phast →
1.6+dfsg-4 →
armhf → 2023-12-25 11:21:35
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| phast 1.6+dfsg-4 (armhf) Mon, 25 Dec 2023 11:19:14 +0000 |
+==============================================================================+
Package: phast
Version: 1.6+dfsg-4
Source Version: 1.6+dfsg-4
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-579e945d-a0e4-42cc-85f1-d506e8ef6152' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/phast-k8iOc3/resolver-nfVbBj' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.3 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.3 MB in 5s (5546 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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://172.17.4.1/private trixie-staging/main phast 1.6+dfsg-4 (dsc) [2044 B]
Get:2 http://172.17.4.1/private trixie-staging/main phast 1.6+dfsg-4 (tar) [1809 kB]
Get:3 http://172.17.4.1/private trixie-staging/main phast 1.6+dfsg-4 (diff) [57.9 kB]
Fetched 1869 kB in 0s (6568 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/phast-k8iOc3/phast-1.6+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/phast-k8iOc3' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, libtmglib-dev, libpcre2-dev, help2man, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), liblapack-dev, libblas-dev, libtmglib-dev, libpcre2-dev, help2man, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [712 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [716 B]
Fetched 2037 B in 0s (0 B/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
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 libblas-dev libblas3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgfortran5
libicu72 liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre2-16-0
libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 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 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 libblas-dev libblas3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgfortran5
libicu72 liblapack-dev liblapack3 libmagic-mgc libmagic1 libpcre2-16-0
libpcre2-32-0 libpcre2-dev libpcre2-posix3 libpipeline1 libsub-override-perl
libtmglib-dev libtmglib3 libtool libuchardet0 libxml2 m4 man-db po-debconf
sbuild-build-depends-main-dummy sensible-utils
0 upgraded, 43 newly installed, 0 to remove and 2 not upgraded.
Need to get 24.8 MB of archives.
After this operation, 100.0 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [904 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-2 [81.2 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.9 [82.3 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.9 [956 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf help2man armhf 1.49.3 [198 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libblas-dev armhf 3.11.0-2 [106 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-7+rpi1 [247 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf liblapack-dev armhf 3.11.0-2 [3007 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libpcre2-16-0 armhf 10.42-4 [211 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libpcre2-32-0 armhf 10.42-4 [201 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libpcre2-posix3 armhf 10.42-4 [55.1 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libpcre2-dev armhf 10.42-4 [648 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libtmglib3 armhf 3.11.0-2 [86.5 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libtmglib-dev armhf 3.11.0-2 [86.2 kB]
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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 autopoint (0.21-14) ...
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Setting up autoconf (2.71-3) ...
Setting up libpcre2-posix3:armhf (10.42-4) ...
Setting up sensible-utils (0.0.20) ...
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Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
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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 automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up liblapack3:armhf (3.11.0-2) ...
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 (0.21-14) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up dh-strip-nondeterminism (1.13.1-1) ...
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Processing triggers for libc-bin (2.37-12+rpi2) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-2 bsdutils_1:2.39.3-2 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-7+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.9 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 gcc-13-base_13.2.0-7+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_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 help2man_1.49.3 hostname_3.23+nmu1 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-7+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-7+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libblas-dev_3.11.0-2 libblas3_3.11.0-2 libblkid1_2.39.3-2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-3 libcap2_1:2.66-4 libcc1-0_13.2.0-7+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.11.9 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libext2fs2_1.47.0-2 libfakeroot_1.32.2-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-7+rpi1 libgcc-s1_13.2.0-7+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran5_13.2.0-7+rpi1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.2-1 libgomp1_13.2.0-7+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 liblapack-dev_3.11.0-2 liblapack3_3.11.0-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblocale-gettext-perl_1.07-6 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.3-2 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231209-1 libnettle8_3.9.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-2 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-16-0_10.42-4 libpcre2-32-0_10.42-4 libpcre2-8-0_10.42-4 libpcre2-dev_10.42-4 libpcre2-posix3_10.42-4 libperl5.36_5.36.0-10 libpipeline1_1.5.7-1 libreadline8_8.2-3 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-2 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-glob-perl_0.11-3 libtext-iconv-perl_1.7-8 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtmglib-dev_3.11.0-2 libtmglib3_3.11.0-2 libtool_2.4.7-7 libubsan1_13.2.0-7+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.3-2 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20231126-1 mount_2.39.3-2 nano_7.2-1 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-10 perl-base_5.36.0-10 perl-modules-5.36_5.36.0-10 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-5 tar_1.34+dfsg-1.3 tzdata_2023c-11 usr-is-merged_38 usrmerge_38 util-linux_2.39.3-2 xz-utils_5.4.5-0.1 zlib1g_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: phast
