Raspbian Package Auto-Building

Build log for phast (1.6+dfsg-1) on armhf

phast → 1.6+dfsg-1 → armhf → 2021-09-05 07:59:48 

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01

+==============================================================================+
| phast 1.6+dfsg-1 (armhf)                     Sun, 05 Sep 2021 07:53:43 +0000 |
+==============================================================================+

Package: phast
Version: 1.6+dfsg-1
Source Version: 1.6+dfsg-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-a54f1b74-b200-495c-a3a4-30a378eb855d' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.3 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.7 MB in 10s (2657 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://salsa.debian.org/med-team/phast.git
Please use:
git clone https://salsa.debian.org/med-team/phast.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1864 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main phast 1.6+dfsg-1 (dsc) [2025 B]
Get:2 http://172.17.0.1/private bookworm-staging/main phast 1.6+dfsg-1 (tar) [1809 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main phast 1.6+dfsg-1 (diff) [53.2 kB]
Fetched 1864 kB in 0s (4648 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phast-0fequ9/phast-1.6+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phast-0fequ9' 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-LDLGYg/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-LDLGYg/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-LDLGYg/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9864 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:
  netbase
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 63 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-LDLGYg/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (66.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12488 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-compat (= 13), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, libf2c2-dev, libatlas-base-dev, help2man
Filtered Build-Depends: debhelper-compat (= 13), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, libf2c2-dev, libatlas-base-dev, help2man
dpkg-deb: building package 'sbuild-build-depends-phast-dummy' in '/<<BUILDDIR>>/resolver-LDLGYg/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-LDLGYg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ Sources [529 B]
Get:5 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ Packages [611 B]
Fetched 2473 B in 0s (11.6 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install 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:
  netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base help2man intltool-debian libarchive-zip-perl libatlas-base-dev
  libatlas3-base libblas-dev libblas3 libdebhelper-perl libelf1 libf2c2
  libf2c2-dev libfile-stripnondeterminism-perl libgfortran5 libicu67
  liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre16-3 libpcre3-dev
  libpcre32-3 libpcrecpp0v5 libpipeline1 libsigsegv2 libsub-override-perl
  libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf
  sensible-utils
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
  libasprintf-dev libgettextpo-dev groff libatlas-doc liblapack-doc
  libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
  www-browser libmail-box-perl
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base help2man intltool-debian libarchive-zip-perl libatlas-base-dev
  libatlas3-base libblas-dev libblas3 libdebhelper-perl libelf1 libf2c2
  libf2c2-dev libfile-stripnondeterminism-perl libgfortran5 libicu67
  liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre16-3 libpcre3-dev
  libpcre32-3 libpcrecpp0v5 libpipeline1 libsigsegv2 libsub-override-perl
  libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf
  sbuild-build-depends-phast-dummy sensible-utils
0 upgraded, 48 newly installed, 0 to remove and 63 not upgraded.
Need to get 29.3 MB of archives.
After this operation, 121 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-LDLGYg/apt_archive ./ sbuild-build-depends-phast-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.1 [192 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [580 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.1 [1056 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf help2man armhf 1.48.5 [143 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libatlas3-base armhf 3.10.3-10+rpi1 [2454 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libatlas-base-dev armhf 3.10.3-10+rpi1 [2601 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libf2c2 armhf 20140711-1 [110 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libf2c2-dev armhf 20140711-1 [118 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf libpcre16-3 armhf 2:8.39-13 [235 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libpcre32-3 armhf 2:8.39-13 [228 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libpcrecpp0v5 armhf 2:8.39-13 [150 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libpcre3-dev armhf 2:8.39-13 [566 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libtmglib3 armhf 3.9.0-3 [96.9 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libtmglib-dev armhf 3.9.0-3 [96.9 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package bsdextrautils.
(Reading database ... 12488 files and directories currently installed.)
Preparing to unpack .../00-bsdextrautils_2.37.2-1_armhf.deb ...
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Unpacking groff-base (1.22.4-6) ...
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Preparing to unpack .../45-libtmglib3_3.9.0-3_armhf.deb ...
Unpacking libtmglib3:armhf (3.9.0-3) ...
Selecting previously unselected package libtmglib-dev:armhf.
Preparing to unpack .../46-libtmglib-dev_3.9.0-3_armhf.deb ...
Unpacking libtmglib-dev:armhf (3.9.0-3) ...
Selecting previously unselected package sbuild-build-depends-phast-dummy.
Preparing to unpack .../47-sbuild-build-depends-phast-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-phast-dummy (0.invalid.0) ...
Setting up libpcrecpp0v5:armhf (2:8.39-13) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up bsdextrautils (2.37.2-1) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libpcre16-3:armhf (2:8.39-13) ...
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up help2man (1.48.5) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libblas3:armhf (3.9.0-3) ...
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
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libpcre32-3:armhf (2:8.39-13) ...
Setting up autopoint (0.21-4) ...
Setting up libgfortran5:armhf (10.2.1-6+rpi1) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libf2c2:armhf (20140711-1) ...
Setting up libf2c2-dev:armhf (20140711-1) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.7) ...
Setting up libblas-dev:armhf (3.9.0-3) ...
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 libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up liblapack3:armhf (3.9.0-3) ...
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 gettext (0.21-4) ...
Setting up libatlas3-base:armhf (3.10.3-10+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libtool (2.4.6-15) ...
Setting up libpcre3-dev:armhf (2:8.39-13) ...
Setting up m4 (1.4.18-5) ...
Setting up libatlas-base-dev:armhf (3.10.3-10+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libtmglib3:armhf (3.9.0-3) ...
Setting up liblapack-dev:armhf (3.9.0-3) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up libtmglib-dev:armhf (3.9.0-3) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.1) ...
Setting up sbuild-build-depends-phast-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-13+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.5.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.2-2 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.3.0-22+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 help2man_1.48.5 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatlas-base-dev_3.10.3-10+rpi1 libatlas3-base_3.10.3-10+rpi1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36.1-8 libbz2-1.0_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.2-2 libf2c2_20140711-1 libf2c2-dev_20140711-1 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran5_10.2.1-6+rpi1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.57+dfsg-3 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-8 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpcre16-3_2:8.39-13 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libpcre3-dev_2:8.39-13 libpcre32-3_2:8.39-13 libpcrecpp0v5_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libreadline8_8.1-1 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-8 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtmglib-dev_3.9.0-3 libtmglib3_3.9.0-3 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libxml2_2.9.10+dfsg-6.7 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.2-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.36.1-8 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phast-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.17 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2

