phast →
1.4+dfsg-1 →
armhf → 2017-11-11 08:38:35
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| phast 1.4+dfsg-1 (armhf) Sat, 11 Nov 2017 08:20:17 +0000 |
+==============================================================================+
Package: phast
Version: 1.4+dfsg-1
Source Version: 1.4+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-865af20c-4a6d-4a45-aee2-0a7895280361' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.1 MB]
Fetched 22.5 MB in 26s (844 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'phast' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/phast.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/phast.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1862 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main phast 1.4+dfsg-1 (dsc) [2007 B]
Get:2 http://172.17.0.1/private buster-staging/main phast 1.4+dfsg-1 (tar) [1808 kB]
Get:3 http://172.17.0.1/private buster-staging/main phast 1.4+dfsg-1 (diff) [51.5 kB]
Fetched 1862 kB in 0s (5283 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phast-hUJ9x5/phast-1.4+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phast-hUJ9x5' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-QyYkvD/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-QyYkvD/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-QyYkvD/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ Packages [430 B]
Fetched 2106 B in 0s (3011 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
e2fsprogs-l10n
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 8 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13092 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man
Filtered Build-Depends: debhelper (>= 10), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man
dpkg-deb: building package 'sbuild-build-depends-phast-dummy' in '/<<BUILDDIR>>/resolver-QyYkvD/apt_archive/sbuild-build-depends-phast-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-phast-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ Sources [515 B]
Get:5 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ Packages [594 B]
Fetched 2442 B in 0s (3557 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install phast build dependencies (apt-based resolver)
-----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
e2fsprogs-l10n
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libblas-dev libblas3 libbsd0
libcroco3 libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0
libicu57 liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre16-3
libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libsigsegv2
libtimedate-perl libtmglib-dev libtmglib3 libtool libxml2 m4 man-db
po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
liblapack-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libblas-dev libblas3 libbsd0
libcroco3 libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0
libicu57 liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre16-3
libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libsigsegv2
libtimedate-perl libtmglib-dev libtmglib3 libtool libxml2 m4 man-db
po-debconf sbuild-build-depends-phast-dummy
0 upgraded, 42 newly installed, 0 to remove and 8 not upgraded.
Need to get 23.6 MB of archives.
After this operation, 82.9 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-QyYkvD/apt_archive ./ sbuild-build-depends-phast-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-2 [95.8 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.14 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-5 [609 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1+nmu1 [74.2 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.10.5 [978 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.5 [162 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.2.0-12 [191 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.7.1-4 [103 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-4 [112 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.7.1-4 [1508 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.7.1-4 [1564 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-4 [235 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-4 [227 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-4 [149 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-4 [565 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libtmglib3 armhf 3.7.1-4 [91.8 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libtmglib-dev armhf 3.7.1-4 [95.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libarchive-zip-perl (1.59-1) ...
Setting up libgfortran4:armhf (7.2.0-12) ...
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Setting up groff-base (1.22.3-9) ...
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No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-4) ...
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Setting up m4 (1.4.18-1) ...
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Setting up libcroco3:armhf (0.6.12-1) ...
Setting up libblas3:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Processing triggers for libc-bin (2.24-17) ...
Setting up autotools-dev (20161112.1+nmu1) ...
Setting up help2man (1.47.5) ...
Setting up libpcrecpp0v5:armhf (2:8.39-4) ...
Setting up libpcre32-3:armhf (2:8.39-4) ...
Setting up libpcre16-3:armhf (2:8.39-4) ...
Setting up bsdmainutils (9.0.14) ...
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 autopoint (0.19.8.1-4) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up libpcre3-dev:armhf (2:8.39-4) ...
Setting up gettext (0.19.8.1-4) ...
Setting up libblas-dev:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up liblapack3:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up liblapack-dev:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libtool (2.4.6-2) ...
Setting up libtmglib3:armhf (3.7.1-4) ...
Setting up po-debconf (1.0.20) ...
Setting up libtmglib-dev:armhf (3.7.1-4) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (10.10.5) ...
Setting up dh-autoreconf (14) ...