Binary: phast
Architecture: any
Version: 1.6+dfsg-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: http://compgen.cshl.edu/phast/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/phast
Vcs-Git: https://salsa.debian.org/med-team/phast.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, libtmglib-dev, libpcre2-dev, help2man
Package-List:
phast deb science optional arch=any
Checksums-Sha1:
5bf657d4f4556f8848c6e4f362b407ec998cf10a 1808800 phast_1.6+dfsg.orig.tar.xz
c0f74aa42bbb46eebe231f0adcb642694330bedf 57936 phast_1.6+dfsg-4.debian.tar.xz
Checksums-Sha256:
7deae15e8bd8ce8e11b251b42795e0595dd86271360b08d15e6ba107ae66863f 1808800 phast_1.6+dfsg.orig.tar.xz
7f5b1adf0df0a8290be8f07117762b2bea42720e2e9b2752e54f680b187f0678 57936 phast_1.6+dfsg-4.debian.tar.xz
Files:
b625b9d3abbe0fdc31468820121b30e9 1808800 phast_1.6+dfsg.orig.tar.xz
2a268ec20d4b5b60d354fae365dc5c3e 57936 phast_1.6+dfsg-4.debian.tar.xz
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-----END PGP SIGNATURE-----
gpgv: Signature made Fri Dec 22 16:28:45 2023 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./phast_1.6+dfsg-4.dsc: no acceptable signature found
dpkg-source: info: extracting phast in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking phast_1.6+dfsg.orig.tar.xz
dpkg-source: info: unpacking phast_1.6+dfsg-4.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 disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-579e945d-a0e4-42cc-85f1-d506e8ef6152
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package phast
dpkg-buildpackage: info: source version 1.6+dfsg-4
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 '/<<PKGBUILDDIR>>'
dh_auto_clean
cd src && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<PKGBUILDDIR>>/src/lib/$dir && make clean ; done
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/base'
rm -f *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/base'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/msa'
rm -f *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/msa'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/feature'
rm -f *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/feature'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/hmm'
rm -f *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/hmm'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/phylo'
rm -f *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/phylo'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/phylo_hmm'
rm -f *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/phylo_hmm'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/motif'
rm -f *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/motif'
rm -f /<<PKGBUILDDIR>>/src/lib/../../lib/*
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/lib'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dless'
rm -f *.o dless.help dlessP.help /<<PKGBUILDDIR>>/src/dless/../../bin/dless /<<PKGBUILDDIR>>/src/dless/../../bin/dlessP
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/dless'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/exoniphy'
rm -f *.o *.help /<<PKGBUILDDIR>>/src/exoniphy/../../bin/exoniphy
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/exoniphy'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phastCons'
rm -f *.o /<<PKGBUILDDIR>>/src/phastCons/../../bin/phastCons phastCons.help
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phastCons'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phastOdds'
rm -f *.o *.help /<<PKGBUILDDIR>>/src/phastOdds/../../bin/phastOdds
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phastOdds'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phastMotif'
rm -f *.o /<<PKGBUILDDIR>>/src/phastMotif/../../bin/phastMotif
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phastMotif'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phyloFit'
rm -f *.o /<<PKGBUILDDIR>>/src/phyloFit/../../bin/phyloFit phyloFit.help
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phyloFit'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phyloBoot'
rm -f *.o *.help /<<PKGBUILDDIR>>/src/phyloBoot/../../bin/phyloBoot
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phyloBoot'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phyloP'
rm -f *.o /<<PKGBUILDDIR>>/src/phyloP/../../bin/phyloP phyloP.help
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phyloP'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/prequel'
rm -f *.o /<<PKGBUILDDIR>>/src/prequel/../../bin/pbsDecode /<<PKGBUILDDIR>>/src/prequel/../../bin/pbsEncode /<<PKGBUILDDIR>>/src/prequel/../../bin/pbsScoreMatrix /<<PKGBUILDDIR>>/src/prequel/../../bin/pbsTrain /<<PKGBUILDDIR>>/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/prequel'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/util'
rm -f *.o *.help /<<PKGBUILDDIR>>/src/util/../../bin/all_dists /<<PKGBUILDDIR>>/src/util/../../bin/base_evolve /<<PKGBUILDDIR>>/src/util/../../bin/chooseLines /<<PKGBUILDDIR>>/src/util/../../bin/clean_genes /<<PKGBUILDDIR>>/src/util/../../bin/consEntropy /<<PKGBUILDDIR>>/src/util/../../bin/convert_coords /<<PKGBUILDDIR>>/src/util/../../bin/display_rate_matrix /<<PKGBUILDDIR>>/src/util/../../bin/draw_tree /<<PKGBUILDDIR>>/src/util/../../bin/eval_predictions /<<PKGBUILDDIR>>/src/util/../../bin/hmm_train /<<PKGBUILDDIR>>/src/util/../../bin/hmm_tweak /<<PKGBUILDDIR>>/src/util/../../bin/hmm_view /<<PKGBUILDDIR>>/src/util/../../bin/indelFit /<<PKGBUILDDIR>>/src/util/../../bin/indelHistory /<<PKGBUILDDIR>>/src/util/../../bin/maf_parse /<<PKGBUILDDIR>>/src/util/../../bin/makeHKY /<<PKGBUILDDIR>>/src/util/../../bin/modFreqs /<<PKGBUILDDIR>>/src/util/../../bin/msa_diff /<<PKGBUILDDIR>>/src/util/../../bin/msa_split /<<PKGBUILDDIR>>/src/util/../../bin/msa_view /<<PKGBUILDDIR>>/src/util/../../bin/phast /<<PKGBUILDDIR>>/src/util/../../bin/phastBias /<<PKGBUILDDIR>>/src/util/../../bin/refeature /<<PKGBUILDDIR>>/src/util/../../bin/stringiphy /<<PKGBUILDDIR>>/src/util/../../bin/treeGen /<<PKGBUILDDIR>>/src/util/../../bin/tree_doctor
