B825F7B5086BFC4: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 5B825F7B5086BFC4: 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-jhnu1A/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-jhnu1A/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-jhnu1A/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-jhnu1A/apt_archive ./ Sources [431 B]
Get:5 copy:/<<BUILDDIR>>/resolver-jhnu1A/apt_archive ./ Packages [522 B]
Fetched 2252 B in 0s (3622 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install prime-phylo 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:
  dirmngr fuse2fs gnupg-l10n libfuse2 libsasl2-modules manpages
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bison bsdmainutils cmake
  cmake-data debhelper dh-autoreconf dh-strip-nondeterminism file flex
  gengetopt gettext gettext-base gfortran gfortran-6 groff-base icu-devtools
  intltool-debian libarchive-zip-perl libarchive13 libbison-dev libblas-common
  libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.61-dev
  libboost-mpi1.61.0 libboost-serialization-dev libboost-serialization1.61-dev
  libboost-serialization1.61.0 libboost1.61-dev libbsd0 libcroco3 libcurl3
  libexpat1 libfile-stripnondeterminism-perl libfl-dev libgfortran-6-dev
  libgfortran3 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins
  libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libjsoncpp1
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
  libltdl-dev libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14
  libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi2 libpciaccess0
  libpipeline1 librtmp1 libsigsegv2 libssh2-1 libtool libunistring0 libxml2
  libxml2-dev m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-common
  po-debconf zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist
  whois vacation codeblocks eclipse ninja-build dh-make gettext-doc
  libasprintf-dev libgettextpo-dev gfortran-doc gfortran-6-doc
  libgfortran3-dbg libcoarrays-dev groff lrzip liblapack-doc-man liblapack-doc
  libboost-doc libboost-graph1.61-dev libboost1.61-doc libboost-atomic1.61-dev
  libboost-chrono1.61-dev libboost-context1.61-dev libboost-coroutine1.61-dev
  libboost-date-time1.61-dev libboost-exception1.61-dev
  libboost-filesystem1.61-dev libboost-graph-parallel1.61-dev
  libboost-iostreams1.61-dev libboost-locale1.61-dev libboost-log1.61-dev
  libboost-math1.61-dev libboost-mpi-python1.61-dev
  libboost-program-options1.61-dev libboost-python1.61-dev
  libboost-random1.61-dev libboost-regex1.61-dev libboost-signals1.61-dev
  libboost-system1.61-dev libboost-test1.61-dev libboost-thread1.61-dev
  libboost-timer1.61-dev libboost-wave1.61-dev libboost1.61-tools-dev
  libmpfrc++-dev libntl-dev krb5-doc krb5-user libhwloc-contrib-plugins
  icu-doc libtool-doc openmpi-doc pciutils gcj-jdk pkg-config less www-browser
  opencl-icd libmail-box-perl
Recommended packages:
  curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
  xdg-user-dirs krb5-locales openmpi-bin xml-core libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bison bsdmainutils cmake
  cmake-data debhelper dh-autoreconf dh-strip-nondeterminism file flex
  gengetopt gettext gettext-base gfortran gfortran-6 groff-base icu-devtools
  intltool-debian libarchive-zip-perl libarchive13 libbison-dev libblas-common
  libblas-dev libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.61-dev
  libboost-mpi1.61.0 libboost-serialization-dev libboost-serialization1.61-dev
  libboost-serialization1.61.0 libboost1.61-dev libbsd0 libcroco3 libcurl3
  libexpat1 libfile-stripnondeterminism-perl libfl-dev libgfortran-6-dev
  libgfortran3 libglib2.0-0 libgssapi-krb5-2 libhwloc-dev libhwloc-plugins
  libhwloc5 libibverbs-dev libibverbs1 libicu-dev libicu57 libjsoncpp1
  libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
  libltdl-dev libltdl7 liblzo2-2 libmagic-mgc libmagic1 libnghttp2-14
  libnl-3-200 libnl-route-3-200 libopenmpi-dev libopenmpi2 libpciaccess0
  libpipeline1 librtmp1 libsigsegv2 libssh2-1 libtool libunistring0 libxml2
  libxml2-dev m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-common
  po-debconf sbuild-build-depends-prime-phylo-dummy zlib1g-dev
0 upgraded, 86 newly installed, 0 to remove and 2 not upgraded.
Need to get 84.9 MB of archives.
