Raspbian Package Auto-Building

Build log for prime-phylo (1.0.11-4+b2) on armhf

prime-phylo → 1.0.11-4+b2 → armhf → 2018-05-04 02:44:35 

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+==============================================================================+
| prime-phylo 1.0.11-4+b2 (armhf)              Fri, 04 May 2018 02:32:21 +0000 |
+==============================================================================+

Package: prime-phylo
Version: 1.0.11-4+b2
Source Version: 1.0.11-4
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-78d1aa0e-3471-4617-9799-4c76ca56575b' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main armhf Packages [12.5 MB]
Fetched 12.5 MB in 8s (1537 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 buster-staging/main prime-phylo 1.0.11-4 (dsc) [2134 B]
Get:2 http://172.17.0.1/private buster-staging/main prime-phylo 1.0.11-4 (tar) [751 kB]
Get:3 http://172.17.0.1/private buster-staging/main prime-phylo 1.0.11-4 (diff) [5892 B]
Fetched 759 kB in 0s (3051 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/prime-phylo-dWdiWl/prime-phylo-1.0.11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/prime-phylo-dWdiWl' 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-IST5bO/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-IST5bO/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-IST5bO/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ Packages [435 B]
Fetched 2111 B in 0s (11.6 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
  libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
  systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15689 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-IST5bO/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-core-dummy sbuild-build-depends-prime-phylo-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ Sources [577 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ Packages [656 B]
Fetched 2566 B in 0s (14.1 kB/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:
  ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
  libpam-systemd libsasl2-modules libssl1.1 openssl systemd-sysv
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-7 groff-base
  ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl
  libarchive13 libbison-dev libblas-dev libblas3 libboost-dev libboost-mpi-dev
  libboost-mpi1.62-dev libboost-mpi1.62.0 libboost-serialization-dev
  libboost-serialization1.62-dev libboost-serialization1.62.0 libboost1.62-dev
  libbsd0 libcroco3 libcurl3 libedit2 libevent-2.1-6 libevent-core-2.1-6
  libevent-pthreads-2.1-6 libfile-stripnondeterminism-perl libgfortran-7-dev
  libgfortran4 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 libopenmpi3 libpciaccess0
  libpipeline1 libpmix2 libpsl5 librhash0 librtmp1 libsigsegv2 libssh2-1
  libssl1.0.2 libtimedate-perl libtool libuv1 libxml2 libxml2-dev m4 man-db
  mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
  po-debconf zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist
  whois vacation cmake-doc ninja-build dh-make dwz flex-doc gettext-doc
  libasprintf-dev libgettextpo-dev gfortran-doc gfortran-7-doc
  libgfortran4-dbg libcoarrays-dev groff lrzip liblapack-doc libboost-doc
  libboost-graph1.62-dev libboost1.62-doc libboost-atomic1.62-dev
  libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
  libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
  libboost-filesystem1.62-dev libboost-graph-parallel1.62-dev
  libboost-iostreams1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
  libboost-math1.62-dev libboost-mpi-python1.62-dev
  libboost-program-options1.62-dev libboost-python1.62-dev
  libboost-random1.62-dev libboost-regex1.62-dev libboost-signals1.62-dev
  libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
  libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
  libboost1.62-tools-dev libmpfrc++-dev libntl-dev krb5-doc krb5-user
  libhwloc-contrib-plugins icu-doc libtool-doc openmpi-doc pciutils gcj-jdk
  pkg-config m4-doc apparmor less www-browser opencl-icd keychain libpam-ssh
  monkeysphere ssh-askpass libmail-box-perl
Recommended packages:
  libfl-dev curl | wget | lynx libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs krb5-locales publicsuffix xauth
  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-7 groff-base
  ibverbs-providers icu-devtools intltool-debian libarchive-zip-perl
  libarchive13 libbison-dev libblas-dev libblas3 libboost-dev libboost-mpi-dev
  libboost-mpi1.62-dev libboost-mpi1.62.0 libboost-serialization-dev
  libboost-serialization1.62-dev libboost-serialization1.62.0 libboost1.62-dev
  libbsd0 libcroco3 libcurl3 libedit2 libevent-2.1-6 libevent-core-2.1-6
  libevent-pthreads-2.1-6 libfile-stripnondeterminism-perl libgfortran-7-dev
  libgfortran4 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 libopenmpi3 libpciaccess0
  libpipeline1 libpmix2 libpsl5 librhash0 librtmp1 libsigsegv2 libssh2-1
  libssl1.0.2 libtimedate-perl libtool libuv1 libxml2 libxml2-dev m4 man-db
  mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
  po-debconf sbuild-build-depends-prime-phylo-dummy zlib1g-dev
0 upgraded, 95 newly installed, 0 to remove and 0 not upgraded.
Need to get 40.2 MB/66.1 MB of archives.
After this operation, 344 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IST5bO/apt_archive ./ sbuild-build-depends-prime-phylo-dummy 0.invalid.0 [944 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf flex armhf 2.6.4-6.1 [427 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf liblzo2-2 armhf 2.08-1.2 [47.6 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2o-1 [888 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libevent-2.1-6 armhf 2.1.8-stable-4 [156 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf openssh-client armhf 1:7.7p1-2 [672 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libbison-dev armhf 2:3.0.4.dfsg-1+b1 [433 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf bison armhf 2:3.0.4.dfsg-1+b1 [743 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf cmake-data all 3.11.1-1 [1386 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive13 armhf 3.2.2-3.1 [251 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.31.1-1 [69.4 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.1-1 [51.4 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.58.0-2 [276 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf librhash0 armhf 1.3.6-2 [97.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libuv1 armhf 1.18.0-3 [86.1 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf cmake armhf 3.11.1-1 [2501 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.2.1 [1013 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf gengetopt armhf 2.22.6+dfsg0-2 [158 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-12 [191 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-12 [232 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-12 [5454 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.2.0-1d1 [1352 B]