Setting up sbuild-build-depends-phast-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-17) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29.1-6+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-12 gcc-7_7.2.0-12 libc6-dev_2.24-17 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha3 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 binutils_2.29.1-6+rpi1 binutils-arm-linux-gnueabihf_2.29.1-6+rpi1 binutils-common_2.29.1-6+rpi1 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 coreutils_8.28-1 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-12 dash_0.5.8-2.5 debconf_1.5.64 debhelper_10.10.5 debianutils_4.8.2 dh-autoreconf_14 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.1-5 dmsetup_2:1.02.142-1 dpkg_1.19.0.4 dpkg-dev_1.19.0.4 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 e2fsprogs-l10n_1.43.7-1 fakeroot_1.22-1 fdisk_2.30.2-0.1 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6-base_6.4.0-6 gcc-7_7.2.0-12 gcc-7-base_7.2.0-12 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-5 gnupg-l10n_2.2.1-5 gnupg-utils_2.2.1-5 gpg_2.2.1-5 gpg-agent_2.2.1-5 gpg-wks-client_2.2.1-5 gpg-wks-server_2.2.1-5 gpgconf_2.2.1-5 gpgsm_2.2.1-5 gpgv_2.2.1-5 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 help2man_1.47.5 hostname_3.18 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.1-2 libapt-pkg5.0_1.6~alpha3 libarchive-zip-perl_1.59-1 libasan4_7.2.0-12 libassuan0_2.4.3-3 libatomic1_7.2.0-12 libattr1_1:2.4.47-2 libaudit-common_1:2.8.1-1 libaudit1_1:2.8.1-1 libbinutils_2.29.1-6+rpi1 libblas-dev_3.7.1-4 libblas3_3.7.1-4 libblkid1_2.30.2-0.1 libbsd0_0.8.6-2 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-17 libc-dev-bin_2.24-17 libc6_2.24-17 libc6-dev_2.24-17 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-12 libcilkrts5_7.2.0-12 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.22-1 libdebconfclient0_0.232 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.19.0.4 libdrm-common_2.4.84-2+rpi1 libdrm2_2.4.84-2+rpi1 libfakeroot_1.22-1 libfdisk1_2.30.2-0.1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-12 libgcc1_1:7.2.0-12 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libgfortran4_7.2.0-12 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-12 libgpg-error0_1.27-4 libhogweed4_3.3-2 libicu57_57.1-8 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 liblapack-dev_3.7.1-4 liblapack3_3.7.1-4 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre16-3_2:8.39-4 libpcre3_2:8.39-4 libpcre3-dev_2:8.39-4 libpcre32-3_2:8.39-4 libpcrecpp0v5_2:8.39-4 libperl5.26_5.26.1-2 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.20.1-2 libss2_1.43.7-1 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 libsystemd0_235-2 libtasn1-6_4.12-2.1 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtmglib-dev_3.7.1-4 libtmglib3_3.7.1-4 libtool_2.4.6-2 libubsan0_7.2.0-12 libudev1_235-2 libunistring2_0.9.7-2 libuuid1_2.30.2-0.1 libxml2_2.9.4+dfsg1-5 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.30.2-0.1 mountall_2.54 multiarch-support_2.24-17 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-2 perl-base_5.26.1-2 perl-modules-5.26_5.26.1-2 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phast-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_235-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017c-1 udev_235-2 util-linux_2.30.2-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Nov 5 23:09:40 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./phast_1.4+dfsg-1.dsc
dpkg-source: info: extracting phast in /<<BUILDDIR>>/phast-1.4+dfsg
dpkg-source: info: unpacking phast_1.4+dfsg.orig.tar.xz
dpkg-source: info: unpacking phast_1.4+dfsg-1.debian.tar.xz
dpkg-source: info: applying clapack.patch
dpkg-source: info: applying do_not_install_to_opt.patch
dpkg-source: info: applying use_debian_packaged_libpcre.patch
dpkg-source: info: applying use_debian_packaged_help2man.patch
dpkg-source: info: applying hardening.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-865af20c-4a6d-4a45-aee2-0a7895280361
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package phast
dpkg-buildpackage: info: source version 1.4+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build phast-1.4+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg'
dh_auto_clean
cd src && make clean
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/$dir && make clean ; done
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif'
rm -f /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../lib/*
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/dless'
rm -f *.o dless.help dlessP.help /<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../../bin/dless /<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../../bin/dlessP
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/dless'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/exoniphy'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.4+dfsg/src/exoniphy/../../bin/exoniphy
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/exoniphy'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastCons'
rm -f *.o /<<BUILDDIR>>/phast-1.4+dfsg/src/phastCons/../../bin/phastCons phastCons.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastCons'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastOdds'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.4+dfsg/src/phastOdds/../../bin/phastOdds
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastOdds'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastMotif'
rm -f *.o /<<BUILDDIR>>/phast-1.4+dfsg/src/phastMotif/../../bin/phastMotif
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastMotif'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloFit'
rm -f *.o /<<BUILDDIR>>/phast-1.4+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloFit'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloBoot'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.4+dfsg/src/phyloBoot/../../bin/phyloBoot
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloBoot'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloP'
rm -f *.o /<<BUILDDIR>>/phast-1.4+dfsg/src/phyloP/../../bin/phyloP phyloP.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloP'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel'