After this operation, 428 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-jhnu1A/apt_archive ./ sbuild-build-depends-prime-phylo-dummy 0.invalid.0 [856 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf cmake-data all 3.6.2-1 [1153 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libarchive13 armhf 3.2.1-2 [250 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-2 [57.5 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-2 [110 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.3+dfsg-2 [262 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.3+dfsg-2 [131 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.14.1-1 [67.7 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libcurl3 armhf 7.50.1-1 [251 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libjsoncpp1 armhf 1.7.4-3 [66.2 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf cmake armhf 3.6.2-1 [2268 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libfl-dev armhf 2.6.1-1 [92.4 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf flex armhf 2.6.1-1 [413 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.28-4 [210 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.28-4 [104 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.28-4 [62.7 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libbison-dev armhf 2:3.0.4.dfsg-1 [433 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf bison armhf 2:3.0.4.dfsg-1 [744 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-1 [2520 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10 [823 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf gengetopt armhf 2.22.6+dfsg0-1 [174 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.1.1-11+rpi1 [166 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.1.1-11+rpi1 [200 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.1.1-11+rpi1 [27.9 MB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.1.1-1 [1370 B]
Get:55 http://172.17.0.1/private stretch-staging/main armhf icu-devtools armhf 57.1-4 [156 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.1-2 [13.9 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-2 [112 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.1-2 [18.9 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf libboost1.61-dev armhf 1.61.0+dfsg-2.1+b1 [6843 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf libboost-dev armhf 1.61.0.2 [3758 B]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libboost-serialization1.61.0 armhf 1.61.0+dfsg-2.1+b1 [105 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf libboost-serialization1.61-dev armhf 1.61.0+dfsg-2.1+b1 [170 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf libltdl7 armhf 2.4.6-2 [386 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libhwloc5 armhf 1.11.4-1+rpi1 [82.8 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf libnl-3-200 armhf 3.2.27-1 [53.4 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libnl-route-3-200 armhf 3.2.27-1 [111 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libibverbs1 armhf 1.2.1-2 [35.4 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libpciaccess0 armhf 0.13.4-1 [47.4 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf ocl-icd-libopencl1 armhf 2.2.9-2 [34.7 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libhwloc-plugins armhf 1.11.4-1+rpi1 [14.9 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libopenmpi2 armhf 2.0.1-5 [1621 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libboost-mpi1.61.0 armhf 1.61.0+dfsg-2.1+b1 [53.9 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf openmpi-common all 2.0.1-5 [146 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf libibverbs-dev armhf 1.2.1-2 [104 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libltdl-dev armhf 2.4.6-2 [159 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libhwloc-dev armhf 1.11.4-1+rpi1 [136 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libopenmpi-dev armhf 2.0.1-5 [997 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf mpi-default-dev armhf 1.7 [4804 B]
Get:79 http://172.17.0.1/private stretch-staging/main armhf libboost-mpi1.61-dev armhf 1.61.0+dfsg-2.1+b1 [71.4 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libboost-mpi-dev armhf 1.61.0.2 [3482 B]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libboost-serialization-dev armhf 1.61.0.2 [3622 B]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libicu-dev armhf 57.1-4 [15.7 MB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.1-2 [1392 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.1-2 [1379 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libxml2-dev armhf 2.9.4+dfsg1-2 [723 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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Setting up liblapack-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libboost-mpi1.61.0 (1.61.0+dfsg-2.1+b1) ...
Setting up libopenmpi-dev (2.0.1-5) ...
update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
Setting up mpi-default-dev (1.7) ...
Setting up libgssapi-krb5-2:armhf (1.14.3+dfsg-2) ...
Setting up libcurl3:armhf (7.50.1-1) ...
Setting up libboost-mpi1.61-dev (1.61.0+dfsg-2.1+b1) ...
Setting up libboost-mpi-dev (1.61.0.2) ...