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


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.5R4UEOk1/trustedkeys.kbx': General error
gpgv: Signature made Mon Aug 30 20:03:36 2021 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_1.6+dfsg-1.dsc
dpkg-source: info: extracting phast in /<<BUILDDIR>>/phast-1.6+dfsg
dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz
dpkg-source: info: unpacking phast_1.6+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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
dpkg-source: info: applying fix_test_makefile.patch

Check disk 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=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-a54f1b74-b200-495c-a3a4-30a378eb855d
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

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

dpkg-buildpackage: info: source package phast
dpkg-buildpackage: info: source version 1.6+dfsg-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg'
dh_auto_clean
cd src && make clean
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/$dir && make clean ; done
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif'
rm -f /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../lib/*
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless'
rm -f *.o dless.help dlessP.help /<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../../bin/dless /<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../../bin/dlessP 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsEncode /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsScoreMatrix /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsTrain /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/util'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/all_dists /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/base_evolve /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/chooseLines /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/clean_genes /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/consEntropy /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/convert_coords /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/draw_tree /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/eval_predictions /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/hmm_train /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/hmm_tweak /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/hmm_view /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/indelFit /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/indelHistory /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/maf_parse /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/makeHKY /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/modFreqs /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_diff /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_split /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_view /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/phast /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/phastBias /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/refeature /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/stringiphy /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/treeGen /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/tree_doctor 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/util'
rm -rf ../bin ../lib ../doc
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg'
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   dh_auto_build -a
	make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.6+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-1.6+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-1.6+dfsg/src/$dir && make ; done	
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/$dir && make ; done
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_eigen.c: In function 'mat_diagonalize':
phast_eigen.c:62:3: warning: implicit declaration of function 'dgeev_' [-Wimplicit-function-declaration]
   62 |   dgeev_(&jobvl, &jobvr, &n, tmp, &n, wr, wi, vl,
      |   ^~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_markov_matrix.c: In function 'mm_exp_higham':
phast_markov_matrix.c:288:5: warning: implicit declaration of function 'dgebal_' [-Wimplicit-function-declaration]
  288 |     dgebal_(&job, &ln, mat, &ln, &ilo, &ihi, scale, &info);
      |     ^~~~~~~
phast_markov_matrix.c:403:3: warning: implicit declaration of function 'dgesv_' [-Wimplicit-function-declaration]
  403 |   dgesv_(&ln, &ln, matU, &ln, ipiv, matV, &ln, &info);
      |   ^~~~~~
phast_markov_matrix.c:428:5: warning: implicit declaration of function 'dgebak_' [-Wimplicit-function-declaration]
  428 |     dgebak_(&job, &side, &ln, &ilo, &ihi, scale, &ln, mat, &ln, &info);
      |     ^~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_matrix.c: In function 'mat_invert':
phast_matrix.c:263:3: warning: implicit declaration of function 'dgetrf_' [-Wimplicit-function-declaration]
  263 |   dgetrf_(&n, &n, (LAPACK_DOUBLE*)tmp, &n, ipiv, &info);
      |   ^~~~~~~
phast_matrix.c:273:3: warning: implicit declaration of function 'dgetri_' [-Wimplicit-function-declaration]
  273 |   dgetri_(&n, (LAPACK_DOUBLE*)tmp, &n, ipiv, work, &lwork, &info);
      |   ^~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_misc.c -o phast_misc.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_stringsplus.c -o phast_stringsplus.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_vector.c -o phast_vector.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar: creating /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_local_alignment.c -o phast_local_alignment.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_maf.c: In function 'maf_read_cats_subset':
phast_maf.c:29:41: warning: variable 'block_no' set but not used [-Wunused-but-set-variable]
   29 |   int i, start_idx, length, max_tuples, block_no,
      |                                         ^~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_msa.c -o phast_msa.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_msa.c: In function 'msa_read_fasta':
phast_msa.c:257:40: warning: variable 'line_no' set but not used [-Wunused-but-set-variable]
  257 |   int maxlen, i, nseqs, j, do_toupper, line_no;
      |                                        ^~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_multi_msa.c -o phast_multi_msa.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_sufficient_stats.c -o phast_sufficient_stats.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_sufficient_stats.c: In function 'ss_from_msas':
