prime-phylo →
1.0.11-1 →
armhf → 2013-07-06 19:16:17
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on
╔══════════════════════════════════════════════════════════════════════════════╗
║ prime-phylo 1.0.11-1 (armhf) 06 Jul 2013 18:54 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: prime-phylo
Version: 1.0.11-1
Source Version: 1.0.11-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/prime-phylo-CJFyc7/prime-phylo-1.0.11' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/prime-phylo-CJFyc7' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-bd34ed37-8763-45c0-bdce-28cf4caff7b5' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging Release.gpg [490 B]
Get:2 http://172.17.0.1 jessie-staging Release [10.8 kB]
Get:3 http://172.17.0.1 jessie-staging/main Sources [6661 kB]
Get:4 http://172.17.0.1 jessie-staging/main armhf Packages [7746 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
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Need to get 757 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main prime-phylo 1.0.11-1 (dsc) [1351 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main prime-phylo 1.0.11-1 (tar) [751 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main prime-phylo 1.0.11-1 (diff) [5029 B]
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-bQ9wTz/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 6 not upgraded.
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Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), 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: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), 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-B0wweM/apt_archive/sbuild-build-depends-prime-phylo-dummy.deb'.
OK
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 extra packages will be installed:
adduser bison bsdmainutils cmake cmake-data debhelper emacsen-common file
flex gengetopt gettext gettext-base gfortran gfortran-4.6 groff-base
intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-dev
libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.49-dev
libboost-mpi1.49.0 libboost-serialization-dev libboost-serialization1.49-dev
libboost-serialization1.49.0 libboost1.49-dev libcroco3 libcurl3-gnutls
libexpat1 libffi6 libgcrypt11 libgfortran3 libglib2.0-0 libgnutls26
libgpg-error0 libgssapi-krb5-2 libibverbs-dev libibverbs1 libicu48 libidn11
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libldap-2.4-2 liblzo2-2 libmagic1 libnettle4 libopenmpi-dev libopenmpi1.3
libp11-kit0 libpipeline1 librtmp0 libsasl2-2 libsigsegv2 libssh2-1
libtasn1-3 libtorque2 libunistring0 libxml2 libxml2-dev m4 man-db
mpi-default-dev openmpi-common po-debconf zlib1g-dev
Suggested packages:
bison-doc wamerican wordlist whois vacation codeblocks eclipse dh-make
gettext-doc gfortran-doc gfortran-4.6-doc libgfortran3-dbg groff lrzip
libboost-doc libboost-graph1.49-dev libboost1.49-doc libboost-chrono1.49-dev
libboost-date-time1.49-dev libboost-filesystem1.49-dev
libboost-graph-parallel1.49-dev libboost-iostreams1.49-dev
libboost-locale1.49-dev libboost-math1.49-dev
libboost-program-options1.49-dev libboost-python1.49-dev
libboost-random1.49-dev libboost-regex1.49-dev libboost-signals1.49-dev
libboost-system1.49-dev libboost-test1.49-dev libboost-thread1.49-dev
libboost-timer1.49-dev libboost-wave1.49-dev xsltproc doxygen docbook-xml
docbook-xsl default-jdk fop rng-tools krb5-doc krb5-user pkg-config less
www-browser libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
ca-certificates libglib2.0-data shared-mime-info krb5-locales
libsasl2-modules xml-core libmail-sendmail-perl
The following NEW packages will be installed:
adduser bison bsdmainutils cmake cmake-data debhelper emacsen-common file
flex gengetopt gettext gettext-base gfortran gfortran-4.6 groff-base
intltool-debian libarchive13 libasprintf0c2 libbison-dev libblas-dev
libblas3 libboost-dev libboost-mpi-dev libboost-mpi1.49-dev
libboost-mpi1.49.0 libboost-serialization-dev libboost-serialization1.49-dev
libboost-serialization1.49.0 libboost1.49-dev libcroco3 libcurl3-gnutls
libexpat1 libffi6 libgcrypt11 libgfortran3 libglib2.0-0 libgnutls26
libgpg-error0 libgssapi-krb5-2 libibverbs-dev libibverbs1 libicu48 libidn11
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libldap-2.4-2 liblzo2-2 libmagic1 libnettle4 libopenmpi-dev libopenmpi1.3
libp11-kit0 libpipeline1 librtmp0 libsasl2-2 libsigsegv2 libssh2-1
libtasn1-3 libtorque2 libunistring0 libxml2 libxml2-dev m4 man-db
mpi-default-dev openmpi-common po-debconf
sbuild-build-depends-prime-phylo-dummy zlib1g-dev
0 upgraded, 73 newly installed, 0 to remove and 6 not upgraded.
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Get:54 http://172.17.0.1/private/ jessie-staging/main libboost1.49-dev armhf 1.49.0-4 [8940 kB]
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Get:72 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 kB]
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Unpacking sbuild-build-depends-prime-phylo-dummy (from .../sbuild-build-depends-prime-phylo-dummy.deb) ...
Setting up libpipeline1:armhf (1.2.4-1) ...
Setting up groff-base (1.22.2-3) ...
Setting up bsdmainutils (9.0.5) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up man-db (2.6.3-7) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.2.1-1) ...
Setting up libgpg-error0:armhf (1.10-3.1) ...
Setting up libgcrypt11:armhf (1.5.2-3) ...
Setting up libp11-kit0:armhf (0.18.3-2) ...
Setting up libtasn1-3:armhf (2.14-3) ...
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Setting up libkeyutils1:armhf (1.5.5-7) ...
Setting up libkrb5support0:armhf (1.10.1+dfsg-5) ...
Setting up libk5crypto3:armhf (1.10.1+dfsg-5) ...
Setting up libkrb5-3:armhf (1.10.1+dfsg-5) ...
Setting up libgssapi-krb5-2:armhf (1.10.1+dfsg-5) ...
Setting up libidn11:armhf (1.25-2) ...
Setting up libsasl2-2:armhf (2.1.25.dfsg1-7) ...
Setting up libldap-2.4-2:armhf (2.4.31-1+nmu2) ...
Setting up libmagic1:armhf (1:5.14-2) ...
Setting up libxml2:armhf (2.9.1+dfsg1-2) ...
