phast →
1.6+dfsg-3 →
armhf → 2021-11-21 06:41:02
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| phast 1.6+dfsg-3 (armhf) Sun, 21 Nov 2021 06:20:46 +0000 |
+==============================================================================+
Package: phast
Version: 1.6+dfsg-3
Source Version: 1.6+dfsg-3
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-a50119ef-cd98-4c15-bf31-e51c2eded938' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.5 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 26.0 MB in 28s (937 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 1869 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main phast 1.6+dfsg-3 (dsc) [2048 B]
Get:2 http://172.17.0.1/private bookworm-staging/main phast 1.6+dfsg-3 (tar) [1809 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main phast 1.6+dfsg-3 (diff) [57.7 kB]
Fetched 1869 kB in 0s (6856 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phast-qgp6o4/phast-1.6+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phast-qgp6o4' 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-YfWcSX/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-YfWcSX/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-YfWcSX/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-YfWcSX/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2666 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 30 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.4 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12500 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, libpcre2-dev, libf2c2-dev, libatlas-base-dev, help2man
Filtered Build-Depends: debhelper-compat (= 13), liblapack-dev, libblas-dev, libtmglib-dev, libpcre2-dev, libf2c2-dev, libatlas-base-dev, help2man
dpkg-deb: building package 'sbuild-build-depends-phast-dummy' in '/<<BUILDDIR>>/resolver-YfWcSX/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-YfWcSX/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ Sources [529 B]
Get:5 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ Packages [610 B]
Fetched 2472 B in 1s (3027 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 bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libatlas-base-dev
libatlas3-base libblas-dev libblas3 libdebhelper-perl libelf1 libf2c2
libf2c2-dev libfile-stripnondeterminism-perl libgfortran5 libicu67
liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre2-16-0 libpcre2-32-0
libpcre2-8-0 libpcre2-dev libpcre2-posix3 libpipeline1 libsigsegv2
libsub-override-perl libtmglib-dev libtmglib3 libtool libuchardet0 libxml2
m4 man-db po-debconf sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libatlas-doc liblapack-doc
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libatlas-base-dev
libatlas3-base libblas-dev libblas3 libdebhelper-perl libelf1 libf2c2
libf2c2-dev libfile-stripnondeterminism-perl libgfortran5 libicu67
liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre2-16-0 libpcre2-32-0
libpcre2-dev libpcre2-posix3 libpipeline1 libsigsegv2 libsub-override-perl
libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf
sbuild-build-depends-phast-dummy sensible-utils
The following packages will be upgraded:
libpcre2-8-0
1 upgraded, 48 newly installed, 0 to remove and 29 not upgraded.
Need to get 29.0 MB of archives.
After this operation, 120 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-YfWcSX/apt_archive ./ sbuild-build-depends-phast-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf libpcre2-8-0 armhf 10.39-2 [213 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.17 [21.5 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-2 [15.5 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf help2man armhf 1.48.5 [143 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-10+rpi1 [234 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf libatlas3-base armhf 3.10.3-11+rpi1 [2287 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libatlas-base-dev armhf 3.10.3-11+rpi1 [2459 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libblas3 armhf 3.10.0-1 [108 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.0-1 [113 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libf2c2 armhf 20140711-1 [110 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libf2c2-dev armhf 20140711-1 [118 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.0-1 [1594 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.0-1 [2872 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf libpcre2-16-0 armhf 10.39-2 [200 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libpcre2-32-0 armhf 10.39-2 [190 kB]
Get:46 http://172.17.0.1/private bookworm-staging/main armhf libpcre2-posix3 armhf 10.39-2 [51.8 kB]
Get:47 http://172.17.0.1/private bookworm-staging/main armhf libpcre2-dev armhf 10.39-2 [629 kB]
Get:48 http://172.17.0.1/private bookworm-staging/main armhf libtmglib3 armhf 3.10.0-1 [95.2 kB]
Get:49 http://172.17.0.1/private bookworm-staging/main armhf libtmglib-dev armhf 3.10.0-1 [94.4 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libpcre2-posix3:armhf (10.39-2) ...
Selecting previously unselected package libpcre2-dev:armhf.
Preparing to unpack .../39-libpcre2-dev_10.39-2_armhf.deb ...
Unpacking libpcre2-dev:armhf (10.39-2) ...
Selecting previously unselected package libtmglib3:armhf.
Preparing to unpack .../40-libtmglib3_3.10.0-1_armhf.deb ...
Unpacking libtmglib3:armhf (3.10.0-1) ...
Selecting previously unselected package libtmglib-dev:armhf.