phast_sufficient_stats.c:140:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
  140 |     else
      |     ^~~~
phast_sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
  142 |       max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1,
      |       ^~~~~~~~~~
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_bed.c -o phast_bed.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_category_map.c -o phast_category_map.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_gff.c -o phast_gff.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_wig.c -o phast_wig.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_hmm.c -o phast_hmm.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_phylo_hmm.c -o phast_phylo_hmm.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_motif.c: In function 'mtf_print':
phast_motif.c:1411:7: warning: '%s' directive argument is null [-Wformat-overflow=]
 1411 |       fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phast_motif.c: In function 'mtf_print_html':
phast_motif.c:1604:7: warning: '%s' directive argument is null [-Wformat-overflow=]
 1604 |       fprintf(F, "<li>%s\n", (char*)lst_get_ptr(notfound, i));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_tfbs.c -o phast_tfbs.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_tfbs.c: In function 'ms_read':
phast_tfbs.c:219:32: warning: variable 'line_no' set but not used [-Wunused-but-set-variable]
  219 |   int i, nseqs, j, do_toupper, line_no;
      |                                ^~~~~~~
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif'
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless'
../munge-help.sh dless.help_src > dless.help
../munge-help.sh dlessP.help_src > dlessP.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
make[3]: *** No rule to make target 'bd_phylo_hmm.o', needed by '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../../bin/dless'.  Stop.
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy'
../munge-help.sh exoniphy.help_src > exoniphy.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy/../../lib  -o /<<BUILDDIR>>/phast-1.6+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-1.6+dfsg/src/exoniphy'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons'
../munge-help.sh phastCons.help_src > phastCons.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons/../../lib  -o /<<BUILDDIR>>/phast-1.6+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-1.6+dfsg/src/phastCons'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds'
../munge-help.sh phastOdds.help_src > phastOdds.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds/../../lib  -o /<<BUILDDIR>>/phast-1.6+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-1.6+dfsg/src/phastOdds'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: 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]
  131 |   int i, j, separate_backgd = 0,
      |             ^~~~~~~~~~~~~~~
gcc  -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif/../../lib  -o /<<BUILDDIR>>/phast-1.6+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-1.6+dfsg/src/phastMotif'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit'
../munge-help.sh phyloFit.help_src > phyloFit.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit/../../lib  -o /<<BUILDDIR>>/phast-1.6+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-1.6+dfsg/src/phyloFit'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot'
../munge-help.sh phyloBoot.help_src > phyloBoot.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot/../../lib  -o /<<BUILDDIR>>/phast-1.6+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-1.6+dfsg/src/phyloBoot'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP'
../munge-help.sh phyloP.help_src > phyloP.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP/../../lib  -o /<<BUILDDIR>>/phast-1.6+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-1.6+dfsg/src/phyloP'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel'
../munge-help.sh pbsDecode.help_src > pbsDecode.help
../munge-help.sh pbsEncode.help_src > pbsEncode.help
../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help
../munge-help.sh pbsTrain.help_src > pbsTrain.help
../munge-help.sh prequel.help_src > prequel.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
make[3]: *** No rule to make target 'simplex_grid.o', needed by '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode'.  Stop.
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/util'
../munge-help.sh base_evolve.help_src > base_evolve.help
../munge-help.sh clean_genes.help_src > clean_genes.help
../munge-help.sh consEntropy.help_src > consEntropy.help
../munge-help.sh indelFit.help_src > indelFit.help
../munge-help.sh indelHistory.help_src > indelHistory.help
../munge-help.sh makeHKY.help_src > makeHKY.help
../munge-help.sh modFreqs.help_src > modFreqs.help
../munge-help.sh msa_diff.help_src > msa_diff.help
../munge-help.sh phast.help_src > phast.help
../munge-help.sh phastBias.help_src > phastBias.help
../munge-help.sh treeGen.help_src > treeGen.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: 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]
  204 |   char tuple_i[mod->order+2], tuple_j[mod->order+2];
      |        ^~~~~~~
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+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 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+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-1.6+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg'
cd test && PATH=/<<BUILDDIR>>/phast-1.6+dfsg/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/test'
*** Testing msa_view ***
msa_view hmrc.ss -i SS --end 10000 > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o PHYLIP > hmrc.ph
msa_view hmrc.ph -i PHYLIP > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm
msa_view hmrc.mpm --in-format MPM > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o SS > hmrc_short_a.ss
msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss
if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi
msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa
msa_view --seqs human,cow hmrc.fa > hm_b.fa
if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa
msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa
if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa
msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa
if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa
msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa
if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --summary -i SS > hmrc_summary
if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi
-e Passed all tests.