rm -f *.o /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/pbsDecode /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/pbsEncode /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/pbsScoreMatrix /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/pbsTrain /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/prequel pbsTrain.help pbsDecode.help pbsEncode.help prequel.help pbsScoreMatrix.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/util'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/indelHistory /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/hmm_train /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/hmm_tweak /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/stringiphy /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/draw_tree /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/clean_genes /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/treeGen /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/base_evolve /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/all_dists /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/tree_doctor /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/msa_diff /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/indelFit /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/consEntropy /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/convert_coords /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/hmm_view /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/phast /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/maf_parse /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/msa_split /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/modFreqs /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/eval_predictions /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/chooseLines /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/display_rate_matrix /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/makeHKY /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/phastBias /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/refeature /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/msa_view
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/util'
rm -rf ../bin ../lib ../doc
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg'
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg'
Type "make package" to create a tarball reflecting the current state of the CVS tree.
(cd src; make DESTDIR= CLAPACKPATH=/usr/lib )
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
mkdir -p ../bin ../lib
for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /<<BUILDDIR>>/phast-1.4+dfsg/src/$dir && make ; done
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/$dir && make ; done
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_matrix.c -o complex_matrix.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c memory_handler.c -o memory_handler.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c lists.c -o lists.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_vector.c -o prob_vector.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_vector.c -o complex_vector.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c numerical_opt.c -o numerical_opt.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c eigen.c -o eigen.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c markov_matrix.c -o markov_matrix.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c vector.c -o vector.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c stringsplus.c -o stringsplus.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c list_of_lists.c -o list_of_lists.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c hashtable.c -o hashtable.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c matrix.c -o matrix.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_matrix.c -o prob_matrix.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c misc.c -o misc.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
ar: creating /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'complex_matrix.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'memory_handler.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'memory_handler.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'lists.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'lists.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'prob_vector.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'prob_vector.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'complex_vector.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'complex_vector.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'numerical_opt.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'numerical_opt.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'eigen.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'eigen.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'markov_matrix.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'markov_matrix.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'vector.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'vector.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'stringsplus.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'stringsplus.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'list_of_lists.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'list_of_lists.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'hashtable.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'hashtable.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'matrix.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'matrix.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'prob_matrix.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'prob_matrix.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'misc.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o memory_handler.o lists.o prob_vector.o complex_vector.o numerical_opt.o eigen.o markov_matrix.o vector.o stringsplus.o list_of_lists.o hashtable.o matrix.o prob_matrix.o misc.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base/../../../lib/libphast.a' seems to have been created in deterministic mode. 'misc.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/base'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c sufficient_stats.c -o sufficient_stats.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf.c -o maf.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
maf.c: In function 'maf_read_cats_subset':
maf.c:29:41: warning: variable 'block_no' set but not used [-Wunused-but-set-variable]
int i, start_idx, length, max_tuples, block_no,
^~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf_block.c -o maf_block.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c local_alignment.c -o local_alignment.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c msa.c -o msa.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
msa.c: In function 'msa_read_fasta':
msa.c:257:40: warning: variable 'line_no' set but not used [-Wunused-but-set-variable]
int maxlen, i, nseqs, j, do_toupper, line_no;
^~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c multi_msa.c -o multi_msa.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'sufficient_stats.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'maf.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'maf.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'maf_block.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'maf_blockX' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'local_alignment.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'local_alignment.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'msa.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'msa.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'multi_msa.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a sufficient_stats.o maf.o maf_block.o local_alignment.o msa.o multi_msa.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa/../../../lib/libphast.a' seems to have been created in deterministic mode. 'multi_msa.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/msa'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c bed.c -o bed.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c wig.c -o wig.