Get:44 http://172.17.0.1/private buster-staging/main armhf libibverbs1 armhf 17.1-1 [38.9 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf ibverbs-providers armhf 17.1-1 [19.3 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-5+b2 [7004 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:50 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.62.0 armhf 1.62.0+dfsg-5+b2 [107 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libboost-serialization1.62-dev armhf 1.62.0+dfsg-5+b2 [172 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libevent-core-2.1-6 armhf 2.1.8-stable-4 [117 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libevent-pthreads-2.1-6 armhf 2.1.8-stable-4 [47.6 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-2.1 [386 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libhwloc5 armhf 1.11.10-1+rpi1 [85.7 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libpciaccess0 armhf 0.14-1 [51.0 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libhwloc-plugins armhf 1.11.10-1+rpi1 [15.4 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libpmix2 armhf 2.1.1~rc1-2 [284 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libopenmpi3 armhf 3.0.1-9+rpi1 [1725 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libboost-mpi1.62.0 armhf 1.62.0+dfsg-5+b2 [54.4 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf openmpi-common all 3.0.1-9+rpi1 [158 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libibverbs-dev armhf 17.1-1 [89.8 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2.1 [158 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libhwloc-dev armhf 1.11.10-1+rpi1 [141 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf openmpi-bin armhf 3.0.1-9+rpi1 [198 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libopenmpi-dev armhf 3.0.1-9+rpi1 [928 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf mpi-default-dev armhf 1.12+rpi1 [5440 B]
Get:68 http://172.17.0.1/private buster-staging/main armhf libboost-mpi1.62-dev armhf 1.62.0+dfsg-5+b2 [72.1 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libboost-mpi-dev armhf 1.62.0.1+b8 [3790 B]
Get:70 http://172.17.0.1/private buster-staging/main armhf libboost-serialization-dev armhf 1.62.0.1+b8 [3926 B]
Get:71 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libxml2-dev armhf 2.9.4+dfsg1-6.1 [672 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libbsd0:armhf.
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Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up liblapack-dev:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libtool (2.4.6-2.1) ...
Setting up libibverbs1:armhf (17.1-1) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libhwloc-dev:armhf (1.11.10-1+rpi1) ...
Setting up libpmix2:armhf (2.1.1~rc1-2) ...
Setting up ibverbs-providers:armhf (17.1-1) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libibverbs-dev:armhf (17.1-1) ...
Setting up libopenmpi3:armhf (3.0.1-9+rpi1) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up openssh-client (1:7.7p1-2) ...
Setting up libboost-mpi1.62.0 (1.62.0+dfsg-5+b2) ...
Setting up libcurl3:armhf (7.58.0-2) ...
Setting up openmpi-bin (3.0.1-9+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: error: no alternatives for mpi
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up cmake (3.11.1-1) ...
Setting up libopenmpi-dev:armhf (3.0.1-9+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up mpi-default-dev (1.12+rpi1) ...
Setting up libboost-mpi1.62-dev (1.62.0+dfsg-5+b2) ...
Setting up libboost-mpi-dev (1.62.0.1+b8) ...
Setting up dh-autoreconf (17) ...
Setting up debhelper (11.2.1) ...
Setting up dh-strip-nondeterminism (0.041-1) ...
Setting up sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.4.0-119-generic armhf (armv8l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bison_2:3.0.4.dfsg-1+b1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 cmake_3.11.1-1 cmake-data_3.11.1-1 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.2.1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.32-2 findutils_4.6.0+git+20171230-2 flex_2.6.4-6.1 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180414-1+rpi1 gengetopt_2.22.6+dfsg0-2 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.2.0-1d1 gfortran-7_7.3.0-12 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 ibverbs-providers_17.1-1 icu-devtools_57.1-9 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libarchive13_3.2.2-3.1 libargon2-0_0~20161029-2 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180414-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-15+rpi1 libbison-dev_2:3.0.4.dfsg-1+b1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.31.1-0.5 libboost-dev_1.62.0.1+b8 libboost-mpi-dev_1.62.0.1+b8 libboost-mpi1.62-dev_1.62.0+dfsg-5+b2 libboost-mpi1.62.0_1.62.0+dfsg-5+b2 libboost-serialization-dev_1.62.0.1+b8 libboost-serialization1.62-dev_1.62.0+dfsg-5+b2 libboost-serialization1.62.0_1.62.0+dfsg-5+b2 libboost1.62-dev_1.62.0+dfsg-5+b2 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+rpi1 libcilkrts5_7.3.0-12 libcom-err2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl3_7.58.0-2 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libedit2_3.1-20170329-1 libevent-2.1-6_2.1.8-stable-4 libevent-core-2.1-6_2.1.8-stable-4 libevent-pthreads-2.1-6_2.1.8-stable-4 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran-7-dev_7.3.0-12 libgfortran4_7.3.0-12 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 libgssapi-krb5-2_1.16-2 libhogweed4_3.4-1 libhwloc-dev_1.11.10-1+rpi1 libhwloc-plugins_1.11.10-1+rpi1 libhwloc5_1.11.10-1+rpi1 libibverbs-dev_17.1-1 libibverbs1_17.1-1 libicu-dev_57.1-9 libicu57_57.1-9 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjson-c3_0.12.1-1.3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 liblapack-dev_3.8.0-1 liblapack3_3.8.0-1 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 libltdl-dev_2.4.6-2.1 libltdl7_2.4.6-2.1 liblz4-1_1.8.1.2-1+rpi1 liblzma5_5.2.2-1.3 liblzo2-2_2.08-1.2 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncursesw5_6.1-1 libnettle6_3.4-1 libnghttp2-14_1.31.1-1 libnl-3-200_3.2.27-2 libnl-route-3-200_3.2.27-2 libnpth0_1.5-3 libnss-systemd_238-4 libopenmpi-dev_3.0.1-9+rpi1 libopenmpi3_3.0.1-9+rpi1 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpciaccess0_0.14-1 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpmix2_2.1.1~rc1-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 libpsl5_0.20.1-1 libreadline7_7.0-3 librhash0_1.3.6-2 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2o-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libuv1_1.18.0-3 libxml2_2.9.4+dfsg1-6.1 libxml2-dev_2.9.4+dfsg1-6.1 libzstd1_1.3.3+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mount_2.31.1-0.5 mpi-default-dev_1.12+rpi1 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 ocl-icd-libopencl1_2.2.12-1 openmpi-bin_3.0.1-9+rpi1 openmpi-common_3.0.1-9+rpi1 openssh-client_1:7.7p1-2 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-prime-phylo-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-4 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5