make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/test'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg'
   create-stamp debian/debhelper-build-stamp
   dh_prep -a
   dh_auto_install --destdir=debian/phast/ -a
	make -j4 install DESTDIR=/<<BUILDDIR>>/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg'
(cd src; make install DESTDIR=/<<BUILDDIR>>/phast-1.6+dfsg/debian/phast )
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
mkdir -p /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/bin/
mkdir -p /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/share/phast/data/
mkdir -p /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/share/man/man1/
cp ../bin/* /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/bin/
cp -R ../data/* /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/share/phast/data/
cp -R ../doc/man/* /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/share/man/man1/
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.6+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_dwz -a -a
   dh_strip -a -a
   dh_makeshlibs -a -a
   dh_shlibdeps -a -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/stringiphy debian/phast/usr/bin/makeHKY debian/phast/usr/bin/msa_split debian/phast/usr/bin/refeature debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/msa_view debian/phast/usr/bin/base_evolve debian/phast/usr/bin/treeGen debian/phast/usr/bin/indelFit debian/phast/usr/bin/consEntropy debian/phast/usr/bin/convert_coords debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/phastCons debian/phast/usr/bin/chooseLines debian/phast/usr/bin/hmm_train debian/phast/usr/bin/exoniphy debian/phast/usr/bin/draw_tree debian/phast/usr/bin/all_dists debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/phyloP debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/phastOdds debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/hmm_view debian/phast/usr/bin/clean_genes debian/phast/usr/bin/maf_parse debian/phast/usr/bin/phyloFit debian/phast/usr/bin/indelHistory debian/phast/usr/bin/modFreqs debian/phast/usr/bin/msa_diff debian/phast/usr/bin/phastMotif debian/phast/usr/bin/phastBias were not linked against ld-linux-armhf.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' in '../phast_1.6+dfsg-1_armhf.deb'.
dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../phast_1.6+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-09-05T07:59:44Z

