Raspbian Package Auto-Building

Build log for phast (1.5+dfsg-1) on armhf

phast → 1.5+dfsg-1 → armhf → 2020-08-15 20:54:56 

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard

+==============================================================================+
| phast 1.5+dfsg-1 (armhf)                     Fri, 14 Aug 2020 19:38:47 +0000 |
+==============================================================================+

Package: phast
Version: 1.5+dfsg-1
Source Version: 1.5+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-ef301d69-9157-4b5f-ba56-76a4e7cdb137' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.8 MB in 29s (863 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 1866 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main phast 1.5+dfsg-1 (dsc) [1988 B]
Get:2 http://172.17.0.1/private bullseye-staging/main phast 1.5+dfsg-1 (tar) [1811 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main phast 1.5+dfsg-1 (diff) [53.1 kB]
Fetched 1866 kB in 1s (2018 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phast-GFEd4z/phast-1.5+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phast-GFEd4z' 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-5fEoSg/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-5fEoSg/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-5fEoSg/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2753 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 packages were automatically installed and are no longer required:
  bsdextrautils libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-5fEoSg/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 (22.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12524 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 (>= 11~), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man
Filtered Build-Depends: debhelper (>= 11~), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man
dpkg-deb: building package 'sbuild-build-depends-phast-dummy' in '/<<BUILDDIR>>/resolver-5fEoSg/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-5fEoSg/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ Sources [518 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ Packages [599 B]
Fetched 2450 B in 1s (3001 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev debhelper dh-autoreconf
  dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man
  intltool-debian libarchive-zip-perl libblas-dev libblas3 libcroco3
  libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgfortran5
  libglib2.0-0 libicu67 liblapack-dev liblapack3 liblocale-gettext-perl
  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
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
  libasprintf-dev libgettextpo-dev groff 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 libglib2.0-data shared-mime-info
  xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev debhelper dh-autoreconf
  dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man
  intltool-debian libarchive-zip-perl libblas-dev libblas3 libcroco3
  libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgfortran5
  libglib2.0-0 libicu67 liblapack-dev liblapack3 liblocale-gettext-perl
  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
0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded.
Need to get 25.0 MB of archives.
After this operation, 97.1 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-5fEoSg/apt_archive ./ sbuild-build-depends-phast-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf liblocale-gettext-perl armhf 1.07-4 [18.1 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.180-1 [162 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.4-1 [1159 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-3 [8287 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.16 [181 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.1.0-6+rpi1 [232 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-13 [235 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-13 [228 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-13 [150 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-13 [566 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libtmglib3 armhf 3.9.0-3 [96.9 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libtmglib-dev armhf 3.9.0-3 [96.9 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 25.0 MB in 13s (1987 kB/s)
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 12524 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-4_armhf.deb ...
Unpacking liblocale-gettext-perl (1.07-4) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../01-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../02-groff-base_1.22.4-5_armhf.deb ...
Unpacking groff-base (1.22.4-5) ...
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Preparing to unpack .../03-libpipeline1_1.5.2-2_armhf.deb ...
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Preparing to unpack .../04-man-db_2.9.3-2_armhf.deb ...
Unpacking man-db (2.9.3-2) ...
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Preparing to unpack .../05-libmagic-mgc_1%3a5.38-5_armhf.deb ...