+------------------------------------------------------------------------------+
| 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 disk space
----------------

Sufficient free space for build

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

Created changelog entry for binNMU version 1.0.11-4+b2

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-78d1aa0e-3471-4617-9799-4c76ca56575b
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

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

dpkg-buildpackage: info: source package prime-phylo
dpkg-buildpackage: info: source version 1.0.11-4+b2
dpkg-buildpackage: info: source distribution buster-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_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_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
	cd obj-arm-linux-gnueabihf && cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON "-GUnix Makefiles" -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 7.3.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- The Fortran compiler identification is GNU 7.3.0
-- 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 7.3.0
-- 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  
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so  
hittade /usr/lib/arm-linux-gnueabihf/libblas.so
-- 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 "2.6.4") 
-- Found MPI_C: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so (found version "3.1") 
-- Found MPI_CXX: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so (found version "3.1") 
-- Found MPI_Fortran: /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_usempif08.so (found version "3.1") 
-- Found MPI: TRUE (found version "3.1")  
-- Boost version: 1.62.0
-- 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/arm-linux-gnueabihf/openmpi/include/openmpi;/usr/lib/arm-linux-gnueabihf/openmpi/include 
included path is  
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    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
	cd obj-arm-linux-gnueabihf && make -j4 -Oline
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
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/Makefile2 all
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/src/cxx/libraries/sfile && /usr/bin/flex -o/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c seqreader.l
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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 */}
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -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
/<<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")) {
          ^~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -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
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c: In function 'seq_print':
/<<PKGBUILDDIR>>/src/cxx/libraries/sfile/sfile.c:265:14: 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;
               ^~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -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>>/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]
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -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
seqreader.l: In function 'seq_read':
seqreader.l:270:9: warning: unused variable 'code' [-Wunused-variable]
At top level:
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c:1864:16: warning: 'input' defined but not used [-Wunused-function]
     static int input  (void)
                ^~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c:1821:17: warning: 'yyunput' defined but not used [-Wunused-function]
     static void yyunput (int c, char * yy_bp )
                 ^~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  4%] Linking C shared library libprime-phylo-sfile.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -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'
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  4%] Built target prime-phylo-sfile
make[2]: 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/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  5%] [BISON][MyParser] Building parser with bison 3.0.4
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  5%] [FLEX][MyScanner] Building scanner with flex 2.6.4
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c NHX.l
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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'
[  7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
/<<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);
                        ~^     ~~~~~~~~
                        %f
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/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'; did you mean 'yytree_parse'? [-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'; did you mean 'pclose'? [-Wimplicit-function-declaration]
NHXparse.y: In function 'read_tree_string':
NHXparse.y:399:3: warning: implicit declaration of function 'read_from_string'; did you mean 'read_tree_string'? [-Wimplicit-function-declaration]
NHXparse.y:404:3: warning: implicit declaration of function 'close_string_buffer' [-Wimplicit-function-declaration]
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c:1597:16: warning: 'input' defined but not used [-Wunused-function]
     static int input  (void)
                ^~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c:1554:17: warning: 'yyunput' defined but not used [-Wunused-function]
     static void yyunput (int c, char * yy_bp )
                 ^~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/PRNG.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PRNG.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ODESolver.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.cc
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.cc:4:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ODESolver.cc:4:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::ODESolver::contd5(std::vector<double>&, beep::Real)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/DiscreteGamma.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscreteGamma.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ProbabilityModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ProbabilityModel.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/Tokenizer.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tokenizer.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.hh:10,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.cc:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.hh:10,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepOption.cc:5:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::option::BeepOptionMap::parseUserSubstModel(beep::option::UserSubstModelOption*, int&, int, char**)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<double> beep::option::BeepOptionMap::getDoubleX3(std::__cxx11::string)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/TimeEstimator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TimeEstimator.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/Probability.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/BranchSwapping.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BranchSwapping.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/PrimeOptionMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.hh:12,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.hh:12,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PrimeOptionMap.cc:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::TmplPrimeOption<T>::parseParams(std::__cxx11::string&, unsigned int, std::vector<T>&) [with T = double]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::__cxx11::string&, unsigned int, std::vector<beep::UserSubstMatrixParams>&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/DiscTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscTree.cc
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscTree.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscTree.cc:6:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscTree.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscTree.cc:6:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::DiscTree::createGridTimes()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/EpochPtSet.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.cc
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.cc:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtSet.cc:5:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'beep::EpochPtSet::EpochPtSet(std::vector<const beep::Node*>, beep::Real, beep::Real, unsigned int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/EdgeDiscTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscTree.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvMRCA.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/EdgeDiscPtMaps.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EdgeDiscPtMaps.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/EpochTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.cc
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.cc:7:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::EpochPtSet; _Alloc = std::allocator<beep::EpochPtSet>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::EpochPtSet>::iterator {aka __gnu_cxx::__normal_iterator<beep::EpochPtSet*, std::vector<beep::EpochPtSet> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochTree.cc:7:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::EpochTree::update()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::EpochPtSet*, std::vector<beep::EpochPtSet> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::EpochPtSet*, std::vector<beep::EpochPtSet> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/EpochPtMaps.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::setWithMin(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator, const T&) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:188:14: note: parameter passing for argument of type 'beep::EpochPtMap<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
  inline void setWithMin(unsigned i, unsigned j, const_iterator start, const T& lowerBound)
              ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::setWithMax(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator, const T&) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:206:14: note: parameter passing for argument of type 'beep::EpochPtMap<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
  inline void setWithMax(unsigned i, unsigned j, const_iterator start, const T& upperBound)
              ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::setWithMin(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator, const T&) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:438:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
  inline void setWithMin(unsigned i, unsigned j, unsigned p, unsigned q,
              ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::setWithMax(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator, const T&) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:461:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
  inline void setWithMax(unsigned i, unsigned j, unsigned p, unsigned q,
              ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::setWithMin(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator, const T&) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:188:14: note: parameter passing for argument of type 'beep::EpochPtMap<beep::Probability>::const_iterator {aka __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
  inline void setWithMin(unsigned i, unsigned j, const_iterator start, const T& lowerBound)
              ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::setWithMax(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator, const T&) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:206:14: note: parameter passing for argument of type 'beep::EpochPtMap<beep::Probability>::const_iterator {aka __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
  inline void setWithMax(unsigned i, unsigned j, const_iterator start, const T& upperBound)
              ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::setWithMin(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator, const T&) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:438:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<beep::Probability>::const_iterator {aka __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
  inline void setWithMin(unsigned i, unsigned j, unsigned p, unsigned q,
              ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::setWithMax(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator, const T&) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:461:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<beep::Probability>::const_iterator {aka __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
  inline void setWithMax(unsigned i, unsigned j, unsigned p, unsigned q,
              ^~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::set(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:162:14: note: parameter passing for argument of type 'beep::EpochPtMap<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
  inline void set(unsigned i, unsigned j, const_iterator start)
              ^~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::set(const EpochTime&, beep::EpochPtMap<T>::const_iterator) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:173:14: note: parameter passing for argument of type 'beep::EpochPtMap<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
