Raspbian Package Auto-Building

phast → 1.5+dfsg-2 → armhf → 2020-10-08 06:21:16

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03

+==============================================================================+
| phast 1.5+dfsg-2 (armhf)                     Thu, 08 Oct 2020 06:01:12 +0000 |
+==============================================================================+

Package: phast
Version: 1.5+dfsg-2
Source Version: 1.5+dfsg-2
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-8c2842ab-4214-46bb-ac73-ae8048ae4e38' 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 [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.4 MB in 24s (1027 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 1871 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main phast 1.5+dfsg-2 (dsc) [1997 B]
Get:2 http://172.17.0.1/private bullseye-staging/main phast 1.5+dfsg-2 (tar) [1811 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main phast 1.5+dfsg-2 (diff) [57.9 kB]
Fetched 1871 kB in 0s (8185 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phast-KjFioH/phast-1.5+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phast-KjFioH' 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-qJTyQ3/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-qJTyQ3/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-qJTyQ3/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-qJTyQ3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2716 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 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 37 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12514 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man
Filtered Build-Depends: debhelper-compat (= 13), liblapack-dev, libblas-dev, libtmglib-dev, libpcre3-dev, help2man
dpkg-deb: building package 'sbuild-build-depends-phast-dummy' in '/<<BUILDDIR>>/resolver-qJTyQ3/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-qJTyQ3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ Sources [520 B]
Get:5 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ Packages [600 B]
Fetched 2453 B in 1s (3291 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
  netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev binutils
  binutils-arm-linux-gnueabihf binutils-common cpp-10 debhelper dh-autoreconf
  dh-strip-nondeterminism dwz file g++-10 gcc-10 gcc-10-base gettext
  gettext-base groff-base help2man intltool-debian libarchive-zip-perl
  libasan6 libatomic1 libbinutils libblas-dev libblas3 libcc1-0 libcroco3
  libctf0 libdebhelper-perl libelf1 libfile-stripnondeterminism-perl
  libgcc-10-dev libgcc-s1 libgfortran5 libglib2.0-0 libgomp1 libicu67
  liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre16-3 libpcre3-dev
  libpcre32-3 libpcrecpp0v5 libpipeline1 libsigsegv2 libstdc++-10-dev
  libstdc++6 libsub-override-perl libtmglib-dev libtmglib3 libtool libubsan1
  libuchardet0 libxml2 m4 man-db po-debconf
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-10-locales
  dh-make gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev groff
  liblapack-doc libstdc++-10-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 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
The following packages will be upgraded:
  binutils binutils-arm-linux-gnueabihf binutils-common cpp-10 g++-10 gcc-10
  gcc-10-base libasan6 libatomic1 libbinutils libcc1-0 libctf0 libgcc-10-dev
  libgcc-s1 libgomp1 libstdc++-10-dev libstdc++6 libubsan1
18 upgraded, 44 newly installed, 0 to remove and 19 not upgraded.
Need to get 58.3 MB of archives.
After this operation, 97.2 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-qJTyQ3/apt_archive ./ sbuild-build-depends-phast-dummy 0.invalid.0 [892 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.2.0-13+rpi1 [31.7 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libctf0 armhf 2.35.1-1+rpi1 [35.3 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf binutils-arm-linux-gnueabihf armhf 2.35.1-1+rpi1 [1707 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libbinutils armhf 2.35.1-1+rpi1 [314 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf binutils-common armhf 2.35.1-1+rpi1 [2214 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf binutils armhf 2.35.1-1+rpi1 [60.1 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10.2.0-13+rpi1 [199 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10.2.0-13+rpi1 [36.1 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 10.2.0-13+rpi1 [84.1 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 10.2.0-13+rpi1 [8180 B]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libasan6 armhf 10.2.0-13+rpi1 [301 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 10.2.0-13+rpi1 [115 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf g++-10 armhf 10.2.0-13+rpi1 [6792 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-10-dev armhf 10.2.0-13+rpi1 [1746 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libgcc-10-dev armhf 10.2.0-13+rpi1 [685 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf gcc-10 armhf 10.2.0-13+rpi1 [12.3 MB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf cpp-10 armhf 10.2.0-13+rpi1 [6249 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 10.2.0-13+rpi1 [409 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.181-1 [161 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.0-2 [1173 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6 [578 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.16 [181 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.0-13+rpi1 [231 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-13 [235 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-13 [228 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-13 [150 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-13 [566 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libtmglib3 armhf 3.9.0-3 [96.9 kB]
Get:62 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
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(Reading database ... 12514 files and directories currently installed.)
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Setting up gcc-10-base:armhf (10.2.0-13+rpi1) ...
(Reading database ... 12514 files and directories currently installed.)
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Setting up libgcc-s1:armhf (10.2.0-13+rpi1) ...
(Reading database ... 12514 files and directories currently installed.)
Preparing to unpack .../0-libgomp1_10.2.0-13+rpi1_armhf.deb ...
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Setting up libstdc++6:armhf (10.2.0-13+rpi1) ...
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(Reading database ... 12513 files and directories currently installed.)
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Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpcre16-3:armhf (2:8.39-13) ...
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Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.0-2) ...