Preparing to unpack .../41-libtmglib-dev_3.10.0-1_armhf.deb ...
Unpacking libtmglib-dev:armhf (3.10.0-1) ...
Selecting previously unselected package sbuild-build-depends-phast-dummy.
Preparing to unpack .../42-sbuild-build-depends-phast-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-phast-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.4-1) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libpcre2-16-0:armhf (10.39-2) ...
Setting up help2man (1.48.5) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libpcre2-32-0:armhf (10.39-2) ...
Setting up libblas3:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up libgfortran5:armhf (11.2.0-10+rpi1) ...
Setting up libpcre2-posix3:armhf (10.39-2) ...
Setting up sensible-utils (0.0.17) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libf2c2:armhf (20140711-1) ...
Setting up libf2c2-dev:armhf (20140711-1) ...
Setting up libelf1:armhf (0.185-2) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libblas-dev:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libfile-stripnondeterminism-perl (1.12.0-2) ...
Setting up liblapack3:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.21-4) ...
Setting up libatlas3-base:armhf (3.10.3-11+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libpcre2-dev:armhf (10.39-2) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up libatlas-base-dev:armhf (3.10.3-11+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libtmglib3:armhf (3.10.0-1) ...
Setting up liblapack-dev:armhf (3.10.0-1) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.0-2) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up libtmglib-dev:armhf (3.10.0-1) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-phast-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37-5+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.3.0-11+rpi1 gcc-10_10.3.0-11+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.9-2+rpi1
Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-3 binutils_2.37-5+rpi1 binutils-arm-linux-gnueabihf_2.37-5+rpi1 binutils-common_2.37-5+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.3.0-11+rpi1 dash_0.5.11+git20210903+057cd650a4ed-1 debconf_1.5.78 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-2 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.3.0-11+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.3.0-11+rpi1 gcc-10-base_10.3.0-11+rpi1 gcc-11-base_11.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 help2man_1.48.5 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.11 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatlas-base-dev_3.10.3-11+rpi1 libatlas3-base_3.10.3-11+rpi1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-5+rpi1 libblas-dev_3.10.0-1 libblas3_3.10.0-1 libblkid1_2.37.2-4 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-5+rpi1 libctf0_2.37-5+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.4-1 libf2c2_20140711-1 libf2c2-dev_20140711-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.0-2 libgcc-10-dev_10.3.0-11+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgfortran5_11.2.0-10+rpi1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack-dev_3.10.0-1 liblapack3_3.10.0-1 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-4 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-16-0_10.39-2 libpcre2-32-0_10.39-2 libpcre2-8-0_10.39-2 libpcre2-dev_10.39-2 libpcre2-posix3_10.39-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libreadline8_8.1-2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.2-2+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.5-1+rpi1 libtasn1-6_4.17.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-4 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtmglib-dev_3.10.0-1 libtmglib3_3.10.0-1 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.5-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.9-2+rpi1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.37.2-4 ncurses-base_6.2+20201114-4 ncurses-bin_6.2+20201114-4 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-phast-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.jXFdpMzn/trustedkeys.kbx': General error
gpgv: Signature made Fri Nov 19 12:55:46 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./phast_1.6+dfsg-3.dsc
dpkg-source: info: extracting phast in /<<BUILDDIR>>/phast-1.6+dfsg
dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz
dpkg-source: info: unpacking phast_1.6+dfsg-3.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 pcre2.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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-a50119ef-cd98-4c15-bf31-e51c2eded938
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 1.6+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg'
dh_auto_clean
cd src && make clean
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/$dir && make clean ; done
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif'
rm -f *.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif'
rm -f /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../lib/*
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless'
rm -f *.o dless.help dlessP.help /<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../../bin/dless /<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../../bin/dlessP
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel'
rm -f *.o /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsEncode /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsScoreMatrix /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsTrain /<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/util'
rm -f *.o *.help /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/all_dists /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/base_evolve /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/chooseLines /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/clean_genes /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/consEntropy /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/convert_coords /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/draw_tree /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/eval_predictions /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/hmm_train /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/hmm_tweak /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/hmm_view /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/indelFit /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/indelHistory /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/maf_parse /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/makeHKY /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/modFreqs /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_diff /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_split /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_view /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/phast /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/phastBias /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/refeature /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/stringiphy /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/treeGen /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/tree_doctor
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/util'
rm -rf ../bin ../lib ../doc
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg'
Type "make package" to create a tarball reflecting the current state of the CVS tree.