Setting up libsigsegv2 (2.9-4) ...
Setting up m4 (1.4.16-5) ...
Setting up flex (2.5.35-10.1) ...
Setting up liblzo2-2:armhf (2.06-1) ...
Setting up libnettle4:armhf (2.7.1-1) ...
Setting up libarchive13:armhf (3.1.2-7) ...
Setting up libffi6:armhf (3.0.13-4) ...
Setting up libglib2.0-0:armhf (2.36.1-2build1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up librtmp0:armhf (2.4+20121230.gitdf6c518-1) ...
Setting up libssh2-1:armhf (1.4.3-1) ...
Setting up libcurl3-gnutls:armhf (7.31.0-2) ...
Setting up libexpat1:armhf (2.1.0-3) ...
Setting up libgfortran3:armhf (4.8.0-7+rpi1) ...
Setting up libicu48:armhf (4.8.1.1-12) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up adduser (3.113+nmu3) ...
Setting up file (1:5.14-2) ...
Setting up gettext-base (0.18.2.1-1) ...
Setting up libbison-dev:armhf (2:2.7.1.dfsg-1) ...
Setting up bison (2:2.7.1.dfsg-1) ...
update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode
Setting up emacsen-common (2.0.5) ...
Setting up cmake-data (2.8.11.1-1) ...
Install cmake-data for emacs
Setting up cmake (2.8.11.1-1) ...
Setting up gettext (0.18.2.1-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20130605) ...
Setting up gengetopt (2.22.6-2) ...
Setting up gfortran-4.6 (4.6.4-2+rpi1) ...
Setting up gfortran (4:4.6.3-8) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
Setting up libblas3 (1.2.20110419-5) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libblas-dev (1.2.20110419-5) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libboost1.49-dev (1.49.0-4) ...
Setting up libboost-dev (1.49.0.1) ...
Setting up libboost-serialization1.49.0 (1.49.0-4) ...
Setting up libboost-serialization1.49-dev (1.49.0-4) ...
Setting up libibverbs1 (1.1.7-1) ...
Setting up libtorque2 (2.4.16+dfsg-1) ...
Setting up libopenmpi1.3 (1.4.5-1) ...
Setting up libboost-mpi1.49.0 (1.49.0-4) ...
Setting up openmpi-common (1.4.5-1) ...
Setting up libibverbs-dev (1.1.7-1) ...
Setting up libopenmpi-dev (1.4.5-1) ...
update-alternatives: using /usr/lib/openmpi/include to provide /usr/include/mpi (mpi) in auto mode
Setting up mpi-default-dev (1.0.1) ...
Setting up libboost-mpi1.49-dev (1.49.0-4) ...
Setting up libboost-mpi-dev (1.49.0.1) ...
Setting up libboost-serialization-dev (1.49.0.1) ...
Setting up liblapack3 (3.4.2+dfsg-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up liblapack-dev (3.4.2+dfsg-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libxml2-dev:armhf (2.9.1+dfsg1-2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Setting up sbuild-build-depends-prime-phylo-dummy (0.invalid.0) ...
Processing triggers for libc-bin ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.0.35-wand5.2 armhf (armv7l)
Toolchain package versions: binutils_2.23.52.20130612-1 dpkg-dev_1.16.10 g++-4.6_4.6.4-2+rpi1 gcc-4.6_4.6.4-2+rpi1 libc6-dev_2.17-6+rpi1 libstdc++6_4.8.0-7+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 linux-libc-dev_3.2.41-2+rpi1
Package versions: adduser_3.113+nmu3 apt_0.9.7.8+rpi1 base-files_7.2 base-passwd_3.5.26 bash_4.2+dfsg-1 binutils_2.23.52.20130612-1 bison_2:2.7.1.dfsg-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.4 build-essential_11.6 bzip2_1.0.6-4 cmake_2.8.11.1-1 cmake-data_2.8.11.1-1 coreutils_8.13-3.5 cpio_2.11+dfsg-1 cpp_4:4.6.3-8 cpp-4.6_4.6.4-2+rpi1 dash_0.5.7-3 debconf_1.5.50 debconf-i18n_1.5.50 debfoster_2.7-1.2 debhelper_9.20130605 debianutils_4.3.4 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 emacsen-common_2.0.5 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-5 flex_2.5.35-10.1 g++_4:4.6.3-8 g++-4.6_4.6.4-2+rpi1 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.4-2+rpi1 gcc-4.6-base_4.6.4-2+rpi1 gcc-4.7-base_4.7.3-4+rpi1 gcc-4.8-base_4.8.0-7+rpi1 gengetopt_2.22.6-2 gettext_0.18.2.1-1 gettext-base_0.18.2.1-1 gfortran_4:4.6.3-8 gfortran-4.6_4.6.4-2+rpi1 gnupg_1.4.12-7 gpgv_1.4.12-7 grep_2.14-2 groff-base_1.22.2-3 gzip_1.6-1 hostname_3.13 initramfs-tools_0.113 initscripts_2.88dsf-41 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 libacl1_2.2.52-1 libapt-pkg4.12_0.9.7.8+rpi1 libarchive13_3.1.2-7 libasprintf0c2_0.18.2.1-1 libattr1_1:2.4.47-1 libbison-dev_2:2.7.1.dfsg-1 libblas-dev_1.2.20110419-5 libblas3_1.2.20110419-5 libblkid1_2.20.1-5.4 libboost-dev_1.49.0.1 libboost-mpi-dev_1.49.0.1 libboost-mpi1.49-dev_1.49.0-4 libboost-mpi1.49.0_1.49.0-4 libboost-serialization-dev_1.49.0.1 