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c genepred.c -o genepred.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c category_map.c -o category_map.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c gff.c -o gff.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a' seems to have been created in deterministic mode. 'bed.oX' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a' seems to have been created in deterministic mode. 'wig.oX' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a' seems to have been created in deterministic mode. 'wig.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a' seems to have been created in deterministic mode. 'genepred.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a' seems to have been created in deterministic mode. 'genepred.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a' seems to have been created in deterministic mode. 'category_map.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a' seems to have been created in deterministic mode. 'category_map.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a' seems to have been created in deterministic mode. 'gff.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a bed.o wig.o genepred.o category_map.o gff.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature/../../../lib/libphast.a' seems to have been created in deterministic mode. 'gff.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/feature'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c em.c -o em.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c hmm.c -o hmm.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a' seems to have been created in deterministic mode. 'em.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a' seems to have been created in deterministic mode. 'hmm.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm/../../../lib/libphast.a' seems to have been created in deterministic mode. 'hmm.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c dgamma.c -o dgamma.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_likelihoods.c -o tree_likelihoods.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_distrib.c -o subst_distrib.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_history.c -o indel_history.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_fit.c -o phylo_fit.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_column.c -o fit_column.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_mods.c -o subst_mods.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_feature.c -o fit_feature.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_em.c -o fit_em.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p.c -o phylo_p.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p_print.c -o phylo_p_print.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c trees.c -o trees.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_mod.c -o indel_mod.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_model.c -o tree_model.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c bgc_hmm.c -o bgc_hmm.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'dgamma.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'phast_cons.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'phast_cons.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'tree_likelihoods.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'tree_likelihoods.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'subst_distrib.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'subst_distrib.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'indel_history.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'indel_history.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'phylo_fit.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'phylo_fit.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'fit_column.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'fit_column.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'subst_mods.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'subst_mods.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'fit_feature.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'fit_feature.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'fit_em.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'fit_em.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'phylo_p.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'phylo_p.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'phylo_p_print.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'phylo_p_print.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'trees.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'trees.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'indel_mod.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'indel_mod.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'tree_model.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'tree_model.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'bgc_hmm.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a dgamma.o phast_cons.o tree_likelihoods.o subst_distrib.o indel_history.o phylo_fit.o fit_column.o subst_mods.o fit_feature.o fit_em.o phylo_p.o phylo_p_print.o trees.o indel_mod.o tree_model.o bgc_hmm.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo/../../../lib/libphast.a' seems to have been created in deterministic mode. 'bgc_hmm.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phylo_hmm.c -o phylo_hmm.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c gap_patterns.c -o gap_patterns.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phylo_hmm.o gap_patterns.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a' seems to have been created in deterministic mode. 'phylo_hmm.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a' seems to have been created in deterministic mode. 'gap_patterns.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phylo_hmm.o gap_patterns.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a' seems to have been created in deterministic mode. 'gap_patterns.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c tfbs.c -o tfbs.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
tfbs.c: In function 'ms_read':
tfbs.c:219:32: warning: variable 'line_no' set but not used [-Wunused-but-set-variable]
int i, nseqs, j, do_toupper, line_no;
^~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c motif.c -o motif.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif/../../../lib/libphast.a tfbs.o motif.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif/../../../lib/libphast.a' seems to have been created in deterministic mode. 'tfbs.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif/../../../lib/libphast.a' seems to have been created in deterministic mode. 'motif.oX' will always be updated. Please consider passing the U flag to ar to avoid the problem.
ar rs /<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif/../../../lib/libphast.a tfbs.o motif.o
make[4]: Warning: Archive '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif/../../../lib/libphast.a' seems to have been created in deterministic mode. 'motif.o' will always be updated. Please consider passing the U flag to ar to avoid the problem.