Setting up cmake (3.6.2-1) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (10) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-3) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26.1-1 dpkg-dev_1.18.10 g++-6_6.1.1-11+rpi1 gcc-6_6.1.1-11+rpi1 libc6-dev_2.24-3 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.3 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.26.1-1 bison_2:3.0.4.dfsg-1 bsdmainutils_9.0.10 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 cmake_3.6.2-1 cmake-data_3.6.2-1 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.1.1-11+rpi1 dash_0.5.8-2.3 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10 debianutils_4.8 dh-autoreconf_12 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-3 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.28-4 findutils_4.6.0+git+20160703-2 flex_2.6.1-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.1.1-11+rpi1 gcc_4:6.1.1-1 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_4.9.3-14 gcc-6_6.1.1-11+rpi1 gcc-6-base_6.1.1-11+rpi1 gengetopt_2.22.6+dfsg0-1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.1.1-1 gfortran-6_6.1.1-11+rpi1 gnupg_2.1.15-3 gnupg-agent_2.1.15-3 gnupg-l10n_2.1.15-3 gpgv_2.1.15-3 grep_2.25-6 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-4 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-4 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.3 libarchive-zip-perl_1.59-1 libarchive13_3.2.1-2 libasan1_4.9.3-14 libasan3_6.1.1-11+rpi1 libassuan0_2.4.3-1 libatomic1_6.1.1-11+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.6-1 libaudit1_1:2.6.6-1 libbison-dev_2:3.0.4.dfsg-1 libblas-common_3.6.1-2 libblas-dev_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.28.2-1 libboost-dev_1.61.0.2 libboost-mpi-dev_1.61.0.2 libboost-mpi1.61-dev_1.61.0+dfsg-2.1+b1 libboost-mpi1.61.0_1.61.0+dfsg-2.1+b1 libboost-serialization-dev_1.61.0.2 libboost-serialization1.61-dev_1.61.0+dfsg-2.1+b1 libboost-serialization1.61.0_1.61.0+dfsg-2.1+b1 libboost1.61-dev_1.61.0+dfsg-2.1+b1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.24-3 libc-dev-bin_2.24-3 libc6_2.24-3 libc6-dev_2.24-3 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.1.1-11+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.0-2 libcurl3_7.50.1-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.10-1 libdebconfclient0_0.217 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.70-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfl-dev_2.6.1-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.1.1-11+rpi1 libgcc1_1:6.1.1-11+rpi1 libgcrypt20_1.7.3-1 libgdbm3_1.8.3-14 libgfortran-6-dev_6.1.1-11+rpi1 libgfortran3_6.1.1-11+rpi1 libglib2.0-0_2.50.0-1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.4-2 libgomp1_6.1.1-11+rpi1 libgpg-error0_1.24-1 libgssapi-krb5-2_1.14.3+dfsg-2 libhogweed4_3.2-1 libhwloc-dev_1.11.4-1+rpi1 libhwloc-plugins_1.11.4-1+rpi1 libhwloc5_1.11.4-1+rpi1 libibverbs-dev_1.2.1-2 libibverbs1_1.2.1-2 libicu-dev_57.1-4 libicu57_57.1-4 libidn11_1.33-1 libisl15_0.17.1-1 libjsoncpp1_1.7.4-3 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.5-2 liblapack-dev_3.6.1-2 liblapack3_3.6.1-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 libltdl-dev_2.4.6-2 libltdl7_2.4.6-2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.28-4 libmagic1_1:5.28-4 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.4-2 libncurses5_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.2-1 libnghttp2-14_1.14.1-1 libnl-3-200_3.2.27-1 libnl-route-3-200_3.2.27-1 libnpth0_1.2-3 libopenmpi-dev_2.0.1-5 libopenmpi2_2.0.1-5 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpciaccess0_0.13.4-1 libpcre3_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-2 libreadline6_6.3-8+b3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libslang2_2.3.0-3+b1 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2j-1 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.1.1-11+rpi1 libstdc++6_6.1.1-11+rpi1 libsystemd0_231-4 libtasn1-6_4.9-4 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160917-1 libtool_2.4.6-2 libubsan0_6.1.1-11+rpi1 libudev1_231-4 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libxml2_2.9.4+dfsg1-2 libxml2-dev_2.9.4+dfsg1-2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.07-1 mawk_1.3.3-17 mount_2.28.2-1 mpi-default-dev_1.7 multiarch-support_2.24-3 nano_2.7.0-1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 ocl-icd-libopencl1_2.2.9-2 openmpi-common_2.0.1-5 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-5 po-debconf_1.0.19 procps_2:3.3.12-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-prime-phylo-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-4 systemd-sysv_231-4 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016g-1 udev_231-4 util-linux_2.28.2-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1