  inline void set(const EpochTime& tm, const_iterator start)
              ^~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::set(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:403:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
  inline void set(unsigned i, unsigned j, unsigned p, unsigned q,
              ^~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::set(beep::EpochTime, beep::EpochTime, beep::EpochPtPtMap<T>::const_iterator) [with T = double]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:418:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<double>::const_iterator {aka __gnu_cxx::__normal_iterator<const double*, std::vector<double> >}' changed in GCC 7.1
  inline void set(EpochTime tm1, EpochTime tm2, const_iterator start)
              ^~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >; _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::set(unsigned int, unsigned int, beep::EpochPtMap<T>::const_iterator) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:162:14: note: parameter passing for argument of type 'beep::EpochPtMap<beep::Probability>::const_iterator {aka __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
  inline void set(unsigned i, unsigned j, const_iterator start)
              ^~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtMap<T>::set(const EpochTime&, beep::EpochPtMap<T>::const_iterator) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:173:14: note: parameter passing for argument of type 'beep::EpochPtMap<beep::Probability>::const_iterator {aka __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
  inline void set(const EpochTime& tm, const_iterator start)
              ^~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::set(unsigned int, unsigned int, unsigned int, unsigned int, beep::EpochPtPtMap<T>::const_iterator) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:403:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<beep::Probability>::const_iterator {aka __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
  inline void set(unsigned i, unsigned j, unsigned p, unsigned q,
              ^~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh: In member function 'void beep::EpochPtPtMap<T>::set(beep::EpochTime, beep::EpochTime, beep::EpochPtPtMap<T>::const_iterator) [with T = beep::Probability]':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:418:14: note: parameter passing for argument of type 'beep::EpochPtPtMap<beep::Probability>::const_iterator {aka __gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
  inline void set(EpochTime tm1, EpochTime tm2, const_iterator start)
              ^~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochPtMaps.cc:5:
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/InvMRCA.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/InvMRCA.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/Node.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Node.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.cc:4:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizers.cc:4:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void beep::StepSizeEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector<double>&) const':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void beep::EquiSplitEdgeDiscretizer::discretizeEdge(const beep::Node*, std::vector<double>&) const':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.cc:6:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeDiscretizer.cc:6:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::TreeDiscretizerOld::update()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tree.cc:7:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Tree.cc:7:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::__cxx11::string)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
/<<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]
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BranchSwapping.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::Probability, std::allocator<beep::Probability> >::iterator {aka __gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BranchSwapping.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.hh:6,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeMCMC.cc:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::OrthologyMCMC::estimateOrthology(bool)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.hh:10,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.cc:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::Tree; _Alloc = std::allocator<beep::Tree>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::Tree>::iterator {aka __gnu_cxx::__normal_iterator<beep::Tree*, std::vector<beep::Tree> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.hh:10,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.cc:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<beep::Tree> beep::TreeIO::readAllBeepTrees(const beep::TreeIOTraits&, std::vector<beep::SetOfNodes>*, std::vector<beep::StrStrMap>*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Tree*, std::vector<beep::Tree> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
/<<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;
                      ^~~~
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.hh:13,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::Tree; _Alloc = std::allocator<beep::Tree>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::Tree>::iterator {aka __gnu_cxx::__normal_iterator<beep::Tree*, std::vector<beep::Tree> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/<<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);
             ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.hh:13,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.cc:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<beep::Tree> beep::TreeInputOutput::readAllBeepTrees(beep::TreeIOTraits&, std::vector<beep::SetOfNodes>*, std::vector<beep::StrStrMap>*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Tree*, std::vector<beep::Tree> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
/<<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);
                              ^~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/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++)
                         ~~^~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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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[ 39%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
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[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/DummyMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DummyMCMC.cc
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[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/SiteRateHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SiteRateHandler.cc
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[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
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[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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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[ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
/<<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;
              ^~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/mcmc/GSRSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/mcmc/GSRSampler.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/mcmc/PosteriorSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/mcmc/MCMCSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/mcmc/MCMCSampler.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/SimpleObserver.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SimpleObserver.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/MultiGSR.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MultiGSR.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/BDTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDTreeGenerator.cc
In file included from /usr/include/c++/7/map:60:0,
                 from /usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:40,
                 from /usr/lib/arm-linux-gnueabihf/openmpi/include/mpi.h:2703,
                 from /usr/include/boost/mpi/config.hpp:20,
                 from /usr/include/boost/mpi/environment.hpp:16,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:8,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDTreeGenerator.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDTreeGenerator.cc:1:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::_Alloc_node; _Key = beep::Node*; _Val = std::pair<beep::Node* const, double>; _KeyOfValue = std::_Select1st<std::pair<beep::Node* const, double> >; _Compare = std::less<beep::Node*>; _Alloc = std::allocator<std::pair<beep::Node* const, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2191:7: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h: In member function 'beep::Node* beep::BDTreeGenerator::generateV(beep::Node*)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h: In member function 'beep::Node* beep::BDTreeGenerator::generateX(beep::Node*, beep::Real)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h: In member function 'virtual bool beep::BDTreeGenerator::generateTree(beep::Tree&, bool)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/MpiMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/BirthDeathMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/MpiMultiGSR.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc
/<<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]
In file included from /usr/include/c++/7/vector:69:0,
                 from /usr/include/boost/archive/detail/helper_collection.hpp:20,
                 from /usr/include/boost/archive/detail/basic_oarchive.hpp:26,
                 from /usr/include/boost/archive/detail/oserializer.hpp:64,
                 from /usr/include/boost/mpi/detail/mpi_datatype_oarchive.hpp:14,
                 from /usr/include/boost/mpi/detail/mpi_datatype_cache.hpp:13,
                 from /usr/include/boost/mpi/datatype.hpp:27,
                 from /usr/include/boost/mpi/communicator.hpp:21,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.hh:11,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc:6:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::SeriGSRvars; _Alloc = std::allocator<beep::SeriGSRvars>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::SeriGSRvars>::iterator {aka __gnu_cxx::__normal_iterator<beep::SeriGSRvars*, std::vector<beep::SeriGSRvars> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /usr/include/boost/archive/detail/helper_collection.hpp:20,
                 from /usr/include/boost/archive/detail/basic_oarchive.hpp:26,
                 from /usr/include/boost/archive/detail/oserializer.hpp:64,
                 from /usr/include/boost/mpi/detail/mpi_datatype_oarchive.hpp:14,
                 from /usr/include/boost/mpi/detail/mpi_datatype_cache.hpp:13,
                 from /usr/include/boost/mpi/datatype.hpp:27,
                 from /usr/include/boost/mpi/communicator.hpp:21,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.hh:11,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MpiMultiGSR.cc:6:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::mpi::packed_iarchive; T = std::vector<beep::SeriGSRvars>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::SeriGSRvars*, std::vector<beep::SeriGSRvars> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::MpiMultiGSR::updateGvars(unsigned int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::SeriGSRvars*, std::vector<beep::SeriGSRvars> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/BirthDeathProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::Probability, std::allocator<beep::Probability> >::iterator {aka __gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:5:
/usr/include/c++/7/bits/stl_vector.h: In member function 'const beep::Node* beep::DiscBirthDeathProbs::getConstLinValsForPath(std::vector<beep::Probability, std::allocator<beep::Probability> >&, beep::DiscTree::Point, beep::DiscTree::Point, bool) const':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >; _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
       vector<_Tp, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:278:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DiscBirthDeathProbs.cc:5:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::DiscBirthDeathProbs::copyLeafBProbs(std::vector<beep::Probability, std::allocator<beep::Probability> >&, unsigned int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::DiscBirthDeathProbs::calcBDProbs(const beep::Node*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In copy constructor 'beep::DiscBirthDeathProbs::DiscBirthDeathProbs(const beep::DiscBirthDeathProbs&)':
/usr/include/c++/7/bits/stl_vector.h:1369:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
  { _M_assign_aux(__first, __last, std::__iterator_category(__first)); }
    ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
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);
                  ^~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc:6:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EpochBDTProbs.cc:6:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::EpochBDTProbs::appendInitVals(beep::EpochBDTProbs::realvec&) const':
/usr/include/c++/7/bits/stl_vector.h:1106:23: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
       { _M_fill_insert(__position, __n, __x); }
         ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::EpochBDTProbs::calcProbsWithinEpochs()':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'beep::fastGEM_BirthDeathProbs::fastGEM_BirthDeathProbs(beep::Tree&, unsigned int, std::vector<double>*, const Real&, const Real&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/PerturbationObservable.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PerturbationObservable.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/LambdaMap.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LambdaMap.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc: In member function 'unsigned int beep::fastGEM::calcMaxProb(unsigned int)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc:136:14: warning: variable 'topRateProb' set but not used [-Wunused-but-set-variable]
  Probability topRateProb = df->operator()(rate);
              ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printSa()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc:1298:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable]
     Real zeroTotalQuotient = 0.0;
          ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printLb()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc:1325:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable]
     Real zeroTotalQuotient = 0.0;
          ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printLt()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/fastGEM.cc:1356:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable]
     Real zeroTotalQuotient = 0.0;
          ^~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ReconciledTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciledTreeModel.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/MaxReconciledTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MaxReconciledTreeModel.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ReconciledTreeTimeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ReconciledTreeTimeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ReconciliationModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationModel.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ReconciliationTimeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeModel.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::__cxx11::string beep::ReconciliationTimeModel::table4os() const':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeModel.cc:319:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs]
     typedef std::map<unsigned, unsigned>::const_iterator MapIter;
                                                          ^~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ReconciliationSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationSampler.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function 'void beep::ReconciliationSampler::setAttributesAndProbabilities()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationSampler.cc:161:17: warning: variable 'p' set but not used [-Wunused-but-set-variable]
     Probability p = calculateDataProbability();
                 ^
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationSampler.cc:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = beep::Probability; _Alloc = std::allocator<beep::Probability>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<beep::Probability, std::allocator<beep::Probability> >::iterator {aka __gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathProbs.hh:9,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationSampler.cc:5:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::ReconciliationSampler::updateC_A(beep::Node*, beep::Node*)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::ReconciliationSampler::updateC_X(beep::Node*, beep::Node*)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::ReconciliationSampler::computePosteriors()':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::Probability*, std::vector<beep::Probability, std::allocator<beep::Probability> > >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ReconciliationTimeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/SetOfNodes.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SetOfNodes.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ReconciliationTimeSampler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeSampler.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function 'const string beep::ReconciliationTimeSampler::table4os() const':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:422:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs]
     typedef std::map<unsigned, unsigned>::const_iterator MapIter;
                                                          ^~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/ReconciliationTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor 'beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const string&)':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:31:3: warning: 'beep::ReconciliationTreeGenerator::R' is initialized with itself [-Winit-self]
   ReconciliationTreeGenerator::
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/HybridBranchSwapping.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridBranchSwapping.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/TopTimeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TopTimeMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/HybridTreeIO.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.cc
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.hh:10,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.cc:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::HybridTree; _Alloc = std::allocator<beep::HybridTree>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::HybridTree>::iterator {aka __gnu_cxx::__normal_iterator<beep::HybridTree*, std::vector<beep::HybridTree> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.hh:10,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeIO.cc:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<beep::HybridTree> beep::HybridTreeIO::readAllHybridTrees(beep::TreeIOTraits, std::vector<beep::SetOfNodes>*, std::vector<beep::StrStrMap>*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::HybridTree*, std::vector<beep::HybridTree> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/HybridTree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTree.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/DLRSOrthoCalculator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/DLRSOrthoCalculator.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/HybridTreeInputOutput.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.cc
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.hh:13,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.cc:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::HybridTree; _Alloc = std::allocator<beep::HybridTree>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::HybridTree>::iterator {aka __gnu_cxx::__normal_iterator<beep::HybridTree*, std::vector<beep::HybridTree> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeInputOutput.hh:13,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridTreeInputOutput.cc:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::vector<beep::HybridTree> beep::HybridTreeInputOutput::readAllHybridTrees(beep::TreeIOTraits&, std::vector<beep::SetOfNodes>*, std::vector<beep::StrStrMap>*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::HybridTree*, std::vector<beep::HybridTree> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/BirthDeathInHybridMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/BDHybridTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc
In file included from /usr/include/c++/7/map:60:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Beep.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/PRNG.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDHybridTreeGenerator.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:1:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::_Alloc_node; _Key = beep::Node*; _Val = std::pair<beep::Node* const, double>; _KeyOfValue = std::_Select1st<std::pair<beep::Node* const, double> >; _Compare = std::less<beep::Node*>; _Alloc = std::allocator<std::pair<beep::Node* const, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2191:7: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h: In member function 'void beep::BDHybridTreeGenerator::generateV(unsigned int)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h: In member function 'void beep::BDHybridTreeGenerator::generateX(unsigned int, beep::Real)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h: In member function 'bool beep::BDHybridTreeGenerator::generateHybridTree(beep::HybridTree&)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<beep::Node*, std::pair<beep::Node* const, double>, std::_Select1st<std::pair<beep::Node* const, double> >, std::less<beep::Node*>, std::allocator<std::pair<beep::Node* const, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<beep::Node* const, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/BirthDeathInHybridProbs.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/HybridBDTreeGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridBDTreeGenerator.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/HybridGuestTreeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/HybridHostTreeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/HybridGuestTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridGuestTreeModel.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/HybridHostTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.cc
In file included from /usr/include/c++/7/vector:69:0,
                 from /usr/include/boost/archive/detail/helper_collection.hpp:20,
                 from /usr/include/boost/archive/detail/basic_oarchive.hpp:26,
                 from /usr/include/boost/archive/detail/oserializer.hpp:64,
                 from /usr/include/boost/mpi/detail/mpi_datatype_oarchive.hpp:14,
                 from /usr/include/boost/mpi/detail/mpi_datatype_cache.hpp:13,
                 from /usr/include/boost/mpi/datatype.hpp:27,
                 from /usr/include/boost/mpi/communicator.hpp:21,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ProbabilityModel.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.cc:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /usr/include/boost/archive/detail/helper_collection.hpp:20,
                 from /usr/include/boost/archive/detail/basic_oarchive.hpp:26,
                 from /usr/include/boost/archive/detail/oserializer.hpp:64,
                 from /usr/include/boost/mpi/detail/mpi_datatype_oarchive.hpp:14,
                 from /usr/include/boost/mpi/detail/mpi_datatype_cache.hpp:13,
                 from /usr/include/boost/mpi/datatype.hpp:27,
                 from /usr/include/boost/mpi/communicator.hpp:21,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Probability.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ProbabilityModel.hh:7,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/HybridHostTreeModel.cc:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::HybridHostTreeModel::setMaxGhosts(unsigned int)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_fill_insert(end(), __new_size - size(), __x);
    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/EnumHybridGuestTreeMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/MatrixCache.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MatrixCache.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/EnumHybridGuestTreeModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LambdaMap.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaMap.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationModel.hh:8,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GuestTreeModel.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::ReconciledTreeTimeModel; _Alloc = std::allocator<beep::ReconciledTreeTimeModel>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::ReconciledTreeTimeModel>::iterator {aka __gnu_cxx::__normal_iterator<beep::ReconciledTreeTimeModel*, std::vector<beep::ReconciledTreeTimeModel> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::ReconciledTreeTimeModel>::iterator {aka __gnu_cxx::__normal_iterator<beep::ReconciledTreeTimeModel*, std::vector<beep::ReconciledTreeTimeModel> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = beep::GuestTreeModel; _Alloc = std::allocator<beep::GuestTreeModel>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::GuestTreeModel>::iterator {aka __gnu_cxx::__normal_iterator<beep::GuestTreeModel*, std::vector<beep::GuestTreeModel> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<beep::GuestTreeModel>::iterator {aka __gnu_cxx::__normal_iterator<beep::GuestTreeModel*, std::vector<beep::GuestTreeModel> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/BeepVector.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LambdaMap.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GammaMap.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/ReconciliationModel.hh:8,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/GuestTreeModel.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void beep::EnumHybridGuestTreeModel::inits()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::ReconciledTreeTimeModel*, std::vector<beep::ReconciledTreeTimeModel> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<beep::GuestTreeModel*, std::vector<beep::GuestTreeModel> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/TransitionHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TransitionHandler.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/CacheSubstitutionModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/CacheSubstitutionModel.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/MatrixTransitionHandler.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MatrixTransitionHandler.cc