libboost-serialization1.49-dev_1.49.0-4 libboost-serialization1.49.0_1.49.0-4 libboost1.49-dev_1.49.0-4 libbz2-1.0_1.0.6-4 libc-bin_2.17-6+rpi1 libc-dev-bin_2.17-6+rpi1 libc6_2.17-6+rpi1 libc6-dev_2.17-6+rpi1 libcap2_1:2.22-1.2 libclass-isa-perl_0.36-5 libcomerr2_1.42.5-1.1 libcroco3_0.6.8-2 libcurl3-gnutls_7.31.0-2 libdb5.1_5.1.29-6 libdbus-1-3_1.6.12-1 libdpkg-perl_1.16.10 libexpat1_2.1.0-3 libffi6_3.0.13-4 libgc1c2_1:7.1-9.1 libgcc1_1:4.8.0-7+rpi1 libgcrypt11_1.5.2-3 libgdbm3_1.8.3-12 libgfortran3_4.8.0-7+rpi1 libglib2.0-0_2.36.1-2build1 libgmp10_2:5.1.2+dfsg-1 libgnutls26_2.12.23-5 libgomp1_4.8.0-7+rpi1 libgpg-error0_1.10-3.1 libgssapi-krb5-2_1.10.1+dfsg-5 libibverbs-dev_1.1.7-1 libibverbs1_1.1.7-1 libicu48_4.8.1.1-12 libidn11_1.25-2 libk5crypto3_1.10.1+dfsg-5 libkeyutils1_1.5.5-7 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 libkrb5-3_1.10.1+dfsg-5 libkrb5support0_1.10.1+dfsg-5 liblapack-dev_3.4.2+dfsg-1 liblapack3_3.4.2+dfsg-1 libldap-2.4-2_2.4.31-1+nmu2 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-2 liblzo2-2_2.06-1 libmagic1_1:5.14-2 libmount1_2.20.1-5.4 libmpc3_1.0.1-1 libmpfr4_3.1.1-1 libncurses5_5.9+20130608-1 libncursesw5_5.9+20130608-1 libnettle4_2.7.1-1 libnih-dbus1_1.0.3-4.1+b1 libnih1_1.0.3-4.1+b1 libopenmpi-dev_1.4.5-1 libopenmpi1.3_1.4.5-1 libp11-kit0_0.18.3-2 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpcre3_1:8.31-2 libpipeline1_1.2.4-1 libprocps0_1:3.3.4-2 libreadline6_6.2+dfsg-0.1 librtmp0_2.4+20121230.gitdf6c518-1 libsasl2-2_2.1.25.dfsg1-7 libselinux1_2.1.13-2 libsemanage-common_2.1.10-2 libsemanage1_2.1.10-2 libsepol1_2.1.9-2 libsigsegv2_2.9-4 libslang2_2.2.4-15 libss2_1.42.5-1.1 libssh2-1_1.4.3-1 libstdc++6_4.8.0-7+rpi1 libstdc++6-4.6-dev_4.6.4-2+rpi1 libswitch-perl_2.16-2 libtasn1-3_2.14-3 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9+20130608-1 libtorque2_2.4.16+dfsg-1 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.2 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.4 libxml2_2.9.1+dfsg1-2 libxml2-dev_2.9.1+dfsg1-2 linux-libc-dev_3.2.41-2+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian8+rpi1 m4_1.4.16-5 make_3.81-8.2 makedev_2.3.1-93 man-db_2.6.3-7 mawk_1.3.3-17 mount_2.20.1-5.4 mountall_2.48 mpi-default-dev_1.0.1 multiarch-support_2.17-6+rpi1 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 openmpi-common_1.4.5-1 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-21+rpi1 perl-base_5.14.2-21+rpi1 perl-modules_5.14.2-21+rpi1 plymouth_0.8.8-6+deb8u1 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-prime-phylo-dummy_0.invalid.0 sed_4.2.2-1 sensible-utils_0.0.9 sysv-rc_2.88dsf-41 sysvinit_2.88dsf-41 sysvinit-utils_2.88dsf-41 tar_1.26+dfsg-6 tzdata_2013c-2 udev_175-7.2 util-linux_2.20.1-5.4 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Tue Dec 18 15:40:38 2012 UTC using DSA key ID C09FD35A
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./prime-phylo_1.0.11-1.dsc
dpkg-source: info: extracting prime-phylo in prime-phylo-1.0.11
dpkg-source: info: unpacking prime-phylo_1.0.11.orig.tar.gz
dpkg-source: info: unpacking prime-phylo_1.0.11-1.debian.tar.gz
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
APT_CONFIG=/var/lib/sbuild/apt.conf
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-bd34ed37-8763-45c0-bdce-28cf4caff7b5
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
previous=N
runlevel=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package prime-phylo
dpkg-buildpackage: source version 1.0.11-1
dpkg-source --before-build prime-phylo-1.0.11
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem=cmake --parallel
dh_testdir -O--buildsystem=cmake -O--parallel
dh_auto_clean -O--buildsystem=cmake -O--parallel
dh_clean -O--buildsystem=cmake -O--parallel
debian/rules build-arch
dh build-arch --buildsystem=cmake --parallel
dh_testdir -a -O--buildsystem=cmake -O--parallel
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
-- The CXX compiler identification is GNU 4.6.4
-- 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
-- The Fortran compiler identification is GNU
-- 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 4.6.4
-- 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
-- Looking for Fortran sgemm
-- Looking for Fortran sgemm - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- A library with BLAS API found.