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Preparing to unpack .../07-file_1%3a5.38-5_armhf.deb ...
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Preparing to unpack .../08-gettext-base_0.19.8.1-10_armhf.deb ...
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Preparing to unpack .../09-libsigsegv2_2.12-2_armhf.deb ...
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Preparing to unpack .../44-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 (1.5.2-2) ...
Setting up libpcre16-3:armhf (2:8.39-13) ...
Setting up libicu67:armhf (67.1-3) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.4-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.2) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up autotools-dev (20180224.1) ...
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 (2.12-2) ...
Setting up libpcre32-3:armhf (2:8.39-13) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libgfortran5:armhf (10.1.0-6+rpi1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libelf1:armhf (0.180-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5+b1) ...
Setting up liblocale-gettext-perl (1.07-4) ...
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 (1.9.0-1) ...
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 libtool (2.4.6-14) ...
Setting up libpcre3-dev:armhf (2:8.39-13) ...
Setting up m4 (1.4.18-4) ...
Setting up help2man (1.47.16) ...
Setting up libtmglib3:armhf (3.9.0-3) ...
Setting up liblapack-dev:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up libtmglib-dev:armhf (3.9.0-3) ...
Setting up automake (1:1.16.2-3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2) ...
Setting up sbuild-build-depends-phast-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35-1+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.1.0-6+rpi1 gcc-10_10.1.0-6+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.1.0-6+rpi1 libstdc++6_10.1.0-6+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-1+b1 aptitude-common_0.8.13-1 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-7 binutils_2.35-1+rpi1 binutils-arm-linux-gnueabihf_2.35-1+rpi1 binutils-common_2.35-1+rpi1 bsdextrautils_2.36-2 bsdutils_1:2.36-2 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.1.0-6+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-2 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.1.0-1+rpi1 g++-10_10.1.0-6+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.1.0-6+rpi1 gcc-10-base_10.1.0-6+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 help2man_1.47.16 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.1.0-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-6+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.35-1+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36-2 libboost-iostreams1.71.0_1.71.0-6+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-3+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.42-2 libcap2-bin_1:2.42-2 libcc1-0_10.1.0-6+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.35-1+rpi1 libctf0_2.35-1+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2 libdpkg-perl_1.20.5+rpi1 libelf1_0.180-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-2 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.1.0-6+rpi1 libgcc-s1_10.1.0-6+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10.1.0-6+rpi1 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.1.0-6+rpi1 libgpg-error0_1.38-2 libhogweed6_3.6-2 libicu67_67.1-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libksba8_1.4.0-2 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.50+dfsg-1+b1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-cap_1:2.42-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre16-3_2:8.39-13 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libpcre3-dev_2:8.39-13 libpcre32-3_2:8.39-13 libpcrecpp0v5_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libreadline8_8.0-4 librust-rand-core-dev_0.5.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsmartcols1_2.36-2 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libstdc++-10-dev_10.1.0-6+rpi1 libstdc++6_10.1.0-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1+b1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtmglib-dev_3.9.0-3 libtmglib3_3.9.0-3 libtool_2.4.6-14 libubsan1_10.1.0-6+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1+b1 libunistring2_0.9.10-4 libuuid1_2.36-2 libxapian30_1.4.15-1 libxml2_2.9.10+dfsg-5+b1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-2 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phast-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-2 xz-utils_5.2.4-1 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.ysidokOS/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct 19 07:15:09 2018 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_1.5+dfsg-1.dsc
dpkg-source: info: extracting phast in /<<BUILDDIR>>/phast-1.5+dfsg
dpkg-source: info: unpacking phast_1.5+dfsg.orig.tar.xz
dpkg-source: info: unpacking phast_1.5+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 disc space
----------------