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib/motif'
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/lib'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/dless'
../munge-help.sh dless.help_src > dless.help
../munge-help.sh dlessP.help_src > dlessP.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../..\" -fno-strict-aliasing -c bd_phylo_hmm.c -o bd_phylo_hmm.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../../bin/dless dless.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../..\" -fno-strict-aliasing -c dlessP.c -o dlessP.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/dless/../../bin/dlessP dlessP.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/dless'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/exoniphy'
../munge-help.sh exoniphy.help_src > exoniphy.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/exoniphy/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/exoniphy'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastCons'
../munge-help.sh phastCons.help_src > phastCons.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/phastCons/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastCons'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastOdds'
../munge-help.sh phastOdds.help_src > phastOdds.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/phastOdds/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastOdds'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastMotif'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
phastMotif.c: In function 'main':
phastMotif.c:131:13: warning: variable 'separate_backgd' set but not used [-Wunused-but-set-variable]
int i, j, separate_backgd = 0,
^~~~~~~~~~~~~~~
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/phastMotif/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phastMotif'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloFit'
../munge-help.sh phyloFit.help_src > phyloFit.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloFit/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloFit'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloBoot'
../munge-help.sh phyloBoot.help_src > phyloBoot.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloBoot/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloBoot'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloP'
../munge-help.sh phyloP.help_src > phyloP.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloP/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/phyloP'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel'
../munge-help.sh pbsTrain.help_src > pbsTrain.help
../munge-help.sh pbsDecode.help_src > pbsDecode.help
../munge-help.sh pbsEncode.help_src > pbsEncode.help
../munge-help.sh prequel.help_src > prequel.help
../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c simplex_grid.c -o simplex_grid.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbs_code.c -o pbs_code.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/pbsDecode pbsDecode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/pbsEncode pbsEncode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/pbsTrain pbsTrain.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/prequel/../../bin/prequel prequel.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/prequel'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/util'
../munge-help.sh phastBias.help_src > phastBias.help
../munge-help.sh indelFit.help_src > indelFit.help
../munge-help.sh modFreqs.help_src > modFreqs.help
../munge-help.sh makeHKY.help_src > makeHKY.help
../munge-help.sh indelHistory.help_src > indelHistory.help
../munge-help.sh clean_genes.help_src > clean_genes.help
../munge-help.sh base_evolve.help_src > base_evolve.help
../munge-help.sh phast.help_src > phast.help
../munge-help.sh treeGen.help_src > treeGen.help
../munge-help.sh msa_diff.help_src > msa_diff.help
../munge-help.sh consEntropy.help_src > consEntropy.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
display_rate_matrix.c: In function 'do_context_dependent_ti_tv':
display_rate_matrix.c:204:8: warning: variable 'tuple_i' set but not used [-Wunused-but-set-variable]
char tuple_i[mod->order+2], tuple_j[mod->order+2];
^~~~~~~
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.4+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.3\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o
<command-line>:0:0: warning: "PHAST_HOME" redefined
<command-line>:0:0: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.4+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src/util'
mkdir -p ../doc/man/
Generating man pages...
USAGE: convert_coords -m <msa_fname> -f <feature_fname> [-s <src_frame>] [-d <dest_frame>] [-p] [-n] [-i PHYLIP|FASTA|MPM]
DESCRIPTION:
Converts coordinates of features in a GFF file according to a multiple
alignment. Will map from the coordinate system of any sequence to any
other sequence; can also map to or from the coordinate system of the
entire alignment. In addition, supports translation of coordinates by
specified offset.
OPTIONS:
-m <msa_fname> (required) Name of file in which alignment is defined.
-f <gff_fname> (required) Name of file in which features are defined (GFF).
-s <src_frame> Index of frame of reference for feature coordinates, as
defined in the GFF file. Use an integer 1-N (if N seqs)
or 0 to indicate the coordinate system of the alignment
as a whole. Default behavior is to match features with
alignment sequences by name (feature by feature).
-d <dest_frame> Index of destination frame of reference. Default is 0
(whole MSA).