(cd src; make DESTDIR= CLAPACKPATH=/usr/lib )
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
mkdir -p ../bin ../lib
for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util ; do cd /<<BUILDDIR>>/phast-1.6+dfsg/src/$dir && make ; done
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/$dir && make ; done
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_eigen.c: In function 'mat_diagonalize':
phast_eigen.c:62:3: warning: implicit declaration of function 'dgeev_' [-Wimplicit-function-declaration]
62 | dgeev_(&jobvl, &jobvr, &n, tmp, &n, wr, wi, vl,
| ^~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_markov_matrix.c: In function 'mm_exp_higham':
phast_markov_matrix.c:288:5: warning: implicit declaration of function 'dgebal_' [-Wimplicit-function-declaration]
288 | dgebal_(&job, &ln, mat, &ln, &ilo, &ihi, scale, &info);
| ^~~~~~~
phast_markov_matrix.c:403:3: warning: implicit declaration of function 'dgesv_' [-Wimplicit-function-declaration]
403 | dgesv_(&ln, &ln, matU, &ln, ipiv, matV, &ln, &info);
| ^~~~~~
phast_markov_matrix.c:428:5: warning: implicit declaration of function 'dgebak_' [-Wimplicit-function-declaration]
428 | dgebak_(&job, &side, &ln, &ilo, &ihi, scale, &ln, mat, &ln, &info);
| ^~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_matrix.c: In function 'mat_invert':
phast_matrix.c:263:3: warning: implicit declaration of function 'dgetrf_' [-Wimplicit-function-declaration]
263 | dgetrf_(&n, &n, (LAPACK_DOUBLE*)tmp, &n, ipiv, &info);
| ^~~~~~~
phast_matrix.c:273:3: warning: implicit declaration of function 'dgetri_' [-Wimplicit-function-declaration]
273 | dgetri_(&n, (LAPACK_DOUBLE*)tmp, &n, ipiv, work, &lwork, &info);
| ^~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_misc.c -o phast_misc.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_misc.c: In function 'make_name_hash':
phast_misc.c:672:46: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from phast_misc.c:16:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_misc.c:672:35: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
672 | pcre2_compile_context *map_re = str_re_new("^[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*(->|=)[[:space:]]*([A-Za-z0-9_]+)[[:space:]]*");
| ^~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_stringsplus.c -o phast_stringsplus.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_stringsplus.c: In function 'str_re_match_sub':
phast_stringsplus.c:501:25: warning: pointer targets in passing argument 2 of 'pcre2_match_8' differ in signedness [-Wpointer-sign]
501 | rc = pcre2_match(re, s->chars, s->length, offset, 0, match_data, NULL);
| ~^~~~~~~
| |
| char *
In file included from phast_stringsplus.c:16:
/usr/include/pcre2.h:935:1: note: expected 'PCRE2_SPTR8' {aka 'const unsigned char *'} but argument is of type 'char *'
935 | PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phast_stringsplus.c: In function 'str_re_match':
phast_stringsplus.c:532:30: warning: passing argument 2 of 'str_re_match_sub' from incompatible pointer type [-Wincompatible-pointer-types]
532 | return str_re_match_sub(s, re, l, 0, nsubexp, NULL);
| ^~
| |
| pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *}
phast_stringsplus.c:488:45: note: expected 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} but argument is of type 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'}
488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp,
| ^
phast_stringsplus.c: In function 'str_re_search':
phast_stringsplus.c:538:28: warning: passing argument 2 of 'str_re_match_sub' from incompatible pointer type [-Wincompatible-pointer-types]
538 | rc = str_re_match_sub(s, re, l, start_offset, nsubexp, &first_match_idx);
| ^~
| |
| pcre2_compile_context_8 * {aka struct pcre2_real_compile_context_8 *}
phast_stringsplus.c:488:45: note: expected 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} but argument is of type 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'}
488 | int str_re_match_sub(String *s, pcre2_code *re, List *l, int offset, int nsubexp,
| ^
phast_stringsplus.c: In function 'str_re_match_sub':
phast_stringsplus.c:504:52: warning: 'ovector' may be used uninitialized in this function [-Wmaybe-uninitialized]
504 | if (first_match != NULL) (*first_match) = ovector[0];
| ~~~~~~~^~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_vector.c -o phast_vector.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar: creating /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/base'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_local_alignment.c -o phast_local_alignment.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_local_alignment.c: In function 'la_read_lav':
phast_local_alignment.c:50:55: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/local_alignment.h:36,
from phast_local_alignment.c:32:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_local_alignment.c:50:44: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
50 | pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{");
| ^~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_maf.c: In function 'maf_read_cats_subset':
phast_maf.c:29:41: warning: variable 'block_no' set but not used [-Wunused-but-set-variable]
29 | int i, start_idx, length, max_tuples, block_no,
| ^~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_msa.c -o phast_msa.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_msa.c: In function 'msa_read_fasta':
phast_msa.c:264:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_msa.c:39:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_msa.c:264:16: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
264 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)");
| ^
phast_msa.c:257:40: warning: variable 'line_no' set but not used [-Wunused-but-set-variable]
257 | int maxlen, i, nseqs, j, do_toupper, line_no;
| ^~~~~~~
phast_msa.c: In function 'msa_read_seq_fasta':
phast_msa.c:1929:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
1929 | descrip_re = str_re_new("^[[:space:]]*>");
| ^~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_msa.c:39:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_msa.c:1929:16: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