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-ef301d69-9157-4b5f-ba56-76a4e7cdb137
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

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

dpkg-buildpackage: info: source package phast
dpkg-buildpackage: info: source version 1.5+dfsg-1
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg'
dh_auto_clean
cd src && make clean
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/$dir && make clean ; done
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/hmm'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo_hmm'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/motif'
rm -f *.o 
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/motif'
rm -f /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../lib/*
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/dless'
rm -f *.o dless.help dlessP.help /<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../../bin/dless /<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../../bin/dlessP 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/dless'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/exoniphy'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.5+dfsg/src/exoniphy/../../bin/exoniphy 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/exoniphy'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phastCons'
rm -f *.o /<<BUILDDIR>>/phast-1.5+dfsg/src/phastCons/../../bin/phastCons phastCons.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phastCons'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phastOdds'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.5+dfsg/src/phastOdds/../../bin/phastOdds 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phastOdds'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phastMotif'
rm -f *.o /<<BUILDDIR>>/phast-1.5+dfsg/src/phastMotif/../../bin/phastMotif 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phastMotif'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloFit'
rm -f *.o /<<BUILDDIR>>/phast-1.5+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloFit'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloBoot'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.5+dfsg/src/phyloBoot/../../bin/phyloBoot 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloBoot'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloP'
rm -f *.o /<<BUILDDIR>>/phast-1.5+dfsg/src/phyloP/../../bin/phyloP phyloP.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloP'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel'
rm -f *.o /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/pbsDecode /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/pbsEncode /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/pbsScoreMatrix /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/pbsTrain /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/util'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/all_dists /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/base_evolve /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/chooseLines /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/clean_genes /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/consEntropy /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/convert_coords /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/display_rate_matrix /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/draw_tree /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/eval_predictions /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/hmm_train /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/hmm_tweak /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/hmm_view /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/indelFit /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/indelHistory /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/maf_parse /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/makeHKY /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/modFreqs /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/msa_diff /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/msa_split /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/msa_view /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/phast /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/phastBias /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/refeature /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/stringiphy /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/treeGen /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/tree_doctor 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/util'
rm -rf ../bin ../lib ../doc
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg'
   dh_clean
 debian/rules build-arch
dh build-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   dh_auto_build -a
	make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.5+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-1.5+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-1.5+dfsg/src/$dir && make ; done	
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/$dir && make ; done
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_matrix.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c complex_vector.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c eigen.c -o 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
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c hashtable.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c list_of_lists.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c lists.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c markov_matrix.c -o 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
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c matrix.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c memory_handler.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c misc.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c numerical_opt.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_matrix.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c prob_vector.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c stringsplus.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c vector.c -o 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-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar: creating /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base/../../../lib/libphast.a complex_matrix.o complex_vector.o eigen.o hashtable.o list_of_lists.o lists.o markov_matrix.o matrix.o memory_handler.o misc.o numerical_opt.o prob_matrix.o prob_vector.o stringsplus.o vector.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/base'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c local_alignment.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf.c -o 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
maf.c: In function 'maf_read_cats_subset':
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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c maf_block.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c msa.c -o 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
msa.c: In function 'msa_read_fasta':
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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c multi_msa.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c sufficient_stats.c -o 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
sufficient_stats.c: In function 'ss_from_msas':
sufficient_stats.c:140:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
  140 |     else
      |     ^~~~
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-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa/../../../lib/libphast.a local_alignment.o maf.o maf_block.o msa.o multi_msa.o sufficient_stats.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/msa'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c bed.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c category_map.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c genepred.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c gff.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c wig.c -o 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-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature/../../../lib/libphast.a bed.o category_map.o genepred.o gff.o wig.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/feature'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/hmm'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c em.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c hmm.c -o 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-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/hmm/../../../lib/libphast.a em.o hmm.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c bgc_hmm.c -o 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
bgc_hmm.c: In function 'bgcHmm':
bgc_hmm.c:241:31: warning: ', ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  241 |       sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars);
