Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/p/phyx/phyx_1.3+ds-1_amd64.buildinfo
Use metasnap for getting required timestamps
New buildinfo file: /tmp/phyx-1.3+ds-1n71ot900/phyx_1.3+ds-1_amd64.buildinfo
Get source package info: phyx=1.3+ds-1
Source URL: http://snapshot.notset.fr/mr/package/phyx/1.3+ds-1/srcfiles?fileinfo=1
env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=autoconf=2.71-2 automake=1:1.16.5-1.3 autopoint=0.21-6 autotools-dev=20220109.1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.38-3 binutils-common=2.38-3 binutils-x86-64-linux-gnu=2.38-3 bsdextrautils=2.38-3 bsdutils=1:2.38-3 build-essential=12.9 bzip2=1.0.8-5 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-19 dash=0.5.11+git20210903+057cd650a4ed-8 debconf=1.5.79 debhelper=13.6 debianutils=5.7-0.1 dh-autoreconf=20 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.7 dpkg-dev=1.21.7 dwz=0.14-1 file=1:5.41-3 findutils=4.9.0-2 g++=4:11.2.0-2 g++-11=11.2.0-19 gcc=4:11.2.0-2 gcc-11=11.2.0-19 gcc-11-base=11.2.0-19 gcc-12-base=12-20220319-1 gettext=0.21-6 gettext-base=0.21-6 grep=3.7-1 groff-base=1.22.4-8 gzip=1.12-1 hdf5-helpers=1.10.7+repack-4 hostname=3.23 init-system-helpers=1.62 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libaec-dev=1.0.6-1 libaec0=1.0.6-1 libarchive-zip-perl=1.68-1 libarmadillo-dev=1:10.8.2+dfsg-1+b1 libarmadillo10=1:10.8.2+dfsg-1+b1 libarpack2=3.8.0-1 libarpack2-dev=3.8.0-1 libasan6=11.2.0-19 libatlas-cpp-0.6-3=0.6.4-3 libatlas-cpp-0.6-dev=0.6.4-3 libatlas-cpp-0.6-tools=0.6.4-3 libatomic1=12-20220319-1 libattr1=1:2.5.1-1 libaudit-common=1:3.0.7-1 libaudit1=1:3.0.7-1+b1 libbinutils=2.38-3 libblas-dev=3.10.0-2 libblas3=3.10.0-2 libblkid1=2.38-3 libbrotli1=1.0.9-2+b3 libbz2-1.0=1.0.8-5 libc-bin=2.33-7 libc-dev-bin=2.33-7 libc6=2.33-7 libc6-dev=2.33-7 libcap-ng0=0.7.9-2.2+b2 libcap2=1:2.44-1 libcc1-0=12-20220319-1 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.38-3 libctf0=2.38-3 libcurl4=7.82.0-2 libcurl4-openssl-dev=7.82.0-2 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.262 libdebhelper-perl=13.6 libdpkg-perl=1.21.7 libelf1=0.186-1 libexpat1=2.4.8-1 libffi8=3.4.2-4 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.2.0-19 libgcc-s1=12-20220319-1 libgcrypt20=1.10.1-2 libgdbm-compat4=1.23-1 libgdbm6=1.23-1 libgfortran5=12-20220319-1 libglib2.0-0=2.72.0-1+b1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.3-4+b1 libgomp1=12-20220319-1 libgpg-error0=1.43-3 libgssapi-krb5-2=1.19.2-2+b1 libhdf5-103-1=1.10.7+repack-4 libhdf5-cpp-103-1=1.10.7+repack-4 libhdf5-dev=1.10.7+repack-4 libhdf5-fortran-102=1.10.7+repack-4 libhdf5-hl-100=1.10.7+repack-4 libhdf5-hl-cpp-100=1.10.7+repack-4 libhdf5-hl-fortran-100=1.10.7+repack-4 libhogweed6=3.7.3-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=12-20220319-1 libjpeg-dev=1:2.1.2-1 libjpeg62-turbo=1:2.1.2-1 libjpeg62-turbo-dev=1:2.1.2-1 libk5crypto3=1.19.2-2+b1 libkeyutils1=1.6.1-3 libkrb5-3=1.19.2-2+b1 libkrb5support0=1.19.2-2+b1 liblapack-dev=3.10.0-2 liblapack3=3.10.0-2 libldap-2.5-0=2.5.11+dfsg-1 liblsan0=12-20220319-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2.1 libmagic-mgc=1:5.41-3 libmagic1=1:5.41-3 libmount1=2.38-3 libmpc3=1.2.1-2 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3-2 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnlopt-cxx-dev=2.7.1-3 libnlopt-cxx0=2.7.1-3 libnlopt-dev=2.7.1-3 