1929 | descrip_re = str_re_new("^[[:space:]]*>");
| ^
phast_msa.c: In function 'msa_format_for_content':
phast_msa.c:2590:22: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_msa.c:39:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_msa.c:2590:9: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
2590 | ss_re = str_re_new("^NSEQS[[:space:]]*=[[:space:]]*([0-9]+)");
| ^
phast_msa.c:2591:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_msa.c:39:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_msa.c:2591:13: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
2591 | phylip_re = str_re_new("^([[:space:]]*([0-9]+))[[:space:]]*[[:space:]]*([0-9]+)");
| ^
phast_msa.c:2592:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
2592 | fasta_re = str_re_new("^>.*");
| ^~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_msa.c:39:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_msa.c:2592:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
2592 | fasta_re = str_re_new("^>.*");
| ^
phast_msa.c:2593:23: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
2593 | lav_re = str_re_new("^#:lav.*");
| ^~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_msa.c:39:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_msa.c:2593:10: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
2593 | lav_re = str_re_new("^#:lav.*");
| ^
phast_msa.c:2594:23: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
2594 | maf_re = str_re_new("^##maf");
| ^~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_msa.c:39:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_msa.c:2594:10: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
2594 | maf_re = str_re_new("^##maf");
| ^
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_multi_msa.c -o phast_multi_msa.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_multi_msa.c: In function 'multimsa_new_from_files':
phast_multi_msa.c:54:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_multi_msa.c:37:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_multi_msa.c:54:38: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
54 | pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)");
| ^~~~~~~~~~
phast_multi_msa.c:55:47: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_multi_msa.c:37:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_multi_msa.c:55:36: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
55 | pcre2_compile_context *alph_re = str_re_new("#[[:space:]]*ALPHABET[[:space:]]*=[[:space:]]*([A-Z]+)");
| ^~~~~~~~~~
phast_multi_msa.c:56:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_multi_msa.c:37:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_multi_msa.c:56:38: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
56 | pcre2_compile_context *format_re = str_re_new("#[[:space:]]*FORMAT[[:space:]]*=[[:space:]]*([A-Z]+)");
| ^~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_sufficient_stats.c -o phast_sufficient_stats.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_sufficient_stats.c: In function 'ss_from_msas':
phast_sufficient_stats.c:140:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
140 | else
| ^~~~
phast_sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
142 | max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1,
| ^~~~~~~~~~
phast_sufficient_stats.c: In function 'ss_read':
phast_sufficient_stats.c:661:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:661:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
661 | nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)");
| ^
phast_sufficient_stats.c:662:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:662:13: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
662 | length_re = str_re_new("LENGTH[[:space:]]*=[[:space:]]*([0-9]+)");
| ^
phast_sufficient_stats.c:663:30: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:663:17: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
663 | tuple_size_re = str_re_new("TUPLE_SIZE[[:space:]]*=[[:space:]]*([0-9]+)");
| ^
phast_sufficient_stats.c:664:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:664:14: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
664 | ntuples_re = str_re_new("NTUPLES[[:space:]]*=[[:space:]]*([0-9]+)");
| ^
phast_sufficient_stats.c:665:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:665:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
665 | names_re = str_re_new("NAMES[[:space:]]*=[[:space:]]*(.*)");
| ^
phast_sufficient_stats.c:666:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:666:11: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
666 | alph_re = str_re_new("ALPHABET[[:space:]]*=[[:space:]]*([-.^A-Za-z ]+)");
| ^
phast_sufficient_stats.c:667:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:667:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
667 | ncats_re = str_re_new("NCATS[[:space:]]*=[[:space:]]*([-0-9]+)");
| ^
phast_sufficient_stats.c:668:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:668:13: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
668 | offset_re = str_re_new("IDX_OFFSET[[:space:]]*=[[:space:]]*([-0-9]+)");
| ^
phast_sufficient_stats.c:669:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:669:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
669 | tuple_re = str_re_new("^([0-9]+)[[:space:]]+([-.^A-Za-z ]+)[[:space:]]+([0-9.[:space:]]+)");
| ^
phast_sufficient_stats.c:670:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
670 | order_re = str_re_new("TUPLE_IDX_ORDER:");
| ^~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_sufficient_stats.c:670:12: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
670 | order_re = str_re_new("TUPLE_IDX_ORDER:");
| ^
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/msa'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_bed.c -o phast_bed.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_bed.c: In function 'gff_print_bed':
phast_bed.c:143:52: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from phast_bed.c:15:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_bed.c:143:41: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