-p <coord_off> Positive coordinate offset. This value will be
added to all coordinates. Useful when
the alignment (or sequence) for which the coordinates
are specified is a sub-alignment of yours.
-n <coord_off> Negative coordinate offset. This value will be
subtracted from all coordinates. Useful when your
alignment is a sub-alignment of the alignment (or
sequence) for which the coordinates are specified.
-i FASTA|PHYLIP|MPM|SS
Alignment format. Default is to guess format from file
contents
PROGRAM: draw_tree
DESCRIPTION: Produces a simple postscript rendering of a tree.
USAGE: draw_tree [-dbvs] <tree.nh>|<tree.mod>
OPTIONS:
<tree_fname> (Required) File name of tree (expected to be in
Newick format, unless filename ends with '.mod', in
which case expected to be a tree model file).
-d Print "diagonal" branches, instead of "right-angle" or
"square" ones (produces a "cladogram", as opposed to a
"phenogram"). This option implies -s.
-b Suppress branch lengths.
-v Vertical layout.
-s Don't draw branches to scale.
Done.
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<BUILDDIR>>/phast-1.4\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg'
(cd src; make install DESTDIR=/<<BUILDDIR>>/phast-1.4+dfsg/debian/phast )
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.4+dfsg/src'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
mkdir -p /<<BUILDDIR>>/phast-1.4+dfsg/debian/phast/usr/bin/
mkdir -p /<<BUILDDIR>>/phast-1.4+dfsg/debian/phast/usr/share/phast/data/
mkdir -p /<<BUILDDIR>>/phast-1.4+dfsg/debian/phast/usr/share/man/man1/
cp ../bin/* /<<BUILDDIR>>/phast-1.4+dfsg/debian/phast/usr/bin/
cp -R ../data/* /<<BUILDDIR>>/phast-1.4+dfsg/debian/phast/usr/share/phast/data/
cp -R ../doc/man/* /<<BUILDDIR>>/phast-1.4+dfsg/debian/phast/usr/share/man/man1/
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.4+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/all_dists debian/phast/usr/bin/hmm_train debian/phast/usr/bin/phastMotif debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/treeGen debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/indelHistory debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/refeature debian/phast/usr/bin/phastCons debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phyloFit debian/phast/usr/bin/msa_view debian/phast/usr/bin/base_evolve debian/phast/usr/bin/consEntropy debian/phast/usr/bin/hmm_view debian/phast/usr/bin/draw_tree debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/dlessP debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/modFreqs debian/phast/usr/bin/clean_genes debian/phast/usr/bin/indelFit debian/phast/usr/bin/chooseLines debian/phast/usr/bin/phastBias debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/phyloP debian/phast/usr/bin/msa_split debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/maf_parse debian/phast/usr/bin/makeHKY debian/phast/usr/bin/prequel debian/phast/usr/bin/convert_coords debian/phast/usr/bin/exoniphy debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/msa_diff debian/phast/usr/bin/phast debian/phast/usr/bin/phastOdds debian/phast/usr/bin/dless were not linked against libblas.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/all_dists debian/phast/usr/bin/hmm_train debian/phast/usr/bin/phastMotif debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/treeGen debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/indelHistory debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/refeature debian/phast/usr/bin/phastCons debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phyloFit debian/phast/usr/bin/msa_view debian/phast/usr/bin/base_evolve debian/phast/usr/bin/consEntropy debian/phast/usr/bin/hmm_view debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/dlessP debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/modFreqs debian/phast/usr/bin/clean_genes debian/phast/usr/bin/indelFit debian/phast/usr/bin/chooseLines debian/phast/usr/bin/phastBias debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/phyloP debian/phast/usr/bin/msa_split debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/maf_parse debian/phast/usr/bin/makeHKY debian/phast/usr/bin/prequel debian/phast/usr/bin/convert_coords debian/phast/usr/bin/exoniphy debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/msa_diff debian/phast/usr/bin/phastOdds debian/phast/usr/bin/dless were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/all_dists debian/phast/usr/bin/hmm_train debian/phast/usr/bin/phastMotif debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/treeGen debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/indelHistory debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/refeature debian/phast/usr/bin/phastCons debian/phast/usr/bin/stringiphy debian/phast/usr/bin/phyloFit debian/phast/usr/bin/msa_view debian/phast/usr/bin/base_evolve debian/phast/usr/bin/consEntropy debian/phast/usr/bin/hmm_view debian/phast/usr/bin/draw_tree debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/dlessP debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/modFreqs debian/phast/usr/bin/clean_genes debian/phast/usr/bin/indelFit debian/phast/usr/bin/chooseLines debian/phast/usr/bin/phastBias debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/phyloP debian/phast/usr/bin/msa_split debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/maf_parse debian/phast/usr/bin/makeHKY debian/phast/usr/bin/prequel debian/phast/usr/bin/convert_coords debian/phast/usr/bin/exoniphy debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/msa_diff debian/phast/usr/bin/phast debian/phast/usr/bin/phastOdds debian/phast/usr/bin/dless were not linked against libtmglib.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.4+dfsg-1_armhf.deb'.