libnlopt0=2.7.1-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpcre2-8-0=10.39-4 libpcre3=2:8.39-14 libperl5.34=5.34.0-4 libpipeline1=1.5.5-1 libpsl5=0.21.0-1.2 libpython3-stdlib=3.10.4-1 libpython3.10-minimal=3.10.4-3 libpython3.10-stdlib=3.10.4-3 libquadmath0=12-20220319-1 libreadline8=8.1.2-1.2 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.28+dfsg-2+b1 libsasl2-modules-db=2.1.28+dfsg-2+b1 libseccomp2=2.5.3-2 libselinux1=3.3-1+b2 libsigsegv2=2.14-1 libsmartcols1=2.38-3 libsqlite3-0=3.38.2-1 libssh2-1=1.10.0-3 libssl-dev=1.1.1n-1 libssl1.1=1.1.1n-1 libstdc++-11-dev=11.2.0-19 libstdc++6=12-20220319-1 libsub-override-perl=0.09-2 libsuperlu-dev=5.3.0+dfsg1-2 libsuperlu5=5.3.0+dfsg1-2 libsystemd0=250.4-1 libsz2=1.0.6-1 libtasn1-6=4.18.0-4 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.7-3 libtsan0=11.2.0-19 libubsan1=12-20220319-1 libuchardet0=0.0.7-1 libudev1=250.4-1 libunistring2=1.0-1 libuuid1=2.38-3 libxml2=2.9.13+dfsg-1 libzstd1=1.5.2+dfsg-1 linux-libc-dev=5.16.18-1 login=1:4.11.1+dfsg1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.10.2-1 mawk=1.3.4.20200120-3+b1 media-types=7.1.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 patch=2.7.6-7 perl=5.34.0-4 perl-base=5.34.0-4 perl-modules-5.34=5.34.0-4 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 python3=3.10.4-1 python3-minimal=3.10.4-1 python3.10=3.10.4-3 python3.10-minimal=3.10.4-3 readline-common=8.1.2-1.2 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 util-linux=2.38-3 util-linux-extra=2.38-3 xz-utils=5.2.5-2.1 zlib1g=1:1.2.11.dfsg-4 zlib1g-dev=1:1.2.11.dfsg-4 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220416T025423Z/ bookworm main
deb-src http://snapshot.notset.fr/archive/debian/20220416T025423Z/ bookworm main
deb http://snapshot.notset.fr/archive/debian/20220414T090031Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d phyx=1.3+ds-1 && mkdir -p /build/phyx-0t0RkU && dpkg-source --no-check -x /*.dsc /build/phyx-0t0RkU/phyx-1.3+ds && chown -R builduser:builduser /build/phyx-0t0RkU" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phyx-0t0RkU/phyx-1.3+ds && env DEB_BUILD_OPTIONS="parallel=12" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1649940782" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/phyx-0t0RkU /tmp/phyx-1.3+ds-1n71ot900 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220414T090031Z unstable main
I: automatically chosen mode: root
I: chroot architecture amd64 is equal to the host's architecture
I: automatically chosen format: null
I: using /tmp/mmdebstrap.lm1sWMYoUE as tempdir
I: running apt-get update...
I: downloading packages with apt...
I: extracting archives...
I: installing essential packages...
I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.lm1sWMYoUE
Reading package lists...
Building dependency tree...
util-linux is already the newest version (2.38-3).
The following NEW packages will be installed:
  fakeroot libfakeroot
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 135 kB of archives.
After this operation, 406 kB of additional disk space will be used.
Get:1 http://snapshot.notset.fr/archive/debian/20220414T090031Z unstable/main amd64 libfakeroot amd64 1.28-1 [48.2 kB]
Get:2 http://snapshot.notset.fr/archive/debian/20220414T090031Z unstable/main amd64 fakeroot amd64 1.28-1 [87.2 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 135 kB in 1s (250 kB/s)
Selecting previously unselected package libfakeroot:amd64.