143 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)");
| ^~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_category_map.c -o phast_category_map.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_category_map.c: In function 'cm_read':
phast_category_map.c:39:31: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/category_map.h:92,
from phast_category_map.c:10:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_category_map.c:39:18: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
39 | cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?");
| ^
phast_category_map.c:40:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/category_map.h:92,
from phast_category_map.c:10:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_category_map.c:40:14: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
40 | ncats_re = str_re_new("^[[:space:]]*NCATS[[:space:]]*=[[:space:]]*([[:digit:]]+)");
| ^
phast_category_map.c:41:26: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/category_map.h:92,
from phast_category_map.c:10:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_category_map.c:41:13: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
41 | fill_re = str_re_new("^[[:space:]]*FILL_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$");
| ^
phast_category_map.c:42:27: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/category_map.h:92,
from phast_category_map.c:10:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_category_map.c:42:14: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
42 | label_re = str_re_new("^[[:space:]]*LABELLING_PRECEDENCE[[:space:]]*=[[:space:]]*(.*)$");
| ^
phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/category_map.h:92,
from phast_category_map.c:10:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_category_map.c:43:15: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
43 | extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$");
| ^
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_gff.c -o phast_gff.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_gff.c: In function 'gff_read_set':
phast_gff.c:56:31: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from phast_gff.c:13:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_gff.c:56:18: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
56 | spec_comment_re = str_re_new("^[[:space:]]*##[[:space:]]*([^[:space:]]+)[[:space:]]+([^[:space:]]+)([[:space:]]+([^[:space:]]+))?");
| ^
phast_gff.c: In function 'gff_new_feature_genomic_pos':
phast_gff.c:272:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from phast_gff.c:13:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_gff.c:272:11: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
272 | posre = str_re_new("(chr[_a-zA-Z0-9]+):([0-9]+)-([0-9]+)([-+])?");
| ^
phast_gff.c: In function 'gff_group':
phast_gff.c:688:23: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
688 | tag_re = str_re_new(tmpstr);
| ^~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from phast_gff.c:13:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_gff.c:688:10: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
688 | tag_re = str_re_new(tmpstr);
| ^
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_wig.c -o phast_wig.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/feature'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_hmm.c -o phast_hmm.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_phylo_p_print.c: In function 'print_feats_generic':
phast_phylo_p_print.c:752:50: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_phylo_p_print.c:17:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_phylo_p_print.c:752:39: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
752 | pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)");
| ^~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_phylo_hmm.c -o phast_phylo_hmm.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_motif.c: In function 'mtf_print':
phast_motif.c:1411:7: warning: '%s' directive argument is null [-Wformat-overflow=]
1411 | fprintf(F, "\t%s\n", (char*)lst_get_ptr(notfound, i));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
phast_motif.c: In function 'mtf_print_html':
phast_motif.c:1604:7: warning: '%s' directive argument is null [-Wformat-overflow=]
1604 | fprintf(F, "<li>%s\n", (char*)lst_get_ptr(notfound, i));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_tfbs.c -o phast_tfbs.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_tfbs.c: In function 'pwm_read':
phast_tfbs.c:147:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_tfbs.c:16:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_tfbs.c:147:11: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
147 | pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)");
| ^
phast_tfbs.c:148:30: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_tfbs.c:16:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_tfbs.c:148:17: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
148 | motif_name_re = str_re_new("^MOTIF[[:space:]]+(.+?)[[:space:]].*");
| ^
phast_tfbs.c: In function 'ms_read':
phast_tfbs.c:229:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from phast_tfbs.c:16:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_tfbs.c:229:16: warning: assignment to 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
229 | descrip_re = str_re_new("[[:space:]]*>[[:space:]]*(.+)");
| ^
phast_tfbs.c:219:32: warning: variable 'line_no' set but not used [-Wunused-but-set-variable]
219 | int i, nseqs, j, do_toupper, line_no;
| ^~~~~~~
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o
ar rs /<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o
make[4]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib/motif'
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/lib'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless'
../munge-help.sh dless.help_src > dless.help
../munge-help.sh dlessP.help_src > dlessP.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
make[3]: *** No rule to make target 'bd_phylo_hmm.o', needed by '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless/../../bin/dless'. Stop.