hittade /usr/lib/libblas.so
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Found BISON: /usr/bin/bison (found version "2.7.12-4996")
-- Found FLEX: /usr/bin/flex (found version "2.5.35")
-- Found MPI_C: /usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/arm-linux-gnueabihf/libdl.so;/usr/lib/arm-linux-gnueabihf/libnsl.so;/usr/lib/arm-linux-gnueabihf/libutil.so;/usr/lib/arm-linux-gnueabihf/libm.so;/usr/lib/arm-linux-gnueabihf/libdl.so
-- Found MPI_CXX: /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/arm-linux-gnueabihf/libdl.so;/usr/lib/arm-linux-gnueabihf/libnsl.so;/usr/lib/arm-linux-gnueabihf/libutil.so;/usr/lib/arm-linux-gnueabihf/libm.so;/usr/lib/arm-linux-gnueabihf/libdl.so
-- Found MPI_Fortran: /usr/lib/openmpi/lib/libmpi_f90.so;/usr/lib/openmpi/lib/libmpi_f77.so;/usr/lib/openmpi/lib/libmpi.so;/usr/lib/openmpi/lib/libopen-rte.so;/usr/lib/openmpi/lib/libopen-pal.so;/usr/lib/arm-linux-gnueabihf/libdl.so;/usr/lib/arm-linux-gnueabihf/libnsl.so;/usr/lib/arm-linux-gnueabihf/libutil.so;/usr/lib/arm-linux-gnueabihf/libm.so;/usr/lib/arm-linux-gnueabihf/libdl.so
-- Boost version: 1.49.0
-- Found the following Boost libraries:
-- mpi
-- serialization
-- Found LibXml2: /usr/lib/arm-linux-gnueabihf/libxml2.so (found version "2.9.1")
mpilib is /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
included path is
-- Configuring done
-- Generating done
-- Build files have been written to: /«PKGBUILDDIR»/obj-arm-linux-gnueabihf
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_build -a -O--buildsystem=cmake -O--parallel
make[1]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -H/«PKGBUILDDIR» -B/«PKGBUILDDIR»/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 84
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 1%] [ 1%] [BISON][MyParser2] Building parser with bison 2.7.12-4996
[FLEX][MyScanner2] Building scanner with flex 2.5.35
cd /«PKGBUILDDIR»/src/cxx/libraries/sfile && /usr/bin/flex -o/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c seqreader.l
cd /«PKGBUILDDIR»/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c gb.y
gb.y: warning: 1 nonterminal useless in grammar
gb.y: warning: 1 rule useless in grammar
gb.y:117.47-58: warning: nonterminal useless in grammar: darwin_entry
gb.y:258.19-61: warning: rule useless in grammar: darwin_entry: TEXT
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'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 85
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 86
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 87
[ 2%] [ 2%] [ 4%] [ 4%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o
Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/«PKGBUILDDIR»/src/cxx/libraries/sfile -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/sfile/gbread.c
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/«PKGBUILDDIR»/src/cxx/libraries/sfile -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/sfile/sfile.c
Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o
Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/«PKGBUILDDIR»/src/cxx/libraries/sfile -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile -I/«PKGBUILDDIR»/src/cxx/libraries/sfile -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/gb.tab.c
/«PKGBUILDDIR»/src/cxx/libraries/sfile/gbread.c: In function 'main':
/«PKGBUILDDIR»/src/cxx/libraries/sfile/gbread.c:17:5: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration]
/«PKGBUILDDIR»/src/cxx/libraries/sfile/sfile.c: In function 'seq_print':
/«PKGBUILDDIR»/src/cxx/libraries/sfile/sfile.c:265:7: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat]
/«PKGBUILDDIR»/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable 'date' set but not used [-Wunused-but-set-variable]
/«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:1377:7: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration]
gb.y: In function 'yyerror':
gb.y:291:8: warning: implicit declaration of function 'linenumber' [-Wimplicit-function-declaration]
gb.y: In function 'add_to_seq':
gb.y:402:9: warning: unused variable 'new_buf' [-Wunused-variable]
seqreader.l: In function 'seq_read':
seqreader.l:271:9: warning: unused variable 'code' [-Wunused-variable]
seqreader.l: At top level:
/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c:1832:17: warning: 'yyunput' defined but not used [-Wunused-function]
/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile/lexer.c:1873:16: warning: 'input' defined but not used [-Wunused-function]
Linking C shared library libprime-phylo-sfile.so
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo-sfile.dir/link.txt --verbose=1
/usr/bin/cc -fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -Wl,-z,relro -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'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 84 85 86 87
[ 4%] Built target prime-phylo-sfile
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 3
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 2
[ 6%] [ 6%] [BISON][MyParser] Building parser with bison 2.7.12-4996
[FLEX][MyScanner] Building scanner with flex 2.5.35
cd /«PKGBUILDDIR»/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c NHX.l
cd /«PKGBUILDDIR»/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c NHXparse.y
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /«PKGBUILDDIR» /«PKGBUILDDIR»/src/cxx/libraries/prime /«PKGBUILDDIR»/obj-arm-linux-gnueabihf /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DependInfo.cmake --color=
Scanning dependencies of target prime-phylo
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 4
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 5
[ 7%] [ 7%] [ 7%] [ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o
Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o
Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/NHXtree.c
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/NHXnode.c
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/NHXannotation.c
Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c
/«PKGBUILDDIR»/src/cxx/libraries/prime/NHXnode.c: In function 'NHX_debug_print':
/«PKGBUILDDIR»/src/cxx/libraries/prime/NHXnode.c:155:2: warning: format '%d' expects argument of type 'int', but argument 3 has type 'double' [-Wformat]
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 6
/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c:1320:17: warning: 'yyunput' defined but not used [-Wunused-function]
/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/lexer.c:1361:16: warning: 'input' defined but not used [-Wunused-function]
[ 9%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime/NHXparse.c
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 7
/«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:1422:7: warning: implicit declaration of function 'yytree_lex' [-Wimplicit-function-declaration]
NHXparse.y: In function 'read_tree':
NHXparse.y:351:5: warning: implicit declaration of function 'close' [-Wimplicit-function-declaration]
NHXparse.y: In function 'read_tree_string':
NHXparse.y:399:3: warning: implicit declaration of function 'read_from_string' [-Wimplicit-function-declaration]
NHXparse.y:404:3: warning: implicit declaration of function 'close_string_buffer' [-Wimplicit-function-declaration]
[ 9%] [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/AnError.cc
Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Beep.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BeepOption.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Hacks.cc
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[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ODESolver.cc
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[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/PRNG.cc
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[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/PrimeOptionMap.cc
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[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ProbabilityModel.cc
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[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/DiscreteGamma.cc
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[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Probability.cc
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[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Tokenizer.cc
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[ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TimeEstimator.cc
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[ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BranchSwapping.cc
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[ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/DiscTree.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/DiscTree.cc
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[ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscPtMaps.cc
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[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscTree.cc
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[ 19%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EpochPtMaps.cc
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[ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EpochPtSet.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EpochPtSet.cc
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[ 20%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochTree.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EpochTree.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EpochTree.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/InvMRCA.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/InvMRCA.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 19
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Node.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Node.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Node.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NodeMap.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/NodeMap.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 20
[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/NodeNodeMap.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/RandomTreeGenerator.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 21
[ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/StrStrMap.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 22
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Tree.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 25%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TreeAnalysis.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 23
[ 26%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TreeDiscretizer.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 24
[ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TreeDiscretizers.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TreeDiscretizers.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TreeMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TreeMCMC.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 25
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIO.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TreeIO.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TreeInputOutput.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]
/«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]
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 26
[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TreeIOTraits.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 27
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TreePerturbationEvent.cc
/«PKGBUILDDIR»/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)':
/«PKGBUILDDIR»/src/cxx/libraries/prime/TreeInputOutput.cc:118:22: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null]
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ConstRateModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 28
[ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Density2P_common.cc
/«PKGBUILDDIR»/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector<beep::SetOfNodes>*, beep::StrStrMap*, std::map<const beep::Node*, beep::Node*>*, std::map<const beep::Node*, unsigned int>*)':
/«PKGBUILDDIR»/src/cxx/libraries/prime/TreeInputOutput.cc:1049:40: warning: 'idInt' may be used uninitialized in this function [-Wuninitialized]
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 29
[ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Density2P_positive.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 32%] /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 30
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/Density2PMCMC.cc
Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeRateMCMC.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -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]