(Reading database ... 
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(Reading database ... 4700 files and directories currently installed.)
Preparing to unpack .../libfakeroot_1.28-1_amd64.deb ...
Unpacking libfakeroot:amd64 (1.28-1) ...
Selecting previously unselected package fakeroot.
Preparing to unpack .../fakeroot_1.28-1_amd64.deb ...
Unpacking fakeroot (1.28-1) ...
Setting up libfakeroot:amd64 (1.28-1) ...
Setting up fakeroot (1.28-1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Processing triggers for libc-bin (2.33-7) ...
I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/
I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220416T025423Z/ bookworm main
deb-src http://snapshot.notset.fr/archive/debian/20220416T025423Z/ bookworm main
deb http://snapshot.notset.fr/archive/debian/20220414T090031Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.lm1sWMYoUE
Get:1 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm InRelease [130 kB]
Hit:2 http://snapshot.notset.fr/archive/debian/20220414T090031Z unstable InRelease
Ign:3 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main Sources
Ign:4 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main amd64 Packages
Ign:3 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main Sources
Ign:4 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main amd64 Packages
Ign:3 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main Sources
Ign:4 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main amd64 Packages
Get:3 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main Sources [12.0 MB]
Get:4 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main amd64 Packages [11.4 MB]
Fetched 23.5 MB in 20s (1199 kB/s)
Reading package lists...
I: installing remaining packages inside the chroot...
I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.lm1sWMYoUE
I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d phyx=1.3+ds-1 && mkdir -p /build/phyx-0t0RkU && dpkg-source --no-check -x /*.dsc /build/phyx-0t0RkU/phyx-1.3+ds && chown -R builduser:builduser /build/phyx-0t0RkU"' exec /tmp/mmdebstrap.lm1sWMYoUE
Reading package lists...
NOTICE: 'phyx' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/phyx.git
Please use:
git clone https://salsa.debian.org/med-team/phyx.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1197 kB of source archives.
Get:1 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main phyx 1.3+ds-1 (dsc) [2025 B]
Get:2 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main phyx 1.3+ds-1 (tar) [1188 kB]
Get:3 http://snapshot.notset.fr/archive/debian/20220416T025423Z bookworm/main phyx 1.3+ds-1 (diff) [7560 B]
Fetched 1197 kB in 1s (1238 kB/s)
Download complete and in download only mode
W: Download is performed unsandboxed as root as file 'phyx_1.3+ds-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied)
dpkg-source: info: extracting phyx in /build/phyx-0t0RkU/phyx-1.3+ds
dpkg-source: info: unpacking phyx_1.3+ds.orig.tar.xz
dpkg-source: info: unpacking phyx_1.3+ds-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying build-more-programs.patch
dpkg-source: info: applying i386.patch
I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/phyx-0t0RkU/phyx-1.3+ds && env DEB_BUILD_OPTIONS="parallel=12" LANG="C.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1649940782" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.lm1sWMYoUE
dpkg-buildpackage: info: source package phyx
dpkg-buildpackage: info: source version 1.3+ds-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --sourcedirectory=src
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/phyx-0t0RkU/phyx-1.3+ds'
rm -rf src/phyx.logfile
if [ -r src/Makefile ]; then \
  /usr/bin/make -C src distclean; \
fi
make[1]: Leaving directory '/build/phyx-0t0RkU/phyx-1.3+ds'
   dh_autoreconf_clean -O--sourcedirectory=src
   dh_clean -O--sourcedirectory=src
 debian/rules binary-arch
dh binary-arch --sourcedirectory=src
   dh_update_autotools_config -a -O--sourcedirectory=src
   dh_autoreconf -a -O--sourcedirectory=src
   dh_auto_configure -a -O--sourcedirectory=src
	cd src && ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for fabs in -lm... yes
checking for nlopt_version in -lnlopt... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for nlopt.h... yes
checking for library containing wrapper_sgesv_... -larmadillo
checking for fenv.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for inline... inline
checking for size_t... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for GNU libc compatible malloc... yes
checking for working strtod... yes
checking for floor... yes
checking for pow... yes
checking for sqrt... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
   dh_auto_build -a -O--sourcedirectory=src
	cd src && make -j10
make[1]: Entering directory '/build/phyx-0t0RkU/phyx-1.3+ds/src'