+------------------------------------------------------------------------------+
| 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 Aug  3 11:30:28 2016 UTC
gpgv:                using RSA key E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./prime-phylo_1.0.11-4.dsc
dpkg-source: info: extracting prime-phylo in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz
dpkg-source: info: unpacking prime-phylo_1.0.11-4.debian.tar.xz
dpkg-source: info: applying fix-gcc-6.patch
dpkg-source: info: applying fix-ftbfs-with-Boost160.patch

Check disc space
----------------

Sufficient free space for build

Hack binNMU version
-------------------

Created changelog entry for binNMU version 1.0.11-4+b1

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-f1ecb379-4131-4a60-9d6d-c2b325aad8a2
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

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

dpkg-buildpackage: info: source package prime-phylo
dpkg-buildpackage: info: source version 1.0.11-4+b1
dpkg-buildpackage: info: source distribution stretch-staging
 dpkg-source --before-build prime-phylo-1.0.11
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean --buildsystem=cmake --parallel
   dh_testdir -O--buildsystem=cmake -O--parallel
   dh_auto_clean -O--buildsystem=cmake -O--parallel
   dh_clean -O--buildsystem=cmake -O--parallel
 debian/rules build-arch
dh build-arch --buildsystem=cmake --parallel
   dh_testdir -a -O--buildsystem=cmake -O--parallel
   dh_update_autotools_config -a -O--buildsystem=cmake -O--parallel
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
-Dofficial_binary_packaging=on \
-Dprime_dynamic=on \
-DCMAKE_INSTALL_PREFIX=/usr \
-DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \
-DCMAKE_BUILD_TYPE=RELEASE
	cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE
-- The CXX compiler identification is GNU 6.1.1
-- 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
-- The Fortran compiler identification is GNU 6.1.1
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- The C compiler identification is GNU 6.1.1
-- 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
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- A library with BLAS API found.
hittade /usr/lib/libblas.so
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Found BISON: /usr/bin/bison (found version "3.0.4") 
-- Found FLEX: /usr/bin/flex (found version "2.6.1") 
-- Found MPI_C: /usr/lib/libmpi.so  
-- Found MPI_CXX: /usr/lib/libmpi_cxx.so;/usr/lib/libmpi.so  
-- Found MPI_Fortran: /usr/lib/libmpi_usempif08.so;/usr/lib/libmpi_usempi_ignore_tkr.so;/usr/lib/libmpi_mpifh.so;/usr/lib/libmpi.so  
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   mpi
--   serialization
-- Found LibXml2: /usr/lib/arm-linux-gnueabihf/libxml2.so (found version "2.9.4") 
mpilib is /usr/lib/openmpi/include/openmpi;/usr/include;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/openmpi/include 
included path is  
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_INSTALL_LOCALSTATEDIR
    CMAKE_INSTALL_SYSCONFDIR