No schema files found: doing nothing.
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Setting up binutils-common:armhf (2.35.1-1+rpi1) ...
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 libgomp1:armhf (10.2.0-13+rpi1) ...
Setting up libasan6:armhf (10.2.0-13+rpi1) ...
Setting up help2man (1.47.16) ...
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 libatomic1:armhf (10.2.0-13+rpi1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libgfortran5:armhf (10.2.0-13+rpi1) ...
Setting up libubsan1:armhf (10.2.0-13+rpi1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libbinutils:armhf (2.35.1-1+rpi1) ...
Setting up libelf1:armhf (0.181-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6) ...
Setting up libcc1-0:armhf (10.2.0-13+rpi1) ...
Setting up cpp-10 (10.2.0-13+rpi1) ...
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 libctf0:armhf (2.35.1-1+rpi1) ...
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 libgcc-10-dev:armhf (10.2.0-13+rpi1) ...
Setting up m4 (1.4.18-4) ...
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 binutils-arm-linux-gnueabihf (2.35.1-1+rpi1) ...
Setting up automake (1:1.16.2-4) ...
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 libstdc++-10-dev:armhf (10.2.0-13+rpi1) ...
Setting up binutils (2.35.1-1+rpi1) ...
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 gcc-10 (10.2.0-13+rpi1) ...
Setting up g++-10 (10.2.0-13+rpi1) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2.1) ...
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.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-1+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-13+rpi1 gcc-10_10.2.0-13+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-7 binutils_2.35.1-1+rpi1 binutils-arm-linux-gnueabihf_2.35.1-1+rpi1 binutils-common_2.35.1-1+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.2.0-13+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 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_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.1.0-1+rpi1 g++-10_10.2.0-13+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.2.0-13+rpi1 gcc-10-base_10.2.0-13+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b1 gcc-8-base_8.4.0-4+rpi1+b1 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 libacl1_2.2.53-8 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-13+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.35.1-1+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36-3 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 libcc1-0_10.2.0-13+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35-2+rpi1 libctf0_2.35.1-1+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.181-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-13+rpi1 libgcc-s1_10.2.0-13+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran5_10.2.0-13+rpi1 libglib2.0-0_2.66.0-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.2.0-13+rpi1 libgpg-error0_1.38-2 libhogweed6_3.6-2 libicu67_67.1-4 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_2.4.51+dfsg-1 libldap-common_2.4.51+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_2.36-3 libmpc3_1.2.0~rc1-1 libmpfr6_4.1.0-3 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.21-2 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_1.5.3-1 libreadline8_8.0-4 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_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.2-1+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-1 libtmglib-dev_3.9.0-3 libtmglib3_3.9.0-3 libtool_2.4.6-14 libubsan1_10.2.0-13+rpi1 libuchardet0_0.0.7-1 libudev1_246.2-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6 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_2.36-3 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_2.96-4 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3 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.72n6taNk/trustedkeys.kbx': General error
gpgv: Signature made Sat Oct  3 08:26:48 2020 UTC
gpgv:                using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv:                issuer "npatra974@gmail.com"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./phast_1.5+dfsg-2.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-2.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
dpkg-source: info: applying arm64.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-8c2842ab-4214-46bb-ac73-ae8048ae4e38
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-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.5+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 binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   dh_auto_build -a
	make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.5+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
prequel.c: In function 'main':
prequel.c:285:32: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 255 [-Wformat-overflow=]
  285 |       sprintf(out_fname, "%s.%s.bin", out_root, n->name);
      |                                ^~~~
prequel.c:285:7: note: 'sprintf' output 6 or more bytes (assuming 261) into a destination of size 256
  285 |       sprintf(out_fname, "%s.%s.bin", out_root, n->name);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prequel.c:253:32: warning: '.fa' directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=]
  253 |       sprintf(out_fname, "%s.%s.fa", out_root, n->name);
      |                                ^~~
prequel.c:253:7: note: 'sprintf' output 5 or more bytes (assuming 260) into a destination of size 256
  253 |       sprintf(out_fname, "%s.%s.fa", out_root, n->name);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
prequel.c:203:32: warning: '.probs' directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=]
  203 |       sprintf(out_fname, "%s.%s.probs", out_root, n->name);
      |                                ^~~~~~
prequel.c:203:7: note: 'sprintf' output 8 or more bytes (assuming 263) into a destination of size 256
  203 |       sprintf(out_fname, "%s.%s.probs", out_root, n->name);
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o PHYLIP > hmrc.ph
msa_view hmrc.ph -i PHYLIP > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm
msa_view hmrc.mpm --in-format MPM > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o SS > hmrc_short_a.ss
msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss
if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi
msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa
msa_view --seqs human,cow hmrc.fa > hm_b.fa
if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa
msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa
if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa
msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa
if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa
msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa
if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --summary -i SS > hmrc_summary
if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi
-e Passed all tests.