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "citations.d" -o "citations.o" "citations.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "log.d" -o "log.o" "log.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "superdouble.d" -o "superdouble.o" "superdouble.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "timer.d" -o "timer.o" "timer.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "sequence.d" -o "sequence.o" "sequence.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_reader.d" -o "seq_reader.o" "seq_reader.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_utils.d" -o "seq_utils.o" "seq_utils.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_models.d" -o "seq_models.o" "seq_models.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "pairwise_alignment.d" -o "pairwise_alignment.o" "pairwise_alignment.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "aa2cdn.d" -o "aa2cdn.o" "aa2cdn.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_aa2cdn.d" -o "main_aa2cdn.o" "main_aa2cdn.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "node.d" -o "node.o" "node.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree.d" -o "tree.o" "tree.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree_reader.d" -o "tree_reader.o" "tree_reader.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree_utils.d" -o "tree_utils.o" "tree_utils.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "bd_sim.d" -o "bd_sim.o" "bd_sim.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_bd_sim.d" -o "main_bd_sim.o" "main_bd_sim.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_sample.d" -o "seq_sample.o" "seq_sample.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_boot.d" -o "main_boot.o" "main_boot.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_bp.d" -o "main_bp.o" "main_bp.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "concat.d" -o "concat.o" "concat.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_cat.d" -o "main_cat.o" "main_cat.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "clean_seq.d" -o "clean_seq.o" "clean_seq.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_clsq.d" -o "main_clsq.o" "main_clsq.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "clean_tree.d" -o "clean_tree.o" "clean_tree.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_cltr.d" -o "main_cltr.o" "main_cltr.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "collapse_tree.d" -o "collapse_tree.o" "collapse_tree.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_colt.d" -o "main_colt.o" "main_colt.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "comp_test.d" -o "comp_test.o" "comp_test.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_comp.d" -o "main_comp.o" "main_comp.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_consq.d" -o "main_consq.o" "main_consq.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_fqfilt.d" -o "main_fqfilt.o" "main_fqfilt.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "log_manip.d" -o "log_manip.o" "log_manip.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_log.d" -o "main_log.o" "main_log.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_info.d" -o "seq_info.o" "seq_info.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_lssq.d" -o "main_lssq.o" "main_lssq.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tree_info.d" -o "tree_info.o" "tree_info.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_lstr.d" -o "main_lstr.o" "main_lstr.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_mono.d" -o "main_mono.o" "main_mono.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_mrca.d" -o "main_mrca.o" "main_mrca.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_mrca_cut.d" -o "main_mrca_cut.o" "main_mrca_cut.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_mrca_name.d" -o "main_mrca_name.o" "main_mrca_name.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_nw.d" -o "main_nw.o" "main_nw.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "polytomy.d" -o "polytomy.o" "polytomy.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_poly.d" -o "main_poly.o" "main_poly.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "recode.d" -o "recode.o" "recode.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_recode.d" -o "main_recode.o" "main_recode.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_revcomp.d" -o "main_revcomp.o" "main_revcomp.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "edlib.d" -o "edlib.o" "edlib.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "relabel.d" -o "relabel.o" "relabel.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rls.d" -o "main_rls.o" "main_rls.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "upgma.d" -o "upgma.o" "upgma.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_upgma.d" -o "main_upgma.o" "main_upgma.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rlt.d" -o "main_rlt.o" "main_rlt.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "nj.d" -o "nj.o" "nj.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_nj.d" -o "main_nj.o" "main_nj.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rmk.d" -o "main_rmk.o" "main_rmk.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rms.d" -o "main_rms.o" "main_rms.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rmt.d" -o "main_rmt.o" "main_rmt.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_rr.d" -o "main_rr.o" "main_rr.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2fa.d" -o "main_s2fa.o" "main_s2fa.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2nex.d" -o "main_s2nex.o" "main_s2nex.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_s2phy.d" -o "main_s2phy.o" "main_s2phy.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "rate_model.d" -o "rate_model.o" "rate_model.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "state_reconstructor.d" -o "state_reconstructor.o" "state_reconstructor.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_nlopt.d" -o "optimize_state_reconstructor_nlopt.o" "optimize_state_reconstructor_nlopt.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "optimize_state_reconstructor_periods_nlopt.d" -o "optimize_state_reconstructor_periods_nlopt.o" "optimize_state_reconstructor_periods_nlopt.