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable 'rparam' [-Wunused-variable]
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[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeRateModel_common.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 32
[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeWeightHandler.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
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[ 35%] [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeWeightMCMC.cc
Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/GammaDensity.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/InvGaussDensity.cc
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function 'void beep::EdgeWeightMCMC::showCurrentTree()':
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/LengthRateModel.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/LogNormDensity.cc
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[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/NormalDensity.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/UniformDensity.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 37
[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/VarRateModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SiteRateHandler.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 38
[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/DummyMCMC.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/MCMCModel.cc
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[ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/StdMCMCModel.cc
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[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/MCMCObject.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SimpleMCMC.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 41
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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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SimpleMCMCPostSample.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
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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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SimpleML.cc
/«PKGBUILDDIR»/src/cxx/libraries/prime/SimpleMCMC.cc: In member function 'virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)':
/«PKGBUILDDIR»/src/cxx/libraries/prime/SimpleMCMC.cc:78:14: warning: variable 'check_number_nonupdate' set but not used [-Wunused-but-set-variable]
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 42
[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/mcmc/MCMCSampler.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 43
[ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/mcmc/GSRSampler.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc
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[ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SimpleObserver.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 45
[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/MpiMCMC.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/MultiGSR.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 46
[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/MpiMultiGSR.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BDTreeGenerator.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:337:41: warning: operation on 'i' may be undefined [-Wsequence-point]
/«PKGBUILDDIR»/src/cxx/libraries/prime/MpiMultiGSR.cc:337:41: warning: operation on 'i' may be undefined [-Wsequence-point]
/«PKGBUILDDIR»/src/cxx/libraries/prime/MpiMultiGSR.cc:337:41: warning: operation on 'i' may be undefined [-Wsequence-point]
/tmp/ccdCGzB7.s: Assembler messages:
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/tmp/ccdCGzB7.s:5076: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
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/tmp/ccdCGzB7.s:5303: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
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/tmp/ccdCGzB7.s:26630: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
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/tmp/ccdCGzB7.s:26684: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:27325: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:27343: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:27379: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:27682: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:27700: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:27736: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28041: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28059: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28095: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28396: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28414: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28450: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28719: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28737: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28773: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28970: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:28987: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:29023: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:29245: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
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/tmp/ccdCGzB7.s:29299: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:30024: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:30041: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/ccdCGzB7.s:30077: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 47
[ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BirthDeathMCMC.cc
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[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BirthDeathProbs.cc
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[ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc
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[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/DiscBirthDeathProbs.cc
/tmp/cciMTv1c.s: Assembler messages:
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/tmp/cciMTv1c.s:10996: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:11033: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
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/tmp/cciMTv1c.s:27257: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc
/tmp/cciMTv1c.s:30866: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:30882: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:30918: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:31980: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:31996: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:32032: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:32341: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:32359: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:32395: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:35635: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:35652: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:35688: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:36078: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:36096: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:36132: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:42703: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:42719: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:42755: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:43045: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:43063: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:43099: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:44027: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:44045: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/tmp/cciMTv1c.s:44081: Warning: swp{b} use is deprecated for ARMv6 and ARMv7
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 51
[ 54%] [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o
Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscBDProbs.cc
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscGSR.cc
/«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]
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning: 'bool beep::EdgeDiscGSR::m_calculatedAtBars' [-Wreorder]
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder]
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'void beep::EdgeDiscGSR::convertDensitiesToProbabilities()':
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscGSR.cc:475:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable 'xpt' set but not used [-Wunused-but-set-variable]
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscGSR.cc:525:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/«PKGBUILDDIR»/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable 'parent' [-Wunused-variable]
/«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]
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EpochBDTMCMC.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 52
[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EpochBDTProbs.cc
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[ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EpochDLTRS.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/GammaMap.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 54
[ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/GuestTreeModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EnumerateReconciliationModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 55
[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 56
[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/fastGEM.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/fastGEM.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 57
[ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/LambdaMap.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]
/«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]
/«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]
/«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]
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 58
[ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/MaxReconciledTreeModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/PerturbationObservable.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 59
[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ReconciledTreeModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc
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[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc
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[ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ReconciliationModel.cc
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[ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ReconciliationSampler.cc
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[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ReconciliationTimeModel.cc
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[ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ReconciliationTimeMCMC.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]
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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 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ReconciliationTimeSampler.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/DLRSOrthoCalculator.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SetOfNodes.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TopTimeMCMC.cc
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[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/HybridBranchSwapping.cc
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[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/HybridTree.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/HybridTree.cc
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[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/HybridTreeIO.cc
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[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/HybridTreeInputOutput.cc
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[ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BDHybridTreeGenerator.cc
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[ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/HybridBDTreeGenerator.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/HybridGuestTreeModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/HybridHostTreeMCMC.cc
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[ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/HybridHostTreeModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 74