make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/test'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg'
   create-stamp debian/debhelper-build-stamp
   dh_testroot -a
   dh_prep -a
   dh_auto_install -a
	make -j4 install DESTDIR=/<<BUILDDIR>>/phast-1.5\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg'
(cd src; make install DESTDIR=/<<BUILDDIR>>/phast-1.5+dfsg/debian/phast )
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.5+dfsg/src'
make[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
mkdir -p /<<BUILDDIR>>/phast-1.5+dfsg/debian/phast/usr/bin/
mkdir -p /<<BUILDDIR>>/phast-1.5+dfsg/debian/phast/usr/share/phast/data/
mkdir -p /<<BUILDDIR>>/phast-1.5+dfsg/debian/phast/usr/share/man/man1/
cp ../bin/* /<<BUILDDIR>>/phast-1.5+dfsg/debian/phast/usr/bin/
cp -R ../data/* /<<BUILDDIR>>/phast-1.5+dfsg/debian/phast/usr/share/phast/data/
cp -R ../doc/man/* /<<BUILDDIR>>/phast-1.5+dfsg/debian/phast/usr/share/man/man1/
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.5+dfsg'
   dh_installdocs -a
   dh_installchangelogs -a
   dh_installman -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_dwz -a -a
   dh_strip -a -a
   dh_makeshlibs -a -a
   dh_shlibdeps -a -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/pbsTrain debian/phast/usr/bin/chooseLines debian/phast/usr/bin/treeGen debian/phast/usr/bin/indelHistory debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/phastOdds debian/phast/usr/bin/dless debian/phast/usr/bin/phyloP debian/phast/usr/bin/hmm_train debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/phastBias debian/phast/usr/bin/maf_parse debian/phast/usr/bin/makeHKY debian/phast/usr/bin/convert_coords debian/phast/usr/bin/msa_diff debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/consEntropy debian/phast/usr/bin/hmm_view debian/phast/usr/bin/stringiphy debian/phast/usr/bin/exoniphy debian/phast/usr/bin/pbsScoreMatrix debian/phast/usr/bin/pbsDecode debian/phast/usr/bin/modFreqs debian/phast/usr/bin/pbsEncode debian/phast/usr/bin/clean_genes debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/msa_view debian/phast/usr/bin/msa_split debian/phast/usr/bin/indelFit debian/phast/usr/bin/draw_tree debian/phast/usr/bin/dlessP debian/phast/usr/bin/prequel debian/phast/usr/bin/phyloFit debian/phast/usr/bin/phastCons debian/phast/usr/bin/phastMotif debian/phast/usr/bin/refeature debian/phast/usr/bin/base_evolve debian/phast/usr/bin/all_dists were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.5+dfsg-2_armhf.deb'.
dpkg-deb: building package 'phast' in '../phast_1.5+dfsg-2_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../phast_1.5+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-10-08T06:20:59Z