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "branch_segment.d" -o "branch_segment.o" "branch_segment.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "cont_models.d" -o "cont_models.o" "cont_models.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "seq_gen.d" -o "seq_gen.o" "seq_gen.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_seqgen.d" -o "main_seqgen.o" "main_seqgen.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_ssort.d" -o "main_ssort.o" "main_ssort.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "sstat.d" -o "sstat.o" "sstat.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_sstat.d" -o "main_sstat.o" "main_sstat.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_sw.d" -o "main_sw.o" "main_sw.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_t2new.d" -o "main_t2new.o" "main_t2new.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_t2nex.d" -o "main_t2nex.o" "main_t2nex.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tcol.d" -o "main_tcol.o" "main_tcol.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tcomb.d" -o "main_tcomb.o" "main_tcomb.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tgen.d" -o "tgen.o" "tgen.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tgen.d" -o "main_tgen.o" "main_tgen.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tlate.d" -o "tlate.o" "tlate.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tlate.d" -o "main_tlate.o" "main_tlate.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_trt.d" -o "main_trt.o" "main_trt.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "tscale.d" -o "tscale.o" "tscale.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_tscale.d" -o "main_tscale.o" "main_tscale.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "vcf_reader.d" -o "vcf_reader.o" "vcf_reader.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_vcf2fa.d" -o "main_vcf2fa.o" "main_vcf2fa.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "bd_fit.d" -o "bd_fit.o" "bd_fit.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_bd_fit.d" -o "main_bd_fit.o" "main_bd_fit.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_contrates.d" -o "main_contrates.o" "main_contrates.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "optimize_cont_models_nlopt.d" -o "optimize_cont_models_nlopt.o" "optimize_cont_models_nlopt.cpp"
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c -fmessage-length=0 -MMD -MP -MF "main_strec.d" -o "main_strec.o" "main_strec.cpp"
building pxaa2cdn
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxaa2cdn" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math aa2cdn.o main_aa2cdn.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
building pxbdsim
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxbdsim" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math bd_sim.o main_bd_sim.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
building pxboot
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxboot" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math seq_sample.o main_boot.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
building pxbp
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxbp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_bp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxaa2cdn.1.in > man/pxaa2cdn.1
cat man/pxboot.1.in > man/pxboot.1
building pxcat
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math concat.o main_cat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
building pxclsq
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxclsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math clean_seq.o main_clsq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxbdsim.1.in > man/pxbdsim.1
building pxcltr
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcltr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math clean_tree.o main_cltr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
building pxcolt
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcolt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math collapse_tree.o main_colt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxbp.1.in > man/pxbp.1
building pxcomp
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math comp_test.o main_comp.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
building pxconsq
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxconsq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_consq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxclsq.1.in > man/pxclsq.1
building pxfqfilt
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxfqfilt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_fqfilt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxcomp.1.in > man/pxcomp.1
building pxlog
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlog" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math log_manip.o main_log.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxcat.1.in > man/pxcat.1
bulding pxlssq
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlssq" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math seq_info.o main_lssq.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxcolt.1.in > man/pxcolt.1
building pxlstr
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxlstr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tree_info.o main_lstr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxcltr.1.in > man/pxcltr.1
building pxmono