dpkg-deb: building package 'phast' in '../phast_1.4+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../phast_1.4+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build phast-1.4+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-11-11T08:37:04Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phast_1.4+dfsg-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Tue, 12 Sep 2017 10:11:38 +0200
Source: phast
Binary: phast
Architecture: armhf
Version: 1.4+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phast - phylogenetic analysis with space/time models
Closes: 875555
Changes:
phast (1.4+dfsg-1) unstable; urgency=medium
.
* Initial release (Closes: #875555)
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Checksums-Sha256:
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Files:
11bed37ec85b5c26ba9fe0bea368e490 23219920 debug optional phast-dbgsym_1.4+dfsg-1_armhf.deb
0ef9937be258038b4e81ae76a54879e7 4698 science optional phast_1.4+dfsg-1_armhf.buildinfo
78a65876b561ef97886511c51839d92b 1239444 science optional phast_1.4+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phast-dbgsym_1.4+dfsg-1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 23219920 bytes: control archive=2348 bytes.
1969 bytes, 12 lines control
4240 bytes, 40 lines md5sums
Package: phast-dbgsym
Source: phast
Version: 1.4+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 25706
Depends: phast (= 1.4+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for phast
Build-Ids: 09789d8622e7f58f4d96401e62e64006201e503d 11db138335a475fd9b0613a6a61a7e6cd8525ee6 1653cc22339bda5687ff478fb27f0915efe8615c 24351197593ac653069a3e4773c172c31acf4d6d 254284d58b2ff0839cc86c7b8ded4f8df42c2c04 3bd391aaae1a4383e3d6775ad6d803f948d13914 3d8fd67caa4533dbd3f61c2d8a69279213b65284 4e00c6a3aba4221259a701e060bdab5411848107 4e58ab7fd6ba020bbe3cd7f78adb358c7b127b71 51406ab15f686cfbc9bd05f19c68189982eb681b 5ead6d50b1f6628faed831eddd76f8c2b3e0fe1f 654c6c2d1f6927e7837474e050d08f2af539fc79 691b17eb7a1cfb2d02c35bb8a4cb27d5b2333803 6b434bfe7810e38d635795807cb94f83001e7a08 702cec2ded61a0235d1d99fce74282918c0b6f8f 7376608fbde7d5af77839fa434d968ca2a3be6bf 7475a89a93e6e7a854835d3194df9a35816f79c3 7e0246a4510aaaad21188f82ffd28b3ab04b1b8e 83bc01d8a559711fb3e860adcd25f6d6bba8f295 91811b6ff5006de0ac5042b8e221737ac44fd0e2 935c4fe3bbcea88ddec1c710427bd1e0a64f52ca 9b9a9f2832435887f6ace0e2815212e424c91643 9f2369e14c4818c343914943ba0ef5b07bc660f5 a1507203a36ad95b26666888b33dc37d5b2a19dd aa11be14c1a792bd30d9a93f86c9b12559b85270 afc71c503fd436495eb40b94b2bc9f9e146669c0 b4584f35a702f62a1760ae5c8398c0803b40b15e b73adf1e297465e48c33f5cf3c50ae3e450a4291 c0d1bdca22be71044e01244960841791bb3150c5 c28cc610b4d04947e1bc1c02d73915d2625837f1 c7fe121c1fdbdde71b747be127ed30e2550633cd d730811744246bc063fa900536b82c871ead20e9 dc876cb5c727281f6c4442e08cdf20974fb003e7 e03065ebcc0569c17a3e7e7edfd1bd896113cccb e37fdcb5dcd74a233f76e59284cd85ff19c30fe4 e44f61f4f6c48096434e6a7adb8d4d01fb33627b e956a6479b0456b60751e8d391a50700c0bf996c eeae8d35b9c9b21d7b15ddf63255960aa9240caf f36e416cea28cc5d2b5a47e4ebf843e8c961a5f3 fa625bbd392f1d2d26ed9ef6fdff01b816746ad0
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phast_1.4+dfsg-1_armhf.deb
--------------------------
new Debian package, version 2.0.