      |                               ^~
bgc_hmm.c:241:7: note: 'sprintf' output 3 or more bytes (assuming 10002) into a destination of size 10000
  241 |       sprintf(warning_str, "%s, %s", warning_str, ((String*)lst_get_ptr(pruned_names, j))->chars);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bgc_hmm.c:241:7: warning: 'sprintf' argument 3 overlaps destination object 'warning_str' [-Wrestrict]
bgc_hmm.c:235:10: note: destination object referenced by 'restrict'-qualified argument 1 was declared here
  235 |     char warning_str[10000];
      |          ^~~~~~~~~~~
bgc_hmm.c:242:29: warning: ')
   ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  242 |     sprintf(warning_str, "%s)\n", warning_str);
      |                             ^~~
bgc_hmm.c:242:5: note: 'sprintf' output between 3 and 10002 bytes into a destination of size 10000
  242 |     sprintf(warning_str, "%s)\n", warning_str);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bgc_hmm.c:242:5: warning: 'sprintf' argument 3 overlaps destination object 'warning_str' [-Wrestrict]
bgc_hmm.c:235:10: note: destination object referenced by 'restrict'-qualified argument 1 was declared here
  235 |     char warning_str[10000];
      |          ^~~~~~~~~~~
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c dgamma.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_column.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_em.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c fit_feature.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_history.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c indel_mod.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_fit.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phylo_p_print.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_distrib.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c subst_mods.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_likelihoods.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c tree_model.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c trees.c -o 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-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo/../../../lib/libphast.a bgc_hmm.o dgamma.o fit_column.o fit_em.o fit_feature.o indel_history.o indel_mod.o phast_cons.o phylo_fit.o phylo_p.o phylo_p_print.o subst_distrib.o subst_mods.o tree_likelihoods.o tree_model.o trees.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo_hmm'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c gap_patterns.c -o 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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phylo_hmm.c -o 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-1.5+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a gap_patterns.o phylo_hmm.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a gap_patterns.o phylo_hmm.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/motif'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c motif.c -o 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
motif.c: In function 'mtf_print':
motif.c:1411:7: warning: '%s' directive argument is null [-Wformat-overflow=]
 1411 |       fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i));
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
motif.c: In function 'mtf_print_html':
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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c tfbs.c -o 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
tfbs.c: In function 'ms_read':
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-1.5+dfsg/src/lib/motif/../../../lib/libphast.a motif.o tfbs.o
ar rs /<<BUILDDIR>>/phast-1.5+dfsg/src/lib/motif/../../../lib/libphast.a motif.o tfbs.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib/motif'
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/lib'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/dless'
../munge-help.sh dless.help_src > dless.help
../munge-help.sh dlessP.help_src > dlessP.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../..\" -fno-strict-aliasing -c bd_phylo_hmm.c -o bd_phylo_hmm.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../../lib  -o /<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../../bin/dless dless.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../..\" -fno-strict-aliasing -c dlessP.c -o dlessP.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../../lib  -o /<<BUILDDIR>>/phast-1.5+dfsg/src/dless/../../bin/dlessP dlessP.o bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/dless'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/exoniphy'
../munge-help.sh exoniphy.help_src > exoniphy.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/exoniphy/../../lib  -o /<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/exoniphy'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phastCons'
../munge-help.sh phastCons.help_src > phastCons.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phastCons/../../lib  -o /<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phastCons'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phastOdds'
../munge-help.sh phastOdds.help_src > phastOdds.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phastOdds/../../lib  -o /<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phastOdds'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phastMotif'
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phastMotif/../../lib  -o /<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phastMotif'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloFit'
../munge-help.sh phyloFit.help_src > phyloFit.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phyloFit/../../lib  -o /<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phyloFit'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloBoot'
../munge-help.sh phyloBoot.help_src > phyloBoot.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phyloBoot/../../lib  -o /<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phyloBoot'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloP'
../munge-help.sh phyloP.help_src > phyloP.help
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phyloP/../../lib  -o /<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/phyloP'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c simplex_grid.c -o simplex_grid.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbs_code.c -o pbs_code.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../lib  -o /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/pbsDecode pbsDecode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../lib  -o /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/pbsEncode pbsEncode.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../lib  -o /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../lib  -o /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/pbsTrain pbsTrain.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../lib  -o /<<BUILDDIR>>/phast-1.5+dfsg/src/prequel/../../bin/prequel prequel.o simplex_grid.o pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src/prequel'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.5+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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+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 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre -Wl,-z,relro -Wl,-z,now 
gcc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/phast-1.5+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.5+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.4\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/src/util/../../lib   -o /<<BUILDDIR>>/phast-1.5+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-1.5+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-1.5+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg'
cd test && PATH=/<<BUILDDIR>>/phast-1.5+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-1.5+dfsg/test'
*** Testing msa_view ***
msa_view hmrc.ss -i SS --end 10000 > hmrc.fa
make[2]: *** wait: No child processes.  Stop.
make[2]: *** Waiting for unfinished jobs....
make[2]: *** wait: No child processes.  Stop.
E: Caught signal ‘Terminated’: terminating immediately
make: *** [debian/rules:8: build-arch] Terminated
make[1]: *** [debian/rules:16: override_dh_auto_test] Terminated
E: Build killed with signal TERM after 1500 minutes of inactivity
--------------------------------------------------------------------------------
Build finished at 2020-08-15T20:54:52Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 0
Build-Time: 90569
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 339
Job: phast_1.5+dfsg-1
Machine Architecture: armhf
Package: phast
Package-Time: 90965
Source-Version: 1.5+dfsg-1
Space: 0
Status: failed
Version: 1.5+dfsg-1
--------------------------------------------------------------------------------
Finished at 2020-08-15T20:54:52Z
Build needed 00:00:00, 0k disc space