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/dless'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy'
../munge-help.sh exoniphy.help_src > exoniphy.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/exoniphy'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons'
../munge-help.sh phastCons.help_src > phastCons.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastCons'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds'
../munge-help.sh phastOdds.help_src > phastOdds.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastOdds'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif'
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phastMotif.c: In function 'main':
phastMotif.c:131:13: warning: variable 'separate_backgd' set but not used [-Wunused-but-set-variable]
131 | int i, j, separate_backgd = 0,
| ^~~~~~~~~~~~~~~
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phastMotif'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit'
../munge-help.sh phyloFit.help_src > phyloFit.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloFit'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot'
../munge-help.sh phyloBoot.help_src > phyloBoot.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloBoot'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP'
../munge-help.sh phyloP.help_src > phyloP.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/phyloP'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel'
../munge-help.sh pbsDecode.help_src > pbsDecode.help
../munge-help.sh pbsEncode.help_src > pbsEncode.help
../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help
../munge-help.sh pbsTrain.help_src > pbsTrain.help
../munge-help.sh prequel.help_src > prequel.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
make[3]: *** No rule to make target 'simplex_grid.o', needed by '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel/../../bin/pbsDecode'. Stop.
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/prequel'
make[3]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/util'
../munge-help.sh base_evolve.help_src > base_evolve.help
../munge-help.sh clean_genes.help_src > clean_genes.help
../munge-help.sh consEntropy.help_src > consEntropy.help
../munge-help.sh indelFit.help_src > indelFit.help
../munge-help.sh indelHistory.help_src > indelHistory.help
../munge-help.sh makeHKY.help_src > makeHKY.help
../munge-help.sh modFreqs.help_src > modFreqs.help
../munge-help.sh msa_diff.help_src > msa_diff.help
../munge-help.sh phast.help_src > phast.help
../munge-help.sh phastBias.help_src > phastBias.help
../munge-help.sh treeGen.help_src > treeGen.help
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
display_rate_matrix.c: In function 'do_context_dependent_ti_tv':
display_rate_matrix.c:204:8: warning: variable 'tuple_i' set but not used [-Wunused-but-set-variable]
204 | char tuple_i[mod->order+2], tuple_j[mod->order+2];
| ^~~~~~~
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
msa_view.c: In function 'fill_with_Ns':
msa_view.c:361:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| char *
In file included from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/gff.h:21,
from /<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/msa.h:19,
from msa_view.c:14:
/<<BUILDDIR>>/phast-1.6+dfsg/src/../include/phast/stringsplus.h:386:45: note: expected 'const unsigned char *' but argument is of type 'char *'
386 | pcre2_code *str_re_new(const unsigned char *re_str);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~
msa_view.c:361:38: warning: initialization of 'pcre2_compile_context_8 *' {aka 'struct pcre2_real_compile_context_8 *'} from incompatible pointer type 'pcre2_code_8 *' {aka 'struct pcre2_real_code_8 *'} [-Wincompatible-pointer-types]
361 | pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)");
| ^~~~~~~~~~
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
gcc -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/phast-1.6+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -L/<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../lib -o /<<BUILDDIR>>/phast-1.6+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src/util'
mkdir -p ../doc/man/
Generating man pages...
USAGE: convert_coords -m <msa_fname> -f <feature_fname> [-s <src_frame>] [-d <dest_frame>] [-p] [-n] [-i PHYLIP|FASTA|MPM]
DESCRIPTION:
Converts coordinates of features in a GFF file according to a multiple
alignment. Will map from the coordinate system of any sequence to any
other sequence; can also map to or from the coordinate system of the
entire alignment. In addition, supports translation of coordinates by
specified offset.
OPTIONS:
-m <msa_fname> (required) Name of file in which alignment is defined.
-f <gff_fname> (required) Name of file in which features are defined (GFF).
-s <src_frame> Index of frame of reference for feature coordinates, as
defined in the GFF file. Use an integer 1-N (if N seqs)
or 0 to indicate the coordinate system of the alignment
as a whole. Default behavior is to match features with
alignment sequences by name (feature by feature).
-d <dest_frame> Index of destination frame of reference. Default is 0
(whole MSA).