In file included from /usr/include/c++/7/map:60:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/Beep.hh:5,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/MatrixTransitionHandler.cc:7:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::_Alloc_node; _Key = char; _Val = std::pair<const char, double>; _KeyOfValue = std::_Select1st<std::pair<const char, double> >; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2191:7: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h: In static member function 'static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::F81(std::map<char, double>)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h: In static member function 'static beep::MatrixTransitionHandler beep::MatrixTransitionHandler::create(std::__cxx11::string, std::map<char, double>*)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/SeqIO.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SeqIO.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/FastCacheSubstitutionModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc
In file included from /usr/include/c++/7/ext/hash_map:60:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1:
/usr/include/c++/7/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
 #warning \
  ^~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/SequenceGenerator.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceGenerator.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/SequenceType.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceType.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: 'std::ostream& beep::operator<<(std::ostream&, const beep::SequenceType&)' has not been declared within beep
 ostream& beep::operator<<(ostream& os, const SequenceType& dt)
          ^~~~
In file included from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceType.cc:8:0:
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a friend
     friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt);
                          ^~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/SubstitutionModel.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SubstitutionModel.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/LA_Vector.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Vector.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/LA_Matrix.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Matrix.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_Matrix.cc:19:5: warning: 'beep::LA_Matrix::dim' is initialized with itself [-Winit-self]
     LA_Matrix::LA_Matrix()
     ^~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/SubstitutionMCMC.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SubstitutionMCMC.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/LA_DiagonalMatrix.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/LA_DiagonalMatrix.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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/SequenceData.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc: In member function 'std::map<char, double> beep::SequenceData::getBaseFrequencies()':
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:288:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int i = 0; i < seqType.alphabetSize(); i++)
                             ~~^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:303:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
                 for (int j = 0; j < seq.length(); j++) {
                                 ~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:6:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
     vector<_Tp, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:60:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:2:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::_Alloc_node; _Key = char; _Val = std::pair<const char, double>; _KeyOfValue = std::_Select1st<std::pair<const char, double> >; _Compare = std::less<char>; _Alloc = std::allocator<std::pair<const char, double> >]':
/usr/include/c++/7/bits/stl_tree.h:2191:7: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:6:
/usr/include/c++/7/bits/stl_vector.h: In member function 'std::map<char, double> beep::SequenceData::getBaseFrequencies()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
    _M_realloc_insert(end(), __x);
    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/map:60:0,
                 from /<<PKGBUILDDIR>>/src/cxx/libraries/prime/SequenceData.cc:2:
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<char, std::pair<const char, double>, std::_Select1st<std::pair<const char, double> >, std::less<char>, std::allocator<std::pair<const char, double> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const char, double> >}' changed in GCC 7.1
  return _M_insert_unique_(__pos, __x, __an);
                                           ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 81%] Linking CXX shared library libprime-phylo.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo.so -o libprime-phylo.so CMakeFiles/prime-phylo.dir/NHXnode.c.o CMakeFiles/prime-phylo.dir/NHXtree.c.o CMakeFiles/prime-phylo.dir/NHXannotation.c.o CMakeFiles/prime-phylo.dir/lexer.c.o CMakeFiles/prime-phylo.dir/NHXparse.c.o CMakeFiles/prime-phylo.dir/AnError.cc.o CMakeFiles/prime-phylo.dir/Beep.cc.o CMakeFiles/prime-phylo.dir/BeepOption.cc.o CMakeFiles/prime-phylo.dir/Hacks.cc.o CMakeFiles/prime-phylo.dir/ODESolver.cc.o CMakeFiles/prime-phylo.dir/PRNG.cc.o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o CMakeFiles/prime-phylo.dir/Probability.cc.o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o CMakeFiles/prime-phylo.dir/DiscTree.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o CMakeFiles/prime-phylo.dir/EpochTree.cc.o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o CMakeFiles/prime-phylo.dir/Node.cc.o CMakeFiles/prime-phylo.dir/NodeMap.cc.o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o CMakeFiles/prime-phylo.dir/Tree.cc.o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o CMakeFiles/prime-phylo.dir/TreeIO.cc.o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o CMakeFiles/prime-phylo.dir/SimpleML.cc.o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o CMakeFiles/prime-phylo.dir/GammaMap.cc.o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o CMakeFiles/prime-phylo.dir/fastGEM.cc.o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o CMakeFiles/prime-phylo.dir/HybridTree.cc.o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o CMakeFiles/prime-phylo.dir/SeqIO.cc.o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o CMakeFiles/prime-phylo.dir/SequenceType.cc.o CMakeFiles/prime-phylo.dir/SequenceData.cc.o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o  -L/usr/lib/arm-linux-gnueabihf/liblapack.so  -L/usr/lib/arm-linux-gnueabihf/libblas.so -Wl,-rpath,/usr/lib/arm-linux-gnueabihf/liblapack.so:/usr/lib/arm-linux-gnueabihf/libblas.so:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi 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make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color=
Scanning dependencies of target primeDLRS
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make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color=
Scanning dependencies of target primeDTLSR
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 83%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o
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[ 83%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/treesize /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color=
Scanning dependencies of target treesize
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make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/applications/primeGEM /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color=
Scanning dependencies of target primeGEM
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[ 83%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o
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[ 83%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/<<PKGBUILDDIR>>/src/cxx/tools/treesize -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/treesize.dir/treesize.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/treesize/treesize.cc
/<<PKGBUILDDIR>>/src/cxx/tools/treesize/treesize.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/treesize/treesize.cc:55:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch]
       switch(args_info.input_format_arg)
             ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 84%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/<<PKGBUILDDIR>>/src/cxx/tools/treesize -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g   -o CMakeFiles/treesize.dir/cmdline.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c: In function 'update_arg':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c:395:9: warning: variable 'stop_char' set but not used [-Wunused-but-set-variable]
   char *stop_char = 0;
         ^~~~~~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c: In function 'cmdline_parser_internal':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c:483:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable]
   int check_required;
       ^~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 85%] Linking CXX executable treesize
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o  -o treesize -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 85%] Built target treesize
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 85%] Generating cmdline.c, cmdline.h
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/showtree /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake --color=
Scanning dependencies of target showtree
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 86%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -I/<<PKGBUILDDIR>>/src/cxx/tools/showtree -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/showtree.dir/showtree.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc
/<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc: In function 'void outputSingleTree(beep::Tree&, beep::TreeIOTraits&, gengetopt_args_info&)':
/<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc:30:20: warning: variable 'nw' set but not used [-Wunused-but-set-variable]
   bool et, nt, bl, nw;
                    ^~
/<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/showtree/showtree.cc:174:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
        if(args_info.tree_number_arg >= Tvec.size())
           ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 86%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree -I/<<PKGBUILDDIR>>/src/cxx/tools/showtree -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g   -o CMakeFiles/showtree.dir/cmdline.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.c
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.c: In function 'cmdline_parser_internal':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree/cmdline.c:554:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable]
   int check_required;
       ^~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 87%] Linking CXX executable showtree
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/showtree && /usr/bin/cmake -E cmake_link_script CMakeFiles/showtree.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o  -o showtree -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 87%] Built target showtree
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 88%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/<<PKGBUILDDIR>>/src/cxx/applications/primeGEM -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /<<PKGBUILDDIR>>/src/cxx/applications/primeGEM/troyo.cc
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make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 89%] Generating cmdline.c, cmdline.h
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/reconcile /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake --color=
Scanning dependencies of target reconcile
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 90%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/<<PKGBUILDDIR>>/src/cxx/applications/primeGEM -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g   -o CMakeFiles/primeGEM.dir/cmdline.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 90%] Linking CXX executable primeGEM
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeGEM.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o  -o primeGEM -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 90%] Built target primeGEM
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 90%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS -I/<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -c /<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS/primeDLRS.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 91%] Linking CXX executable primeDLRS
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/<<PKGBUILDDIR>>/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/reconcile.dir/Rootalyzer.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/reconcile/Rootalyzer.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 92%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDLRS.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeDLRS.dir/primeDLRS.cc.o  -o primeDLRS -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:/usr/lib/arm-linux-gnueabihf/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 92%] Built target primeDLRS