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmono" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mono.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxconsq.1.in > man/pxconsq.1
cat man/pxlog.1.in > man/pxlog.1
building pxmrca
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrca" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
building pxmrcacut
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrcacut" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca_cut.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxmono.1.in > man/pxmono.1
building pxmrcaname
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxmrcaname" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_mrca_name.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxlssq.1.in > man/pxlssq.1
building pxnw
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxnw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_nw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxmrcaname.1.in > man/pxmrcaname.1
building pxpoly
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxpoly" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math polytomy.o main_poly.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxfqfilt.1.in > man/pxfqfilt.1
building pxrecode
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrecode" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math recode.o main_recode.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxmrca.1.in > man/pxmrca.1
building pxrevcomp
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrevcomp" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_revcomp.o edlib.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxpoly.1.in > man/pxpoly.1
building pxrls
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrls" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math relabel.o main_rls.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxrevcomp.1.in > man/pxrevcomp.1
building pxupgma
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxupgma" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math upgma.o main_upgma.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxlstr.1.in > man/pxlstr.1
cat man/pxnw.1.in > man/pxnw.1
cat man/pxrecode.1.in > man/pxrecode.1
building pxrlt
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrlt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math relabel.o main_rlt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
building pxnj
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxnj" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math nj.o main_nj.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
building pxrmk
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrmk" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rmk.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxrls.1.in > man/pxrls.1
building pxrms
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrms" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rms.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxmrcacut.1.in > man/pxmrcacut.1
cat man/pxupgma.1.in > man/pxupgma.1
building pxrmt
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrmt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rmt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
building pxrr
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxrr" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_rr.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
building pxs2fa
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_s2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxrlt.1.in > man/pxrlt.1
cat man/pxrmk.1.in > man/pxrmk.1
cat man/pxrms.1.in > man/pxrms.1
building pxs2nex
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_s2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
building pxs2phy
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxs2phy" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_s2phy.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
building pxseqgen
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxseqgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_seqgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo
cat man/pxnj.1.in > man/pxnj.1
building pxssort
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxssort" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_ssort.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxs2phy.1.in > man/pxs2phy.1
building pxsstat
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxsstat" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math sstat.o main_sstat.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
cat man/pxrr.1.in > man/pxrr.1
cat man/pxrmt.1.in > man/pxrmt.1
building pxsw
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxsw" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_sw.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
building pxt2new
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxt2new" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_t2new.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxssort.1.in > man/pxssort.1
building pxt2nex
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxt2nex" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_t2nex.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxsstat.1.in > man/pxsstat.1
building pxtcol
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtcol" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_tcol.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxs2fa.1.in > man/pxs2fa.1
building pxtcomb