-p <coord_off> Positive coordinate offset. This value will be
added to all coordinates. Useful when
the alignment (or sequence) for which the coordinates
are specified is a sub-alignment of yours.
-n <coord_off> Negative coordinate offset. This value will be
subtracted from all coordinates. Useful when your
alignment is a sub-alignment of the alignment (or
sequence) for which the coordinates are specified.
-i FASTA|PHYLIP|MPM|SS
Alignment format. Default is to guess format from file
contents
PROGRAM: draw_tree
DESCRIPTION: Produces a simple postscript rendering of a tree.
USAGE: draw_tree [-dbvs] <tree.nh>|<tree.mod>
OPTIONS:
<tree_fname> (Required) File name of tree (expected to be in
Newick format, unless filename ends with '.mod', in
which case expected to be a tree model file).
-d Print "diagonal" branches, instead of "right-angle" or
"square" ones (produces a "cladogram", as opposed to a
"phenogram"). This option implies -s.
-b Suppress branch lengths.
-v Vertical layout.
-s Don't draw branches to scale.
Done.
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg'
cd test && PATH=/<<BUILDDIR>>/phast-1.6+dfsg/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/test'
*** Testing msa_view ***
msa_view hmrc.ss -i SS --end 10000 > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o PHYLIP > hmrc.ph
msa_view hmrc.ph -i PHYLIP > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm
msa_view hmrc.mpm --in-format MPM > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o SS > hmrc_short_a.ss
msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss
if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi
msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa
msa_view --seqs human,cow hmrc.fa > hm_b.fa
if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa
msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa
if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa
msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa
if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa
msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa
if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --summary -i SS > hmrc_summary
if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi
-e Passed all tests.
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/test'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install --destdir=debian/phast/ -a
make -j4 install DESTDIR=/<<BUILDDIR>>/phast-1.6\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg'
(cd src; make install DESTDIR=/<<BUILDDIR>>/phast-1.6+dfsg/debian/phast )
make[2]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
mkdir -p /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/bin/
mkdir -p /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/share/phast/data/
mkdir -p /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/share/man/man1/
cp ../bin/* /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/bin/
cp -R ../data/* /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/share/phast/data/
cp -R ../doc/man/* /<<BUILDDIR>>/phast-1.6+dfsg/debian/phast/usr/share/man/man1/
make[2]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<BUILDDIR>>/phast-1.6+dfsg'
dh_installexamples
find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/phast-1.6+dfsg'
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
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/indelFit debian/phast/usr/bin/treeGen debian/phast/usr/bin/stringiphy debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/maf_parse debian/phast/usr/bin/phastOdds debian/phast/usr/bin/makeHKY debian/phast/usr/bin/consEntropy debian/phast/usr/bin/phyloFit debian/phast/usr/bin/modFreqs debian/phast/usr/bin/phyloP debian/phast/usr/bin/clean_genes debian/phast/usr/bin/chooseLines debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/hmm_train debian/phast/usr/bin/draw_tree debian/phast/usr/bin/exoniphy debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/msa_diff debian/phast/usr/bin/phastCons debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/convert_coords debian/phast/usr/bin/phastMotif debian/phast/usr/bin/base_evolve debian/phast/usr/bin/phastBias debian/phast/usr/bin/msa_view debian/phast/usr/bin/msa_split debian/phast/usr/bin/all_dists debian/phast/usr/bin/refeature debian/phast/usr/bin/indelHistory debian/phast/usr/bin/hmm_view were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'phast' in '../phast_1.6+dfsg-3_armhf.deb'.
dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../phast_1.6+dfsg-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-11-21T06:40:50Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phast_1.6+dfsg-3_armhf.changes:
-------------------------------
Format: 1.8
Date: Fri, 19 Nov 2021 13:17:54 +0100
Source: phast
Binary: phast phast-dbgsym
Architecture: armhf
Version: 1.6+dfsg-3
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phast - phylogenetic analysis with space/time models
Closes: 1000000 1000163
Changes:
phast (1.6+dfsg-3) unstable; urgency=medium
.
* Port to pcre2
Closes: #1000000, #1000163
Checksums-Sha1:
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Checksums-Sha256:
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Files:
8675cbf85156fee58f6267b98394f731 24046528 debug optional phast-dbgsym_1.6+dfsg-3_armhf.deb
613fdc4ddea5e3af7b7dcfd6ef547ce6 5395 science optional phast_1.6+dfsg-3_armhf.buildinfo
537c77582a95cc85214a9ef325a1c8f4 2389188 science optional phast_1.6+dfsg-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phast-dbgsym_1.6+dfsg-3_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 24046528 bytes: control archive=2100 bytes.