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 93%] Generating cmdline.c, cmdline.h
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/reroot /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake --color=
Scanning dependencies of target reroot
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 93%] Building CXX object src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR -I/<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR/idolatrous.cc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 94%] Linking CXX executable primeDTLSR
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/<<PKGBUILDDIR>>/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g   -o CMakeFiles/reconcile.dir/cmdline.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile/cmdline.c
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[ 95%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDTLSR.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/primeDTLSR.dir/idolatrous.cc.o  -o primeDTLSR -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:/usr/lib/arm-linux-gnueabihf/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 95%] Built target primeDTLSR
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend
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[ 95%] Generating cmdline.c, cmdline.h
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake --color=
Scanning dependencies of target tree2leafnames
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make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 96%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot -I/<<PKGBUILDDIR>>/src/cxx/tools/reroot -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g   -o CMakeFiles/reroot.dir/cmdline.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/cmdline.c
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[ 97%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile -I/<<PKGBUILDDIR>>/src/cxx/tools/reconcile -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc
/<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
   char *ofilename = "mpr.out";
                     ^~~~~~~~~
/<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)':
/<<PKGBUILDDIR>>/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < gtree.getNumberOfNodes(); i++) {
                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~
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[ 97%] Linking CXX executable reconcile
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g   -o CMakeFiles/tree2leafnames.dir/cmdline.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c: In function 'update_arg':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c:388:9: warning: variable 'stop_char' set but not used [-Wunused-but-set-variable]
   char *stop_char = 0;
         ^~~~~~~~~
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c: In function 'cmdline_parser_internal':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames/cmdline.c:472:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable]
   int check_required;
       ^~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 97%] Generating cmdline.c, cmdline.h
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/chainsaw /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake --color=
Scanning dependencies of target chainsaw
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 98%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o  -o reconcile -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 98%] Built target reconcile
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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[ 98%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g   -o CMakeFiles/chainsaw.dir/cmdline.c.o   -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.c
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.c: In function 'cmdline_parser_internal':
/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw/cmdline.c:539:7: warning: variable 'check_required' set but not used [-Wunused-but-set-variable]
   int check_required;
       ^~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames/tree2leafnames.cc
/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames/tree2leafnames.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/tree2leafnames/tree2leafnames.cc:51:11: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch]
     switch(args_info.input_format_arg)
           ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 98%] Linking CXX executable tree2leafnames
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o  -o tree2leafnames -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 98%] Built target tree2leafnames
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/chainsaw.dir/chainsaw.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector<beep::SetOfNodes>*, beep::StrStrMap*)':
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc:90:9: warning: enumeration value 'guest_tree_format__NULL' not handled in switch [-Wswitch]
   switch(ai.guest_tree_format_arg)
         ^
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadHostTree(gengetopt_args_info&)':
/<<PKGBUILDDIR>>/src/cxx/tools/chainsaw/chainsaw.cc:114:9: warning: enumeration value 'host_tree_format__NULL' not handled in switch [-Wswitch]
   switch(ai.host_tree_format_arg)
         ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 99%] Linking CXX executable chainsaw
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o  -o chainsaw -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 99%] Built target chainsaw
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/c++  -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot -I/<<PKGBUILDDIR>>/src/cxx/tools/reroot -I/usr/lib/arm-linux-gnueabihf/openmpi/include/openmpi -I/usr/lib/arm-linux-gnueabihf/openmpi/include -I/usr/lib/arm-linux-gnueabihf/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>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g   -std=gnu++98 -o CMakeFiles/reroot.dir/reroot.cc.o -c /<<PKGBUILDDIR>>/src/cxx/tools/reroot/reroot.cc
/<<PKGBUILDDIR>>/src/cxx/tools/reroot/reroot.cc: In function 'int main(int, char**)':
/<<PKGBUILDDIR>>/src/cxx/tools/reroot/reroot.cc:76:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch]
       switch(args_info.input_format_arg)
             ^
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Linking CXX executable reroot
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/cmake -E cmake_link_script CMakeFiles/reroot.dir/link.txt --verbose=1
/usr/bin/c++  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g  -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o  -o reroot -Wl,-rpath,/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/arm-linux-gnueabihf/openmpi/lib:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi_cxx.so /usr/lib/arm-linux-gnueabihf/openmpi/lib/libmpi.so -lboost_mpi -lboost_serialization ../../libraries/sfile/libprime-phylo-sfile.so 
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target reroot
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
   dh_auto_test -a -O--buildsystem=cmake -O--parallel
 fakeroot debian/rules binary-arch
dh binary-arch --buildsystem=cmake --parallel
   dh_testroot -a -O--buildsystem=cmake -O--parallel
   dh_prep -a -O--buildsystem=cmake -O--parallel
   dh_auto_install -a -O--buildsystem=cmake -O--parallel
	cd obj-arm-linux-gnueabihf && make -j4 -Oline install DESTDIR=/<<PKGBUILDDIR>>/debian/prime-phylo AM_UPDATE_INFO_DIR=no
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
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/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f CMakeFiles/Makefile2 all
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'
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=
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]: Nothing to be done for 'src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build'.
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[  4%] Built target prime-phylo-sfile
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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'
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=
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make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build
make[3]: Nothing to be done for 'src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build'.
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 81%] Built target prime-phylo
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make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/tools/treesize /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/applications/primeDTLSR /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/cxx/applications/primeDLRS /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
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Install the project...
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/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Debug"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/chainsaw.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/mcmc_analysis.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/primeDLRS.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/primeDTLSR.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/primeGEM.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/reconcile.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/reroot.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/showtree.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/tree2leafnames.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/share/man/man1/treesize.1
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo-sfile.so" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeGEM
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeGEM" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeDTLSR
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeDTLSR" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeDLRS
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/primeDLRS" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/treesize
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/treesize" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/showtree
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/showtree" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/reconcile
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/reconcile" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/reroot
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/reroot" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/tree2leafnames
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/tree2leafnames" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/chainsaw
-- Set runtime path of "/<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/chainsaw" to "/usr/lib/prime-phylo"
-- Installing: /<<PKGBUILDDIR>>/debian/prime-phylo/usr/bin/mcmc_analysis
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
   dh_installdocs -a -O--buildsystem=cmake -O--parallel
   dh_installchangelogs -a -O--buildsystem=cmake -O--parallel
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   dh_link -a -O--buildsystem=cmake -O--parallel
   dh_strip_nondeterminism -a -O--buildsystem=cmake -O--parallel
   dh_compress -a -O--buildsystem=cmake -O--parallel
   dh_fixperms -a -O--buildsystem=cmake -O--parallel
   dh_missing -a -O--buildsystem=cmake -O--parallel
   dh_strip -a -O--buildsystem=cmake -O--parallel
   debian/rules override_dh_makeshlibs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_makeshlibs -pprime-phylo -Xprime-phylo.so -Xprime-phylo-sfile.so
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_shlibdeps -a -O--buildsystem=cmake -O--parallel
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/tree2leafnames contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/chainsaw contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/treesize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/primeGEM contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/primeDTLSR contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/reroot contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/reconcile contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/showtree contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so'
dpkg-shlibdeps: warning: debian/prime-phylo/usr/bin/primeDLRS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/prime-phylo/usr/bin/tree2leafnames debian/prime-phylo/usr/bin/chainsaw debian/prime-phylo/usr/bin/treesize debian/prime-phylo/usr/bin/primeGEM debian/prime-phylo/usr/bin/primeDTLSR debian/prime-phylo/usr/bin/reroot debian/prime-phylo/usr/bin/reconcile debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so debian/prime-phylo/usr/bin/showtree debian/prime-phylo/usr/bin/primeDLRS were not linked against libmpi_cxx.so.40 (they use none of the library's symbols)
   dh_installdeb -a -O--buildsystem=cmake -O--parallel
   dh_gencontrol -a -O--buildsystem=cmake -O--parallel
   dh_md5sums -a -O--buildsystem=cmake -O--parallel
   dh_builddeb -a -O--buildsystem=cmake -O--parallel
dpkg-deb: building package 'prime-phylo-dbgsym' in '../prime-phylo-dbgsym_1.0.11-4+b2_armhf.deb'.
dpkg-deb: building package 'prime-phylo' in '../prime-phylo_1.0.11-4+b2_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../prime-phylo_1.0.11-4+b2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build prime-phylo-1.0.11
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-05-04T02:44:32Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