-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_build -a -O--buildsystem=cmake -O--parallel
	make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -H/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  1%] [BISON][MyParser2] Building parser with bison 3.0.4
[  1%] [FLEX][MyScanner2] Building scanner with flex 2.6.1
cd /<<PKGBUILDDIR>>/src/cxx/libraries/sfile && /usr/bin/flex -o/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c seqreader.l
cd /<<PKGBUILDDIR>>/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c gb.y
gb.y: warning: 1 nonterminal useless in grammar [-Wother]
gb.y: warning: 1 rule useless in grammar [-Wother]
gb.y:117.47-58: warning: nonterminal useless in grammar: darwin_entry [-Wother]
 %type <entry>   gb_entry fasta_entry ig_entry darwin_entry
                                               ^^^^^^^^^^^^
gb.y:258.19-61: warning: rule useless in grammar [-Wother]
 darwin_entry	: TEXT {$$ = NULL; /* Not implemented yet */}
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/libraries/sfile /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake --color=
Scanning dependencies of target prime-phylo-sfile
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o
[  2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o
[  2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o
[  3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g -fPIC   -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o   -c /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g -fPIC   -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o   -c /<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g -fPIC   -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/<<PKGBUILDDIR>>/src/cxx/libraries/sfile -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g -fPIC   -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c: In function 'main':
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/gbread.c:17:10: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration]
     if (!strcmp(argv[opt], "-d")) {
          ^~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c: In function 'seq_print':
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:265:17: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=]
       printf("%9d", char_counter + 1);
                 ^
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable 'date' set but not used [-Wunused-but-set-variable]
   char *top, *date;
               ^~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c: In function 'yyparse':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c:1237:16: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration]
       yychar = yylex ();
                ^~~~~
gb.y: In function 'yyerror':
gb.y:291:70: warning: implicit declaration of function 'linenumber' [-Wimplicit-function-declaration]
gb.y: In function 'add_to_seq':
gb.y:402:9: warning: unused variable 'new_buf' [-Wunused-variable]
seqreader.l: In function 'seq_read':
seqreader.l:271:9: warning: unused variable 'code' [-Wunused-variable]
At top level:
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c:1875:16: warning: 'input' defined but not used [-Wunused-function]
     static int input  (void)
                ^~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c:1832:17: warning: 'yyunput' defined but not used [-Wunused-function]
     static void yyunput (int c, char * yy_bp )
                 ^~~~~~~
[  4%] Linking C shared library libprime-phylo-sfile.so
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1
/usr/bin/cc  -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g  -fPIE -pie -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo-sfile.so -o libprime-phylo-sfile.so CMakeFiles/prime-phylo-sfile.dir/gbread.c.o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -Wl,-rpath,:::::::::::::::::::: 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  4%] Built target prime-phylo-sfile
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  5%] [BISON][MyParser] Building parser with bison 3.0.4
[  5%] [FLEX][MyScanner] Building scanner with flex 2.6.1
cd /<<PKGBUILDDIR>>/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c NHX.l
cd /<<PKGBUILDDIR>>/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c NHXparse.y
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/libraries/prime /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake --color=
Scanning dependencies of target prime-phylo
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  5%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o
[  6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o
[  6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g -fPIC   -o CMakeFiles/prime-phylo.dir/NHXtree.c.o   -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXtree.c
[  7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g -fPIC   -o CMakeFiles/prime-phylo.dir/lexer.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g -fPIC   -o CMakeFiles/prime-phylo.dir/NHXnode.c.o   -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g -fPIC   -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o   -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXannotation.c
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c: In function 'NHX_debug_print':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/NHXnode.c:155:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'double' [-Wformat=]
  fprintf(stderr, "BW:\t%d\n", l->arg.t);
                         ^
[  8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -fexceptions -g -fPIC   -o CMakeFiles/prime-phylo.dir/NHXparse.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c:1363:16: warning: 'input' defined but not used [-Wunused-function]
     static int input  (void)
                ^~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c:1320:17: warning: 'yyunput' defined but not used [-Wunused-function]
     static void yyunput (int c, char * yy_bp )
                 ^~~~~~~
[  8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/AnError.cc
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c: In function 'yytree_parse':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c:64:25: warning: implicit declaration of function 'yytree_lex' [-Wimplicit-function-declaration]
 #define yylex           yytree_lex
                         ^
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c:1280:16: note: in expansion of macro 'yylex'
       yychar = yylex ();
                ^~~~~
NHXparse.y: In function 'read_tree':
NHXparse.y:351:5: warning: implicit declaration of function 'close' [-Wimplicit-function-declaration]
NHXparse.y: In function 'read_tree_string':
NHXparse.y:399:3: warning: implicit declaration of function 'read_from_string' [-Wimplicit-function-declaration]
NHXparse.y:404:3: warning: implicit declaration of function 'close_string_buffer' [-Wimplicit-function-declaration]
[  9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Beep.cc
[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.cc
[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Hacks.cc
[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/NodeMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeMap.cc
[ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NodeNodeMap.cc
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/RandomTreeGenerator.cc
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StrStrMap.cc
[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tree.cc
[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeAnalysis.cc
[ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.cc
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.cc
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc
[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.cc
[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc
[ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIOTraits.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc: In constructor 'beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const Real&)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null]
     sprAccPropCnt(0, 0)
                       ^
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null]
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:34:23: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null]
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreePerturbationEvent.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc:118:22: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null]
    buf[ bytes_read ]=NULL;
                      ^~~~
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ConstRateModel.cc