[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 75
[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/CacheSubstitutionModel.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc
In file included from /usr/include/c++/4.6/ext/hash_map:61:0,
from /«PKGBUILDDIR»/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8,
from /«PKGBUILDDIR»/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1:
/usr/include/c++/4.6/backward/backward_warning.h:33:2: 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]
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[ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/MatrixCache.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 77
[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/TransitionHandler.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/MatrixTransitionHandler.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 78
[ 81%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SeqIO.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SeqIO.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 79
[ 82%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SequenceGenerator.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
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[ 82%] [ 83%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SequenceType.cc
Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SequenceData.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SequenceData.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 83%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SubstitutionModel.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:288:54: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/«PKGBUILDDIR»/src/cxx/libraries/prime/SequenceData.cc:303:48: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 81
[ 84%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/SubstitutionMCMC.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 82
[ 85%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/LA_Vector.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 85%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/LA_Matrix.cc
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 83
[ 86%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime -I/«PKGBUILDDIR»/src/cxx/libraries/prime -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/«PKGBUILDDIR»/src/cxx/libraries -I/usr/lib/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -c /«PKGBUILDDIR»/src/cxx/libraries/prime/LA_DiagonalMatrix.cc
Linking CXX shared library libprime-phylo.so
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -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/liblapack.so -L/usr/lib/libblas.so -llapack -lblas -lxml2 /usr/lib/openmpi/lib/libmpi_cxx.so /usr/lib/openmpi/lib/libmpi.so /usr/lib/openmpi/lib/libopen-rte.so /usr/lib/openmpi/lib/libopen-pal.so -ldl -lnsl -lutil -lm -ldl -lboost_mpi-mt -lboost_serialization-mt ../sfile/libprime-phylo-sfile.so -lnsl -lutil -lm -lboost_mpi-mt -lboost_serialization-mt -Wl,-rpath,/usr/lib/liblapack.so:/usr/lib/libblas.so:/usr/lib/openmpi/lib:/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83
[ 86%] Built target prime-phylo
make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend
make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend
make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend
make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.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/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]: 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]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
[ 86%] [ 86%] Generating cmdline.c, cmdline.h
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
Generating cmdline.c, cmdline.h
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
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=
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 primeDTLSR
Scanning dependencies of target primeDLRS
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
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'
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
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/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
Scanning dependencies of target treesize
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build
Scanning dependencies of target primeGEM
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build
[ 87%] [ 87%] make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
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make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
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Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o
Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o
[ 88%] cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/applications/primeDTLSR -I/«PKGBUILDDIR»/src/cxx/applications/primeDTLSR -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /«PKGBUILDDIR»/src/cxx/applications/primeDTLSR/idolatrous.cc
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/applications/primeDLRS -I/«PKGBUILDDIR»/src/cxx/applications/primeDLRS -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -c /«PKGBUILDDIR»/src/cxx/applications/primeDLRS/primeDLRS.cc
[ 89%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/«PKGBUILDDIR»/src/cxx/applications/primeGEM -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /«PKGBUILDDIR»/src/cxx/applications/primeGEM/troyo.cc
Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/«PKGBUILDDIR»/src/cxx/tools/treesize -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -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]
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[ 90%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/treesize -I/«PKGBUILDDIR»/src/cxx/tools/treesize -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/treesize.dir/cmdline.c.o -c /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/treesize/cmdline.c
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Linking CXX executable treesize
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM -I/«PKGBUILDDIR»/src/cxx/applications/primeGEM -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/applications/primeGEM/cmdline.c
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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=
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/reroot -I/«PKGBUILDDIR»/src/cxx/tools/reroot -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/reroot.dir/reroot.cc.o -c /«PKGBUILDDIR»/src/cxx/tools/reroot/reroot.cc
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/usr/bin/c++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -rdynamic ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/openmpi/lib/libmpi_cxx.so /usr/lib/openmpi/lib/libmpi.so /usr/lib/openmpi/lib/libopen-rte.so /usr/lib/openmpi/lib/libopen-pal.so -ldl -lnsl -lutil -lm -ldl -lnsl -lutil -lm -lboost_mpi-mt -lboost_serialization-mt -Wl,-rpath,/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:/usr/lib/openmpi/lib:
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/reroot && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/reroot -I/«PKGBUILDDIR»/src/cxx/tools/reroot -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/reroot.dir/cmdline.c.o -c /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/reroot/cmdline.c
/«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]
make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
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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
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=
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Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o
cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/tree2leafnames -I/«PKGBUILDDIR»/src/cxx/tools/tree2leafnames -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -c /«PKGBUILDDIR»/src/cxx/tools/tree2leafnames/tree2leafnames.cc
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
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=
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/«PKGBUILDDIR»/src/cxx/tools/chainsaw -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -o CMakeFiles/chainsaw.dir/chainsaw.cc.o -c /«PKGBUILDDIR»/src/cxx/tools/chainsaw/chainsaw.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]
/«PKGBUILDDIR»/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)':
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/«PKGBUILDDIR»/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)':
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/«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]
/«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]
Linking CXX executable tree2leafnames
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/usr/bin/c++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -rdynamic ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/openmpi/lib/libmpi_cxx.so /usr/lib/openmpi/lib/libmpi.so /usr/lib/openmpi/lib/libopen-rte.so /usr/lib/openmpi/lib/libopen-pal.so -ldl -lnsl -lutil -lm -ldl -lnsl -lutil -lm -lboost_mpi-mt -lboost_serialization-mt ../../libraries/sfile/libprime-phylo-sfile.so -Wl,-rpath,/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/openmpi/lib:/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:
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cd /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -I/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/tools/chainsaw -I/«PKGBUILDDIR»/src/cxx/tools/chainsaw -I/usr/lib/openmpi/include -I/usr/lib/openmpi/include/openmpi -I/usr/lib/openmpi/include/openmpi/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 -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]
Linking CXX executable reconcile
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -rdynamic ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/openmpi/lib/libmpi_cxx.so /usr/lib/openmpi/lib/libmpi.so /usr/lib/openmpi/lib/libopen-rte.so /usr/lib/openmpi/lib/libopen-pal.so -ldl -lnsl -lutil -lm -ldl -lnsl -lutil -lm -lboost_mpi-mt -lboost_serialization-mt ../../libraries/sfile/libprime-phylo-sfile.so -Wl,-rpath,/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/openmpi/lib:/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:
/«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]
/«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]
Linking CXX executable reroot
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -rdynamic ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/openmpi/lib/libmpi_cxx.so /usr/lib/openmpi/lib/libmpi.so /usr/lib/openmpi/lib/libopen-rte.so /usr/lib/openmpi/lib/libopen-pal.so -ldl -lnsl -lutil -lm -ldl -lnsl -lutil -lm -lboost_mpi-mt -lboost_serialization-mt ../../libraries/sfile/libprime-phylo-sfile.so -Wl,-rpath,/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/openmpi/lib:/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:
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Linking CXX executable chainsaw
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -rdynamic ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/openmpi/lib/libmpi_cxx.so /usr/lib/openmpi/lib/libmpi.so /usr/lib/openmpi/lib/libopen-rte.so /usr/lib/openmpi/lib/libopen-pal.so -ldl -lnsl -lutil -lm -ldl -lnsl -lutil -lm -lboost_mpi-mt -lboost_serialization-mt ../../libraries/sfile/libprime-phylo-sfile.so -Wl,-rpath,/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/prime:/usr/lib/openmpi/lib:/«PKGBUILDDIR»/obj-arm-linux-gnueabihf/src/cxx/libraries/sfile:
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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/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=
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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/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/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.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/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=
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]: 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]: 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=
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build
make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build
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make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
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/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 89 90
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for `src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build'.