Finished
--------

I: Built successfully

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


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


phast_1.6+dfsg-1_armhf.changes:
-------------------------------

Format: 1.8
Date: Mon, 30 Aug 2021 21:53:58 +0200
Source: phast
Binary: phast phast-dbgsym
Architecture: armhf
Version: 1.6+dfsg-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 phast      - phylogenetic analysis with space/time models
Changes:
 phast (1.6+dfsg-1) unstable; urgency=medium
 .
   * Fix watchfile to detect new versions on github (routine-update)
   * New upstream version
   * Standards-Version: 4.6.0 (routine-update)
   * watch file standard 4 (routine-update)
   * Build-Depends: libf2c2-dev, libatlas-base-dev
Checksums-Sha1:
 08c7ed94eda9ba800edc3554612837ad586b0fde 24210344 phast-dbgsym_1.6+dfsg-1_armhf.deb
 861d8dd049380faea4d5357ff44593f0ccf3c324 5330 phast_1.6+dfsg-1_armhf.buildinfo
 2ac4a8c73eccbb612a7c32e6e6daf61689e20448 1137252 phast_1.6+dfsg-1_armhf.deb
Checksums-Sha256:
 5d305fc656a4558c31fdc2af50b59b88d2da4933aa6b7437ee59de74a1da3b39 24210344 phast-dbgsym_1.6+dfsg-1_armhf.deb
 5370605b310bf556246de0ac9a612e691c72159ff93877ae219ce54f700c10dd 5330 phast_1.6+dfsg-1_armhf.buildinfo
 602f042e0652cd71041df0cfebbde3ea44c95d32e64bdda815554d38785eab0d 1137252 phast_1.6+dfsg-1_armhf.deb
Files:
 86d33084bd91cc3861f0a5a9cdf89e90 24210344 debug optional phast-dbgsym_1.6+dfsg-1_armhf.deb
 7f473057c93c67102f1fcc0030b2b031 5330 science optional phast_1.6+dfsg-1_armhf.buildinfo
 63bc994e2ec6dff0e14151de6c0db278 1137252 science optional phast_1.6+dfsg-1_armhf.deb