1682 bytes, 12 lines control
3583 bytes, 34 lines md5sums
Package: phast-dbgsym
Source: phast
Version: 1.6+dfsg-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 26044
Depends: phast (= 1.6+dfsg-3)
Section: debug
Priority: optional
Description: debug symbols for phast
Build-Ids: 072f85582c59f972f09a704c124fbab9f59eb302 22ccc2c2b7a35e0f94f42332cca181fe324af7e5 323a0938ce3f074fcae65a8d97eade07d5c0d077 32fb3d92a083f38b6188851e56d108199023f313 3bdf37958f76ddb5229cc02582563484a54a23c4 4229b0481caa4ca047c0a1b1be40597482543ddf 4ab5239b96545a0a1f83f85b87083f6cec06b4b5 4dd24aaed6b4da1b5cbce27ed114ff61d46ea3be 5ded8649576a9e281abad6dc67d0eadc16ecbc98 67c4e04945b42498d46615c071aa03f776365d59 68f1a456db3fa3877ebd3d1c6591dfb43559bf42 6ace266f761538f910cd3478226d1aed60d9db5d 6dab3ea716e6059a4758799debb85f676b3b11df 7cc82215da9c6e3585c94257fd7b0e7ec15aad3c 7cf720edbb64338663319f816429531e51c7816e 8dede43dffeacd1bbe4809ba2cdd93d2d9a64acc 8ff37012cc835258362d36efb2e72f995195edb7 916d998eeb2933f5a81eb5e4e76c21bebe23d3dd 9a08014c90e5e5eefe9404da61b96642aad3127a 9f3fbc30db4f5d4d6570eeca4e91e34f4d9cd126 b577a24792a2dce1fde9f9a784276ecdd07a0611 b801227fb5f3a7a242b282dde4905516cac928fa bc999f66bd06acda81518dbcb9c25d585ea1b4b0 c549c03263986c7e59fd1c562471f7c5d08721eb c9c7ef76b24188097d64fe281e980ea4d9b1684b ca69eb181d8eb45c90a4a0869afb5ddb7a770dcc cf4cc3997349c8f9d20c40a7e56107df4412e8d0 db2997791138b5c5983736397351b2f872253e04 e501bed73b284c90b4adc0f7dfbc0f06cbf75dcb e767fe43c043ae2f2d28430b7058b35b916c1651 ec4e7f4c74472722ce8bda354cf5c7e32ae2a17c f196989d320513a6ef2d9549c52c184a969091f3 f62ba6c41cb92ea3cda6139bc08d67fa6caa77ce
drwxr-xr-x root/root 0 2021-11-19 12:17 ./
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phast_1.6+dfsg-3_armhf.deb
--------------------------
new Debian package, version 2.0.
size 2389188 bytes: control archive=5532 bytes.
1112 bytes, 22 lines control
14785 bytes, 195 lines md5sums
Package: phast
Version: 1.6+dfsg-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 20446
Depends: libc6 (>= 2.29), liblapack3 | liblapack.so.3, libpcre2-8-0 (>= 10.22)
Section: science
Priority: optional
Homepage: http://compgen.cshl.edu/phast/
Description: phylogenetic analysis with space/time models
PHAST is a software package for comparative and evolutionary genomics.
It consists of about half a dozen major programs, plus more than a dozen
utilities for manipulating sequence alignments, phylogenetic trees, and
genomic annotations. For the most part, PHAST focuses on two kinds of
applications: the identification of novel functional elements, including
protein-coding exons and evolutionarily conserved sequences; and
statistical phylogenetic modeling, including estimation of model
parameters, detection of signatures of selection, and reconstruction of
ancestral sequences.
.
PHAST does not support phylogeny reconstruction or sequence alignment,
and it is designed for use with DNA sequences only (see Comparison).
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drwxr-xr-x root/root 0 2021-11-19 12:17 ./usr/share/phast/data/phastCons/
-rw-r--r-- root/root 103302 2021-11-19 12:17 ./usr/share/phast/data/phastCons/simple-coding-indels.hmm
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 190068
Build-Time: 805
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 346
Job: phast_1.6+dfsg-3
Machine Architecture: armhf
Package: phast
Package-Time: 1204
Source-Version: 1.6+dfsg-3
Space: 190068
Status: successful
Version: 1.6+dfsg-3
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Finished at 2021-11-21T06:40:50Z
Build needed 00:20:04, 190068k disc space