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for `src/cxx/tools/treesize/CMakeFiles/treesize.dir/build'.
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for `src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build'.
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 88
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 99 100
[ 88%] Built target primeGEM
make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend
[ 88%] [ 91%] [ 91%] Built target primeDLRS
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'
Built target treesize
make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend
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=
Built target primeDTLSR
make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.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/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=
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=
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/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=
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]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
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 -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build
make[3]: 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/build
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for `src/cxx/tools/showtree/CMakeFiles/showtree.dir/build'.
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 95 96
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for `src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build'.
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
[ 93%] /usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 91 92
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for `src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build'.
make[3]: Nothing to be done for `src/cxx/tools/reroot/CMakeFiles/reroot.dir/build'.
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 97 98
Built target showtree
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 93 94
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'
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=
[ 95%] Built target reconcile
[ 99%] [ 99%] Built target reroot
Built target tree2leafnames
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'
make[3]: Nothing to be done for `src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build'.
make[3]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_report /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 1
[100%] Built target chainsaw
make[2]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /«PKGBUILDDIR»/obj-arm-linux-gnueabihf/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for `preinstall'.
make[2]: Leaving directory `/«PKGBUILDDIR»/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "Debug"
-- Installing: /«PKGBUILDDIR»/debian/prime-phylo/usr/share/man/man1/primeGEM.1
-- Installing: /«PKGBUILDDIR»/debian/prime-phylo/usr/share/man/man1/primeDTLSR.1
-- Installing: /«PKGBUILDDIR»/debian/prime-phylo/usr/share/man/man1/primeDLRS.1
-- Installing: /«PKGBUILDDIR»/debian/prime-phylo/usr/share/man/man1/treesize.1
-- Installing: /«PKGBUILDDIR»/debian/prime-phylo/usr/share/man/man1/showtree.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/tree2leafnames.1
-- 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/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
dh_installman -a -O--buildsystem=cmake -O--parallel
dh_lintian -a -O--buildsystem=cmake -O--parallel
dh_perl -a -O--buildsystem=cmake -O--parallel
dh_link -a -O--buildsystem=cmake -O--parallel
dh_compress -a -O--buildsystem=cmake -O--parallel
dh_fixperms -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-sfile.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.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: 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: 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: 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: 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: 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: 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: 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: 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: 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: package could avoid a useless dependency if debian/prime-phylo/usr/bin/reroot debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so debian/prime-phylo/usr/bin/chainsaw debian/prime-phylo/usr/bin/tree2leafnames debian/prime-phylo/usr/bin/showtree debian/prime-phylo/usr/bin/primeDLRS debian/prime-phylo/usr/bin/primeGEM debian/prime-phylo/usr/bin/reconcile debian/prime-phylo/usr/bin/primeDTLSR debian/prime-phylo/usr/bin/treesize were not linked against libutil.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/prime-phylo/usr/bin/reroot debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so debian/prime-phylo/usr/bin/chainsaw debian/prime-phylo/usr/bin/tree2leafnames debian/prime-phylo/usr/bin/showtree debian/prime-phylo/usr/bin/primeDLRS debian/prime-phylo/usr/bin/primeGEM debian/prime-phylo/usr/bin/reconcile debian/prime-phylo/usr/bin/primeDTLSR debian/prime-phylo/usr/bin/treesize were not linked against libmpi_cxx.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/prime-phylo/usr/bin/reroot debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so debian/prime-phylo/usr/bin/chainsaw debian/prime-phylo/usr/bin/tree2leafnames debian/prime-phylo/usr/bin/showtree debian/prime-phylo/usr/bin/primeDLRS debian/prime-phylo/usr/bin/primeGEM debian/prime-phylo/usr/bin/reconcile debian/prime-phylo/usr/bin/primeDTLSR debian/prime-phylo/usr/bin/treesize were not linked against libnsl.so.1 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/prime-phylo/usr/bin/reroot debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so debian/prime-phylo/usr/bin/chainsaw debian/prime-phylo/usr/bin/tree2leafnames debian/prime-phylo/usr/bin/showtree debian/prime-phylo/usr/bin/primeDLRS debian/prime-phylo/usr/bin/primeGEM debian/prime-phylo/usr/bin/reconcile debian/prime-phylo/usr/bin/primeDTLSR debian/prime-phylo/usr/bin/treesize were not linked against libdl.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/prime-phylo/usr/bin/reroot debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so debian/prime-phylo/usr/bin/chainsaw debian/prime-phylo/usr/bin/tree2leafnames debian/prime-phylo/usr/bin/showtree debian/prime-phylo/usr/bin/primeDLRS debian/prime-phylo/usr/bin/primeGEM debian/prime-phylo/usr/bin/reconcile debian/prime-phylo/usr/bin/primeDTLSR debian/prime-phylo/usr/bin/treesize were not linked against libopen-pal.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/prime-phylo/usr/bin/reroot debian/prime-phylo/usr/lib/prime-phylo/libprime-phylo.so debian/prime-phylo/usr/bin/chainsaw debian/prime-phylo/usr/bin/tree2leafnames debian/prime-phylo/usr/bin/showtree debian/prime-phylo/usr/bin/primeDLRS debian/prime-phylo/usr/bin/primeGEM debian/prime-phylo/usr/bin/reconcile debian/prime-phylo/usr/bin/primeDTLSR debian/prime-phylo/usr/bin/treesize were not linked against libopen-rte.so.0 (they use none of the library's symbols)
dh_installdeb -a -O--buildsystem=cmake -O--parallel
dh_gencontrol -a -O--buildsystem=cmake -O--parallel
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package prime-phylo: unused substitution variable ${perl:Depends}
dh_md5sums -a -O--buildsystem=cmake -O--parallel
dh_builddeb -a -O--buildsystem=cmake -O--parallel
dpkg-deb: building package `prime-phylo' in `../prime-phylo_1.0.11-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../prime-phylo_1.0.11-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build prime-phylo-1.0.11
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20130706-1914
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
prime-phylo_1.0.11-1_armhf.changes:
───────────────────────────────────
Format: 1.8
Date: Mon, 17 Dec 2012 14:11:13 +0100
Source: prime-phylo
Binary: prime-phylo
Architecture: armhf
Version: 1.0.11-1
Distribution: jessie-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Erik Sjolund <erik.sjolund@gmail.com>
Description:
prime-phylo - bayesian estimation of gene trees taking the species tree into ac
Closes: 684039
Changes:
prime-phylo (1.0.11-1) unstable; urgency=low
.