[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_common.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector<beep::SetOfNodes>*, beep::StrStrMap*, std::map<const beep::Node*, beep::Node*>*, std::map<const beep::Node*, unsigned int>*)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc:1049:22: warning: 'idInt' may be used uninitialized in this function [-Wmaybe-uninitialized]
  new_node = S.addNode(l, r, idInt, name);
             ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2P_positive.cc
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Density2PMCMC.cc
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC.cc
[ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc
[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateModel_common.cc
[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightHandler.cc
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightMCMC.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc: In member function 'void beep::EdgeRateMCMC_common<Templ_EdgeRateModel>::generateRates() [with Templ_EdgeRateModel = beep::gbmRateModel]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:104:30: warning: unused variable 'fparam' [-Wunused-variable]
                         Real fparam = std::log(rate) -  0.5 * variance * (rtime - 3.0 * ltime);
                              ^~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable 'rparam' [-Wunused-variable]
                         Real rparam = variance * (rtime + ltime);
                              ^~~~~~
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaDensity.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function 'void beep::EdgeWeightMCMC::showCurrentTree()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < t.size(); i++)
                         ~~^~~~~~~~~~
[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvGaussDensity.cc
[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LengthRateModel.cc
[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LogNormDensity.cc
[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/NormalDensity.cc
[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/UniformDensity.cc
[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/VarRateModel.cc
[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o
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[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o
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[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MCMCModel.cc
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/StdMCMCModel.cc
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MCMCObject.cc
[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMC.cc
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMCPostSample.cc
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleML.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMC.cc: In member function 'virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleMCMC.cc:78:14: warning: variable 'check_number_nonupdate' set but not used [-Wunused-but-set-variable]
     unsigned check_number_nonupdate = 0;
              ^~~~~~~~~~~~~~~~~~~~~~
[ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o
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/<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function 'virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc:337:6: warning: operation on 'i' may be undefined [-Wsequence-point]
    p[++i] = geneFams[i]->initStateProb();//updateDataProbability();
      ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc:337:6: warning: operation on 'i' may be undefined [-Wsequence-point]
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc:337:6: warning: operation on 'i' may be undefined [-Wsequence-point]
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc
[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc
[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc
[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscBDProbs.cc
[ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc
[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTMCMC.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:8:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor 'beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: 'beep::EdgeDiscGSR::m_calculatedAtAndBelow' will be initialized after [-Wreorder]
         bool m_calculatedAtAndBelow;
              ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning:   'bool beep::EdgeDiscGSR::m_calculatedAtBars' [-Wreorder]
         bool m_calculatedAtBars;
              ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning:   when initialized here [-Wreorder]
     EdgeDiscGSR::EdgeDiscGSR(Tree* G,
     ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'void beep::EdgeDiscGSR::convertDensitiesToProbabilities()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:475:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < m_G->getNumberOfNodes(); i++) {
                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable 'xpt' set but not used [-Wunused-but-set-variable]
                     Point xpt = x.getPt();
                           ^~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:525:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < m_G->getNumberOfNodes(); i++) {
                         ~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable 'parent' [-Wunused-variable]
             Node *parent = u->getParent();
                   ^~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscGSR.cc:897:18: warning: unused variable 'timeStep' [-Wunused-variable]
             Real timeStep = u->isLeaf() ? 1.0 : m_DS->getTimestep(xPoint.first);
                  ^~~~~~~~
[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc
[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochDLTRS.cc
[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaMap.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc: In member function 'std::__cxx11::string beep::EpochBDTProbs::getDebugInfo(bool, bool, bool) const':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc:661:1: internal compiler error: Segmentation fault
 }
 ^
0x690f8f crash_signal
	../../src/gcc/toplev.c:333
0x40969b et_set_father
	../../src/gcc/et-forest.c:525
0x3aebef calculate_dominance_info(cdi_direction)
	../../src/gcc/dominance.c:658
0x66d54f try_shrink_wrapping(edge_def**, bitmap_head*, rtx_insn*)
	../../src/gcc/shrink-wrap.c:695
0x4731a7 thread_prologue_and_epilogue_insns()
	../../src/gcc/function.c:6069
0x473a7f rest_of_handle_thread_prologue_and_epilogue
	../../src/gcc/function.c:6591
0x473a7f execute
	../../src/gcc/function.c:6633
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See <file:///usr/share/doc/gcc-6/README.Bugs> for instructions.
[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GuestTreeModel.cc
[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumerateReconciliationModel.cc
[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc
[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++   -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -I/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fPIE -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -Wreorder -Wall -fexceptions -g -fPIC   -std=gnu++98 -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc
The bug is not reproducible, so it is likely a hardware or OS problem.
src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make:1973: recipe for target 'src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o' failed
make[3]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
CMakeFiles/Makefile2:136: recipe for target 'src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all' failed
make[2]: *** [src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Makefile:152: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_auto_build: make -j4 returned exit code 2
debian/rules:10: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2016-10-02T23:42:05Z

Finished
--------


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

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

Build Architecture: armhf
Build-Space: 0
Build-Time: 509
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 480
Job: prime-phylo_1.0.11-4
Machine Architecture: armhf
Package: prime-phylo
Package-Time: 1035
Source-Version: 1.0.11-4
Space: 0
Status: failed
Version: 1.0.11-4+b1
--------------------------------------------------------------------------------
Finished at 2016-10-02T23:42:05Z
Build needed 00:00:00, 0k disc space
Raspbian Package Auto-Building

Build log for prime-phylo (1.0.11-4+b1) on armhf