Finished
--------

I: Built successfully

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


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


phast_1.5+dfsg-2_armhf.changes:
-------------------------------

Format: 1.8
Date: Sat, 03 Oct 2020 12:51:30 +0530
Source: phast
Binary: phast phast-dbgsym
Architecture: armhf
Version: 1.5+dfsg-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <npatra974@gmail.com>
Description:
 phast      - phylogenetic analysis with space/time models
Closes: 911983
Changes:
 phast (1.5+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * Standards-Version: 4.5.0 (routine-update)
   * debhelper-compat 13 (routine-update)
   * Add salsa-ci file (routine-update)
   * Rules-Requires-Root: no (routine-update)
   * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
     Repository-Browse.
   * Add patch to fix tests on arm64 (Closes: #911983)
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 6de0dc9c352ff2171830bb1bbb541537859a9206 4888 phast_1.5+dfsg-2_armhf.buildinfo
 31f796d18c597dd84be42dbfc7dc8f27efe7b691 1308400 phast_1.5+dfsg-2_armhf.deb
Checksums-Sha256:
 9e76875098963eec4b4f7522383a78326620d73bd85f8b6323d33f61a3fec4a9 29880168 phast-dbgsym_1.5+dfsg-2_armhf.deb
 f141a34c580ba5b1681fd373418a567fe2741344f3383cf958c6d4cecd807baf 4888 phast_1.5+dfsg-2_armhf.buildinfo
 2446943c5cdf01ee39436cc0189ae635af36bb15b296d58d1ddb0b749ff54d74 1308400 phast_1.5+dfsg-2_armhf.deb
Files:
 46c92c7dbefd6c94e7dae23b4ea3c734 29880168 debug optional phast-dbgsym_1.5+dfsg-2_armhf.deb
 9295fdff7d8d3c4d6e392473a2e9e3be 4888 science optional phast_1.5+dfsg-2_armhf.buildinfo
 e8aad7bfb39b754770f5b149caa3bc30 1308400 science optional phast_1.5+dfsg-2_armhf.deb

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


phast-dbgsym_1.5+dfsg-2_armhf.deb
---------------------------------

 new Debian package, version 2.0.
 size 29880168 bytes: control archive=2392 bytes.
    1969 bytes,    12 lines      control              
    4325 bytes,    41 lines      md5sums              
 Package: phast-dbgsym
 Source: phast
 Version: 1.5+dfsg-2
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 32083
 Depends: phast (= 1.5+dfsg-2)
 Section: debug
 Priority: optional
 Description: debug symbols for phast
 Build-Ids: 002f55e5fea81fe76becfbf356482300004f6184 04f727a0953a469daaa0cd49fba9d1b8501d7c1f 08358a24d40a08d8e2047fed7faa7b6839fb826e 0dd81d5d470b57801ad035adeff9aa19ed82e3c3 15a261a91551670b04c5477842444fe4d82332dd 222d7ca2d56ea69bc8b1c4d652ee9c13e5bbbab0 22926158713e68ae5c1fd61cee7cc101ed3db531 31f861ad243ac77711b8e42868cc01af562f4710 35477c741d8dce67c80f7b567d1482f0f2970559 3611a8b30143e6d5c9b225fed36d9785233acb27 366580e72c17268b4a96e7a51f743a40897e27f3 3b6014933a8c97909b10c9c094b5d8cf61dfee74 4344a240c01d423cf188988a24b321a957283118 4735b08b842a379265703c48f187215b72434e57 47ad4142c0d20d87e5e44b0eecc69d993d436d7a 4a4e47d3217f83976ed84a37ee6e4e0da319fcad 4b50096f56ee3ce95bee14fdbdab31d07649ab38 534219243ad9c15629ca4cba59f2abfcedf351cb 610cbcd56b3b4de0d8c4fa3f33eb7cc84d19ddf3 6da2af3bbb8cdae7bbaddbbf3afd24406cb35e30 76b4a81b25d3b5572aef7393657b4f1a575825a4 7e860d308323af7ec2a3821fd9c7fbe73eea8b67 8baa8b96b22cec91816039d5004d8fb1a2124a89 954c94cf0f44897526d7ce3ffa83c0b9fff6366e 9c0ff87cb0b69f7287f1e278386ae4dcbc4b0ebe a4e329625c56fb5f6c1e6fc5b3de7c4128c91b19 a64f74f34c9e4b629febf5ecf3a8e9428c86f6b7 a81d01b080b04569311e9ac50d63d4043d65f41c ad69e7079982fcb8a9717e2f7cd3b8d31a5cc2ad b2d0a30aa73f8224db16fad2e0e1f5a66db50e03 b36bf7764d3ce1215596d6c238f61fc3a7d7b8b4 b5f9f874fdf360b5e35f45fc3d3052117fcbc603 b86cafaa939a0f9dd9f0255289bfbedb9c85df19 b96b6b8f0c8972b1063b85af9bd09c98131c2f4e ca60147ccfa4b25e69f215607c97542b54fbf910 d3e8534e2bbef736a454b4ac10228037d49c24f9 eeea841fb523dcbdd274577a46f8670d0e475688 ef48c75a0eb1ca297b5c7fb16dcede10810472d4 f704453b7997dfc224df648e2486299260121c59 ff429d1a1ab259d2973ccb21b4a58a3ef53b1ff3