* Initial release (Closes: #684039)
Checksums-Sha1:
05666f496fc68f9320fac4c383c55d7d803ddd06 973792 prime-phylo_1.0.11-1_armhf.deb
Checksums-Sha256:
13cb04589849c8e534b5cf9b4d642b631517c7b6bb4b1539d907a6424103e615 973792 prime-phylo_1.0.11-1_armhf.deb
Files:
c7087736ee25b78d84ceb868c8dd8459 973792 science optional prime-phylo_1.0.11-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
prime-phylo_1.0.11-1_armhf.deb
──────────────────────────────
new debian package, version 2.0.
size 973792 bytes: control archive=1591 bytes.
1112 bytes, 19 lines control
1653 bytes, 26 lines md5sums
Package: prime-phylo
Version: 1.0.11-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2401
Depends: perl, libblas3 | libblas.so.3 | libatlas3-base, libboost-mpi1.49.0 (>= 1.49.0-1), libboost-serialization1.49.0 (>= 1.49.0-1), libc6 (>= 2.7), libgcc1 (>= 1:4.4.0), liblapack3 | liblapack.so.3 | libatlas3-base, libopenmpi1.3, libstdc++6 (>= 4.6), 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.
drwxr-xr-x root/root 0 2013-07-06 19:13 ./
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/share/
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/share/man/
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/share/man/man1/
-rw-r--r-- root/root 987 2013-07-06 19:13 ./usr/share/man/man1/primeGEM.1.gz
-rw-r--r-- root/root 1992 2013-07-06 19:13 ./usr/share/man/man1/primeDTLSR.1.gz
-rw-r--r-- root/root 2154 2013-07-06 19:13 ./usr/share/man/man1/primeDLRS.1.gz
-rw-r--r-- root/root 608 2013-07-06 19:13 ./usr/share/man/man1/treesize.1.gz
-rw-r--r-- root/root 904 2013-07-06 19:13 ./usr/share/man/man1/showtree.1.gz
-rw-r--r-- root/root 654 2013-07-06 19:13 ./usr/share/man/man1/reconcile.1.gz
-rw-r--r-- root/root 886 2013-07-06 19:13 ./usr/share/man/man1/reroot.1.gz
-rw-r--r-- root/root 494 2013-07-06 19:13 ./usr/share/man/man1/tree2leafnames.1.gz
-rw-r--r-- root/root 653 2013-07-06 19:13 ./usr/share/man/man1/chainsaw.1.gz
-rw-r--r-- root/root 1284 2013-07-06 19:13 ./usr/share/man/man1/mcmc_analysis.1.gz
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/share/doc/
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/share/doc/prime-phylo/
-rw-r--r-- root/root 7324 2012-12-18 15:07 ./usr/share/doc/prime-phylo/copyright
-rw-r--r-- root/root 160 2012-12-18 15:07 ./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
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/share/lintian/
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 1167 2012-12-18 15:07 ./usr/share/lintian/overrides/prime-phylo
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/lib/
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/lib/prime-phylo/
-rw-r--r-- root/root 2001624 2013-07-06 19:13 ./usr/lib/prime-phylo/libprime-phylo.so
-rw-r--r-- root/root 42756 2013-07-06 19:13 ./usr/lib/prime-phylo/libprime-phylo-sfile.so
drwxr-xr-x root/root 0 2013-07-06 19:13 ./usr/bin/
-rwxr-xr-x root/root 33128 2012-12-17 15:52 ./usr/bin/mcmc_analysis
-rwxr-xr-x root/root 35120 2013-07-06 19:13 ./usr/bin/primeGEM
-rwxr-xr-x root/root 76356 2013-07-06 19:13 ./usr/bin/primeDTLSR
-rwxr-xr-x root/root 76288 2013-07-06 19:13 ./usr/bin/primeDLRS
-rwxr-xr-x root/root 18212 2013-07-06 19:13 ./usr/bin/treesize
-rwxr-xr-x root/root 26672 2013-07-06 19:13 ./usr/bin/showtree
-rwxr-xr-x root/root 34848 2013-07-06 19:13 ./usr/bin/reconcile
-rwxr-xr-x root/root 47200 2013-07-06 19:13 ./usr/bin/reroot
-rwxr-xr-x root/root 18204 2013-07-06 19:13 ./usr/bin/tree2leafnames
-rwxr-xr-x root/root 26604 2013-07-06 19:13 ./usr/bin/chainsaw
lrwxrwxrwx root/root 0 2013-07-06 19:13 ./usr/share/man/man1/primeGSRf.1.gz -> primeDLRS.1.gz
lrwxrwxrwx root/root 0 2013-07-06 19:13 ./usr/bin/primeGSRf -> primeDLRS
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 97468
Build-Time: 598
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 514
Job: prime-phylo_1.0.11-1
Machine Architecture: armhf
Package: prime-phylo
Package-Time: 1176
Source-Version: 1.0.11-1
Space: 97468
Status: successful
Version: 1.0.11-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20130706-1914
Build needed 00:19:36, 97468k disc space