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtcomb" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_tcomb.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxt2nex.1.in > man/pxt2nex.1
building pxtgen
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtgen" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tgen.o main_tgen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
cat man/pxs2nex.1.in > man/pxs2nex.1
cat man/pxseqgen.1.in > man/pxseqgen.1
cat man/pxtcomb.1.in > man/pxtcomb.1
cat man/pxtcol.1.in > man/pxtcol.1
building pxtlate
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtlate" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tlate.o main_tlate.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
building pxtrt
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtrt" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_trt.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
building pxtscale
cat man/pxtgen.1.in > man/pxtgen.1
building pxvcf2fa
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxtscale" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math tscale.o main_tscale.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wl,-z,relro -Wl,-z,now
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -o "pxvcf2fa" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math vcf_reader.o main_vcf2fa.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o -Wl,-z,relro -Wl,-z,now
building pxbdfit
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxbdfit" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math bd_fit.o main_bd_fit.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo
cat man/pxt2new.1.in > man/pxt2new.1
cat man/pxsw.1.in > man/pxsw.1
cat man/pxtlate.1.in > man/pxtlate.1
cat man/pxvcf2fa.1.in > man/pxvcf2fa.1
cat man/pxtscale.1.in > man/pxtscale.1
cat man/pxbdfit.1.in > man/pxbdfit.1
cat man/pxtrt.1.in > man/pxtrt.1
building pxcontrates
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxcontrates" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_contrates.o optimize_cont_models_nlopt.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo
cat man/pxcontrates.1.in > man/pxcontrates.1
building pxstrec
g++ -g -O2 -ffile-prefix-map=/build/phyx-0t0RkU/phyx-1.3+ds=. -fstack-protector-strong -Wformat -Werror=format-security -o "pxstrec" -O3 -std=c++14 -fopenmp -Wall -DOMP -ftree-vectorize -ffast-math main_strec.o ./utils.o ./citations.o ./log.o ./superdouble.o ./timer.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -llapack -lblas -lpthread -lm -lnlopt -larmadillo # -lgfortran
cat man/pxstrec.1.in > man/pxstrec.1
make[1]: Leaving directory '/build/phyx-0t0RkU/phyx-1.3+ds/src'
   create-stamp debian/debhelper-build-stamp
   dh_testroot -a -O--sourcedirectory=src
   dh_prep -a -O--sourcedirectory=src
   debian/rules override_dh_auto_install
make[1]: Entering directory '/build/phyx-0t0RkU/phyx-1.3+ds'
mkdir -p /build/phyx-0t0RkU/phyx-1.3+ds/debian/phyx/usr/bin
dh_auto_install -- PREFIX=/build/phyx-0t0RkU/phyx-1.3+ds/debian/phyx/usr
	cd src && make -j10 install DESTDIR=/build/phyx-0t0RkU/phyx-1.3\+ds/debian/phyx AM_UPDATE_INFO_DIR=no PREFIX=/build/phyx-0t0RkU/phyx-1.3\+ds/debian/phyx/usr
make[2]: Entering directory '/build/phyx-0t0RkU/phyx-1.3+ds/src'
mkdir -p /build/phyx-0t0RkU/phyx-1.3+ds/debian/phyx/usr/bin && install -m 0755 px* /build/phyx-0t0RkU/phyx-1.3+ds/debian/phyx/usr/bin
mkdir -p /build/phyx-0t0RkU/phyx-1.3+ds/debian/phyx/usr/share/man/man1 && install -m 0755 man/px*.1 /build/phyx-0t0RkU/phyx-1.3+ds/debian/phyx/usr/share/man/man1
make[2]: Leaving directory '/build/phyx-0t0RkU/phyx-1.3+ds/src'
#echo "#!/usr/bin/python3" > /build/phyx-0t0RkU/phyx-1.3+ds/debian/phyx/usr/bin/Phyx_Gui
#cat src/Phyx_Gui.py >> /build/phyx-0t0RkU/phyx-1.3+ds/debian/phyx/usr/bin/Phyx_Gui
make[1]: Leaving directory '/build/phyx-0t0RkU/phyx-1.3+ds'
   dh_installdocs -a -O--sourcedirectory=src
   dh_installchangelogs -a -O--sourcedirectory=src
   dh_installexamples -a -O--sourcedirectory=src
   dh_installman -a -O--sourcedirectory=src
   dh_installsystemduser -a -O--sourcedirectory=src
   dh_perl -a -O--sourcedirectory=src
   dh_link -a -O--sourcedirectory=src
   dh_strip_nondeterminism -a -O--sourcedirectory=src
   debian/rules override_dh_compress
make[1]: Entering directory '/build/phyx-0t0RkU/phyx-1.3+ds'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/build/phyx-0t0RkU/phyx-1.3+ds'
   dh_fixperms -a -O--sourcedirectory=src
   dh_missing -a -O--sourcedirectory=src
   dh_dwz -a -O--sourcedirectory=src
   dh_strip -a -O--sourcedirectory=src
   dh_makeshlibs -a -O--sourcedirectory=src
   dh_shlibdeps -a -O--sourcedirectory=src
   dh_installdeb -a -O--sourcedirectory=src
   dh_gencontrol -a -O--sourcedirectory=src
   dh_md5sums -a -O--sourcedirectory=src
   dh_builddeb -a -O--sourcedirectory=src
dpkg-deb: building package 'phyx' in '../phyx_1.3+ds-1_amd64.deb'.
dpkg-deb: building package 'phyx-dbgsym' in '../phyx-dbgsym_1.3+ds-1_amd64.deb'.
 dpkg-genbuildinfo --build=any -O../phyx_1.3+ds-1_amd64.buildinfo
 dpkg-genchanges --build=any -O../phyx_1.3+ds-1_amd64.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
I: running special hook: sync-out /build/phyx-0t0RkU /tmp/phyx-1.3+ds-1n71ot900
I: cleaning package lists and apt cache...
I: removing tempdir /tmp/mmdebstrap.lm1sWMYoUE...
I: success in 545.6305 seconds
md5: phyx-dbgsym_1.3+ds-1_amd64.deb: OK
md5: phyx_1.3+ds-1_amd64.deb: OK
sha1: phyx-dbgsym_1.3+ds-1_amd64.deb: OK
sha1: phyx_1.3+ds-1_amd64.deb: OK
sha256: phyx-dbgsym_1.3+ds-1_amd64.deb: OK
sha256: phyx_1.3+ds-1_amd64.deb: OK
Checksums: OK