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drwxr-xr-x root/root         0 2020-10-03 07:21 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2020-10-03 07:21 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root     46272 2020-10-03 07:21 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/phast.debug
drwxr-xr-x root/root         0 2020-10-03 07:21 ./usr/share/
drwxr-xr-x root/root         0 2020-10-03 07:21 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-10-03 07:21 ./usr/share/doc/phast-dbgsym -> phast


phast_1.5+dfsg-2_armhf.deb
--------------------------

 new Debian package, version 2.0.
 size 1308400 bytes: control archive=4728 bytes.
    1097 bytes,    22 lines      control              
   12208 bytes,   165 lines      md5sums              
 Package: phast
 Version: 1.5+dfsg-2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 22650
 Depends: libc6 (>= 2.29), liblapack3 | liblapack.so.3, libpcre3
 Section: science
 Priority: optional
 Homepage: http://compgen.cshl.edu/phast/
 Description: phylogenetic analysis with space/time models
  PHAST is a software package for comparative and evolutionary genomics.
  It consists of about half a dozen major programs, plus more than a dozen
  utilities for manipulating sequence alignments, phylogenetic trees, and
  genomic annotations. For the most part, PHAST focuses on two kinds of
  applications: the identification of novel functional elements, including
  protein-coding exons and evolutionarily conserved sequences; and
  statistical phylogenetic modeling, including estimation of model
  parameters, detection of signatures of selection, and reconstruction of
  ancestral sequences.
  .
  PHAST does not support phylogeny reconstruction or sequence alignment,
  and it is designed for use with DNA sequences only (see Comparison).

drwxr-xr-x root/root         0 2020-10-03 07:21 ./
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drwxr-xr-x root/root         0 2020-10-03 07:21 ./usr/bin/
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-rwxr-xr-x root/root    472696 2020-10-03 07:21 ./usr/bin/chooseLines
-rwxr-xr-x root/root    503512 2020-10-03 07:21 ./usr/bin/clean_genes
-rwxr-xr-x root/root    474368 2020-10-03 07:21 ./usr/bin/consEntropy
-rwxr-xr-x root/root    472696 2020-10-03 07:21 ./usr/bin/convert_coords
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-rwxr-xr-x root/root    597160 2020-10-03 07:21 ./usr/bin/dlessP
-rwxr-xr-x root/root    472696 2020-10-03 07:21 ./usr/bin/draw_tree
-rwxr-xr-x root/root    480888 2020-10-03 07:21 ./usr/bin/eval_predictions
-rwxr-xr-x root/root    539928 2020-10-03 07:21 ./usr/bin/exoniphy
-rwxr-xr-x root/root    505464 2020-10-03 07:21 ./usr/bin/hmm_train
-rwxr-xr-x root/root    501368 2020-10-03 07:21 ./usr/bin/hmm_tweak
-rwxr-xr-x root/root    501368 2020-10-03 07:21 ./usr/bin/hmm_view
-rwxr-xr-x root/root    494896 2020-10-03 07:21 ./usr/bin/indelFit
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+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
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Build Architecture: armhf
Build-Space: 224344
Build-Time: 825
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 314
Job: phast_1.5+dfsg-2
Machine Architecture: armhf
Package: phast
Package-Time: 1187
Source-Version: 1.5+dfsg-2
Space: 224344
Status: successful
Version: 1.5+dfsg-2
--------------------------------------------------------------------------------
Finished at 2020-10-08T06:20:59Z
Build needed 00:19:47, 224344k disc space

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