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


phast-dbgsym_1.6+dfsg-1_armhf.deb
---------------------------------

 new Debian package, version 2.0.
 size 24210344 bytes: control archive=2088 bytes.
    1682 bytes,    12 lines      control              
    3583 bytes,    34 lines      md5sums              
 Package: phast-dbgsym
 Source: phast
 Version: 1.6+dfsg-1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 26191
 Depends: phast (= 1.6+dfsg-1)
 Section: debug
 Priority: optional
 Description: debug symbols for phast
 Build-Ids: 0ca320b5561e846235a5573ed86eb1c3380edfd6 11eb81b73aee0685396fb8e64406ca6d81042942 13235f4c8672ff407973cc66cfb05717c264e750 145a726a1eb4110645638c7b9a6fbbefe5a1670e 24fe4b61e4692a6bd79c494670d51ef47157bc2d 282595a59ff02690773cb61656547426977fd2bf 2f1ce5df3c5039d389a6673b1f25e30ed25f1fcd 30a39623c2ebbdfa030402ae21a7d333f3b41d23 345f73c4f37911beadcebd1cabac2bea06e7fd17 5cea63b4104fa3c9bc8e66a6cbac70db7c48c676 6311d78daf2202f96a3e6e1b89d8176c33cda642 68574e87ea1ad831d3d5e3b30ce9e2b9a23b3d4c 6e00eb63b93a4c1539245129ae51a03b2f9c8a3c 6ee36072d7b16018ec208f270bb461818c146936 78685df98b7b180ae82326f59a98ae1097f0efef 7a4a6a547713eeef64debcd8932b82d8bbdbd67c 7b4f40c0fbe656bdd877acbfa9c9c832ce987e3e 82a72f4c535349470185dbb8634cf627bacabd0b 8f538716fb29800b82867a33c3b4638c1ecd2b81 920237d4badb9a4b941c1c776d9566223c06c1bf 98bd88877f491ed7c9627ebeda0ab31c1984f669 a0fdbe108cc6bd458afe3e42089b5ee1937d28a6 a86d8b85e795e99562f6e85bc1a70e8717664a17 b719454f0a54dda6dbad721d93d75bed47ff225b ba883e3465e09298c4d40178f2d59f88a9d28e00 cb083240a77d369316e5fc7e3cae1f34e1633a93 d012f68680974e686da6af598f63e592498ac2ad d5b091f4705f23c815be434e336df870a1cc35af d757d8bbb57f92be71b8ffccf2eb23a84c168f99 e2202721c2e6a0e15d9addc7dc94cf10f800c3f1 e2d2231d0f53b1a6f6c854d1aca5a91c052597c9 f07ebfd6536feb19ba9f3a27dab81f5a89d6a23f fdff73c75b30ac9d0c0c3e0fbe388d6a0f0ce953

drwxr-xr-x root/root         0 2021-08-30 19:53 ./
drwxr-xr-x root/root         0 2021-08-30 19:53 ./usr/
drwxr-xr-x root/root         0 2021-08-30 19:53 ./usr/lib/
drwxr-xr-x root/root         0 2021-08-30 19:53 ./usr/lib/debug/
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lrwxrwxrwx root/root         0 2021-08-30 19:53 ./usr/share/doc/phast-dbgsym -> phast


phast_1.6+dfsg-1_armhf.deb
--------------------------

 new Debian package, version 2.0.
 size 1137252 bytes: control archive=4584 bytes.
    1097 bytes,    22 lines      control              
   11849 bytes,   158 lines      md5sums              
 Package: phast
 Version: 1.6+dfsg-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 19130
 Depends: libc6 (>= 2.29), liblapack3 | liblapack.so.3, libpcre3
 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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-rwxr-xr-x root/root    539928 2021-08-30 19:53 ./usr/bin/exoniphy
-rwxr-xr-x root/root    505464 2021-08-30 19:53 ./usr/bin/hmm_train
-rwxr-xr-x root/root    501368 2021-08-30 19:53 ./usr/bin/hmm_tweak
-rwxr-xr-x root/root    501368 2021-08-30 19:53 ./usr/bin/hmm_view
-rwxr-xr-x root/root    494896 2021-08-30 19:53 ./usr/bin/indelFit
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-rwxr-xr-x root/root    568424 2021-08-30 19:53 ./usr/bin/phyloFit
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drwxr-xr-x root/root         0 2021-08-30 19:53 ./usr/share/phast/data/phastCons/
-rw-r--r-- root/root    103302 2021-08-30 19:53 ./usr/share/phast/data/phastCons/simple-coding-indels.hmm
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| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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| Summary                                                                      |
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Build Architecture: armhf
Build-Space: 187588
Build-Time: 217
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 125
Job: phast_1.6+dfsg-1
Machine Architecture: armhf
Package: phast
Package-Time: 361
Source-Version: 1.6+dfsg-1
Space: 187588
Status: successful
Version: 1.6+dfsg-1
--------------------------------------------------------------------------------
Finished at 2021-09-05T07:59:44Z
Build needed 00:06:01, 187588k disk space