prime-phylo_1.0.11-4+b2_armhf.changes:
--------------------------------------

Format: 1.8
Date: Wed, 03 Aug 2016 11:20:36 +0000
Source: prime-phylo (1.0.11-4)
Binary: prime-phylo
Binary-Only: yes
Architecture: armhf
Version: 1.0.11-4+b2
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
 prime-phylo - bayesian estimation of gene trees taking the species tree into ac
Changes:
 prime-phylo (1.0.11-4+b2) buster-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
Checksums-Sha1:
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 bbf06fa025a146dc8bb5d72b99709fd49819c87c 7387 prime-phylo_1.0.11-4+b2_armhf.buildinfo
 2a71063349d3399b72a6721567e09a5f37ec55d9 675392 prime-phylo_1.0.11-4+b2_armhf.deb
Checksums-Sha256:
 16d5bc479a3d27b39a7baa4a4675c5356d6b754a763817d390b052725dcfdab3 8942240 prime-phylo-dbgsym_1.0.11-4+b2_armhf.deb
 7a4bf191344cc16c891f8011c32cb493a0181e80899f33200388279a31ff3a77 7387 prime-phylo_1.0.11-4+b2_armhf.buildinfo
 686ade849148ce67cab3fd0f79f3988e1f855a28fe5aca9fe4d1dcc7131f9789 675392 prime-phylo_1.0.11-4+b2_armhf.deb
Files:
 5036ffc1acd46167225a42cd0dadb2ab 8942240 debug optional prime-phylo-dbgsym_1.0.11-4+b2_armhf.deb
 feb28b276ec386a88b66f8e41b8f7c4f 7387 science optional prime-phylo_1.0.11-4+b2_armhf.buildinfo
 be679ef8d1003dd12b2c83a24818fa9f 675392 science optional prime-phylo_1.0.11-4+b2_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


prime-phylo-dbgsym_1.0.11-4+b2_armhf.deb
----------------------------------------

 new Debian package, version 2.0.
 size 8942240 bytes: control archive=1056 bytes.
     816 bytes,    12 lines      control              
    1166 bytes,    11 lines      md5sums              
 Package: prime-phylo-dbgsym
 Source: prime-phylo (1.0.11-4)
 Version: 1.0.11-4+b2
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 9381
 Depends: prime-phylo (= 1.0.11-4+b2)
 Section: debug
 Priority: optional
 Description: debug symbols for prime-phylo
 Build-Ids: 282f151693117ea2382e35e8d5119daa5773f926 33480ad291ce7e5532d280a4765c2556a6493686 3b18b893042f36ec0ebe995fff0a6212c76b3447 44db01b3b928df52cbd7d38c76af2faee218b86b 6c7ca94f47fa83afd79160bfbb6704fd24b48807 85af7711c5ce99ab8266c034c1531bf2822178b7 98b843b28b6fb5a6c356a458118c6b3e9d03246d afacd20bf6bdfce38fc103e8e036b68753839260 d113a9515d4e77e64a61c11dc45610093eca1407 ddce04ed92a2f91b6a1888562e1c380141bdf70b fb94f1d0c68e60b1b8bf4800d0d4678d278f0452

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lrwxrwxrwx root/root         0 2016-08-03 11:20 ./usr/share/doc/prime-phylo-dbgsym -> prime-phylo


prime-phylo_1.0.11-4+b2_armhf.deb
---------------------------------

 new Debian package, version 2.0.
 size 675392 bytes: control archive=1624 bytes.
    1085 bytes,    20 lines      control              
    1665 bytes,    26 lines      md5sums              
 Package: prime-phylo
 Source: prime-phylo (1.0.11-4)
 Version: 1.0.11-4+b2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2425
 Depends: perl:any, libblas3 | libblas.so.3, libboost-mpi1.62.0, libboost-serialization1.62.0, libc6 (>= 2.23), libgcc1 (>= 1:4.0), liblapack3 | liblapack.so.3, libopenmpi3, libstdc++6 (>= 5.2), libxml2 (>= 2.7.4)
 Suggests: njplot, treeviewx, muscle, probalign, mafft, python-biopython, mrbayes, phyml, raxml
 Section: science
 Priority: optional
 Homepage: http://prime.sbc.su.se
 Description: bayesian estimation of gene trees taking the species tree into account
  PrIME (Probabilistic Integrated Models of Evolution) is a package
  supporting inference of evolutionary parameters in a Bayesian framework
  using Markov chain Monte Carlo simulation. A distinguishing feature of
  PrIME is that the species tree is taken into account when analyzing gene
  trees.
  .
  The input data to PrIME is a multiple sequence alignment in FASTA format
  and the output data contains trees in Newick format.

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drwxr-xr-x root/root         0 2016-08-03 11:20 ./usr/bin/
-rwxr-xr-x root/root     26304 2016-08-03 11:20 ./usr/bin/chainsaw
-rwxr-xr-x root/root     33128 2012-12-17 15:52 ./usr/bin/mcmc_analysis
-rwxr-xr-x root/root     79368 2016-08-03 11:20 ./usr/bin/primeDLRS
-rwxr-xr-x root/root     83464 2016-08-03 11:20 ./usr/bin/primeDTLSR
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-rwxr-xr-x root/root     34444 2016-08-03 11:20 ./usr/bin/reconcile
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-rwxr-xr-x root/root     18036 2016-08-03 11:20 ./usr/bin/tree2leafnames
-rwxr-xr-x root/root     18056 2016-08-03 11:20 ./usr/bin/treesize
drwxr-xr-x root/root         0 2016-08-03 11:20 ./usr/lib/
drwxr-xr-x root/root         0 2016-08-03 11:20 ./usr/lib/prime-phylo/
-rw-r--r-- root/root     42408 2016-08-03 11:20 ./usr/lib/prime-phylo/libprime-phylo-sfile.so
-rw-r--r-- root/root   1996292 2016-08-03 11:20 ./usr/lib/prime-phylo/libprime-phylo.so
drwxr-xr-x root/root         0 2016-08-03 11:20 ./usr/share/
drwxr-xr-x root/root         0 2016-08-03 11:20 ./usr/share/doc/
drwxr-xr-x root/root         0 2016-08-03 11:20 ./usr/share/doc/prime-phylo/
-rw-r--r-- root/root       222 2016-08-03 11:20 ./usr/share/doc/prime-phylo/changelog.Debian.armhf.gz
-rw-r--r-- root/root       504 2016-08-03 11:20 ./usr/share/doc/prime-phylo/changelog.Debian.gz
-rw-r--r-- root/root       505 2012-12-17 15:52 ./usr/share/doc/prime-phylo/changelog.gz
-rw-r--r-- root/root      7324 2016-07-25 20:47 ./usr/share/doc/prime-phylo/copyright
drwxr-xr-x root/root         0 2016-08-03 11:20 ./usr/share/man/
drwxr-xr-x root/root         0 2016-08-03 11:20 ./usr/share/man/man1/
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-rw-r--r-- root/root      2154 2016-08-03 11:20 ./usr/share/man/man1/primeDLRS.1.gz
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-rw-r--r-- root/root       987 2016-08-03 11:20 ./usr/share/man/man1/primeGEM.1.gz
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-rw-r--r-- root/root       654 2016-08-03 11:20 ./usr/share/man/man1/reconcile.1.gz
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-rw-r--r-- root/root       608 2016-08-03 11:20 ./usr/share/man/man1/treesize.1.gz


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| Post Build                                                                   |
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| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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| Summary                                                                      |
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Build Architecture: armhf
Build-Space: 108040
Build-Time: 247
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 467
Job: prime-phylo_1.0.11-4
Machine Architecture: armhf
Package: prime-phylo
Package-Time: 731
Source-Version: 1.0.11-4
Space: 108040
Status: successful
Version: 1.0.11-4+b2
--------------------------------------------------------------------------------
Finished at 2018-05-04T02:44:32Z
Build needed 00:12:11, 108040k disk space