size 1239444 bytes: control archive=4744 bytes.
1133 bytes, 22 lines control
12208 bytes, 165 lines md5sums
Package: phast
Version: 1.4+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 22271
Depends: libblas3 | libblas.so.3, libc6 (>= 2.23), liblapack3 | liblapack.so.3, libpcre3, libtmglib3
Section: science
Priority: optional
Homepage: http://compgen.cshl/edu/phast
Description: phylogenetic analysis with space/time models
PHAST is a software package for comparative and evolutionary genomics.
It consists of about half a dozen major programs, plus more than a dozen
utilities for manipulating sequence alignments, phylogenetic trees, and
genomic annotations. For the most part, PHAST focuses on two kinds of
applications: the identification of novel functional elements, including
protein-coding exons and evolutionarily conserved sequences; and
statistical phylogenetic modeling, including estimation of model
parameters, detection of signatures of selection, and reconstruction of
ancestral sequences.
.
PHAST does not support phylogeny reconstruction or sequence alignment,
and it is designed for use with DNA sequences only (see Comparison).
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-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc4.mod
-rw-r--r-- root/root 62237 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.gc5.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cds-2.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc1.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc2.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc3.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc4.mod
-rw-r--r-- root/root 62237 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.gc5.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cds-3.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc1.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc2.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc3.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc4.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cns.gc5.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.cns.mod
-rw-r--r-- root/root 49950 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc1.mod
-rw-r--r-- root/root 49950 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc2.mod
-rw-r--r-- root/root 49950 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc3.mod
-rw-r--r-- root/root 49950 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc4.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.gc5.mod
-rw-r--r-- root/root 49950 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.ncns.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc1.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc2.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc3.mod
-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.gc4.mod
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-rw-r--r-- root/root 49949 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/mammals/r3.noncoding.mod
-rw-r--r-- root/root 529 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models
-rw-r--r-- root/root 549 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-gc1
-rw-r--r-- root/root 549 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-gc2
-rw-r--r-- root/root 549 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-gc3
-rw-r--r-- root/root 549 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-gc4
-rw-r--r-- root/root 549 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-gc5
-rw-r--r-- root/root 523 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-no-cns
-rw-r--r-- root/root 539 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-no-cns-gc1
-rw-r--r-- root/root 539 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-no-cns-gc2
-rw-r--r-- root/root 539 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-no-cns-gc3
-rw-r--r-- root/root 539 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-no-cns-gc4
-rw-r--r-- root/root 539 2017-09-12 08:11 ./usr/share/phast/data/exoniphy/models-no-cns-gc5
drwxr-xr-x root/root 0 2017-09-12 08:11 ./usr/share/phast/data/phastCons/
-rw-r--r-- root/root 103302 2017-09-12 08:11 ./usr/share/phast/data/phastCons/simple-coding-indels.hmm
-rw-r--r-- root/root 584 2017-09-12 08:11 ./usr/share/phast/data/phastCons/simple-coding.hmm
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 180272
Build-Time: 656
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 302
Job: phast_1.4+dfsg-1
Machine Architecture: armhf
Package: phast
Package-Time: 1007
Source-Version: 1.4+dfsg-1
Space: 180272
Status: successful
Version: 1.4+dfsg-1
--------------------------------------------------------------------------------
Finished at 2017-11-11T08:37:04Z
Build needed 00:16:47, 180272k disc space