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/util'
rm -rf ../bin ../lib ../doc
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/$dir && make ; done
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /<<PKGBUILDDIR>>/src/lib/$dir && make ; done
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/base'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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:
/<<PKGBUILDDIR>>/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:]]*");
| ^~~~~~~~~~
phast_misc.c: In function ‘phast_fclose’:
phast_misc.c:301:5: warning: pointer ‘f’ used after ‘fclose’ [-Wuse-after-free]
301 | unregister_open_file(f);
| ^~~~~~~~~~~~~~~~~~~~~~~
phast_misc.c:300:5: note: call to ‘fclose’ here
300 | fclose(f);
| ^~~~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 [-Wmaybe-uninitialized]
504 | if (first_match != NULL) (*first_match) = ovector[0];
| ~~~~~~~^~~
phast_stringsplus.c:491:15: note: ‘ovector’ was declared here
491 | PCRE2_SIZE *ovector;
| ^~~~~~~
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/lib/base/../../../lib/libphast.a
ar rs /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/src/lib/base'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/msa'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/../include/phast/local_alignment.h:36,
from phast_local_alignment.c:32:
/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/../include/phast/gff.h:21,
from /<<PKGBUILDDIR>>/src/../include/phast/msa.h:19,
from phast_msa.c:39:
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/../include/phast/gff.h:21,
from /<<PKGBUILDDIR>>/src/../include/phast/msa.h:19,
from phast_multi_msa.c:37:
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/../include/phast/gff.h:21,
from /<<PKGBUILDDIR>>/src/../include/phast/msa.h:19,
from /<<PKGBUILDDIR>>/src/../include/phast/sufficient_stats.h:20,
from phast_sufficient_stats.c:11:
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/src/lib/msa'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/feature'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/../include/phast/gff.h:21,
from phast_bed.c:15:
/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/../include/phast/gff.h:21,
from /<<PKGBUILDDIR>>/src/../include/phast/category_map.h:92,
from phast_category_map.c:10:
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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:56:38: 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 /<<PKGBUILDDIR>>/src/../include/phast/gff.h:21,
from phast_gff.c:13:
/<<PKGBUILDDIR>>/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:56:25: 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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<PKGBUILDDIR>>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<PKGBUILDDIR>>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<PKGBUILDDIR>>/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/src/lib/feature'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/hmm'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o
ar rs /<<PKGBUILDDIR>>/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/hmm'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/phylo'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/../include/phast/gff.h:21,
from /<<PKGBUILDDIR>>/src/../include/phast/msa.h:19,
from phast_phylo_p_print.c:17:
/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/src/lib/phylo'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/phylo_hmm'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o
ar rs /<<PKGBUILDDIR>>/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/phylo_hmm'
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/lib/motif'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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:1411:21: 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:1604:23: 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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/lib/../..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/../include/phast/gff.h:21,
from /<<PKGBUILDDIR>>/src/../include/phast/msa.h:19,
from phast_tfbs.c:16:
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 *
/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o
ar rs /<<PKGBUILDDIR>>/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/lib/motif'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/lib'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dless'
../munge-help.sh dless.help_src > dless.help
../munge-help.sh dlessP.help_src > dlessP.help
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/src/dless/../../bin/dless'. Stop.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/dless'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/exoniphy'
../munge-help.sh exoniphy.help_src > exoniphy.help
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/exoniphy/../../lib -o /<<PKGBUILDDIR>>/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/exoniphy'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phastCons'
../munge-help.sh phastCons.help_src > phastCons.help
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/phastCons/../../lib -o /<<PKGBUILDDIR>>/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phastCons'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phastOdds'
../munge-help.sh phastOdds.help_src > phastOdds.help
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/phastOdds/../../lib -o /<<PKGBUILDDIR>>/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phastOdds'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phastMotif'
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/phastMotif/../../lib -o /<<PKGBUILDDIR>>/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phastMotif'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phyloFit'
../munge-help.sh phyloFit.help_src > phyloFit.help
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/phyloFit/../../lib -o /<<PKGBUILDDIR>>/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phyloFit'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phyloBoot'
../munge-help.sh phyloBoot.help_src > phyloBoot.help
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/phyloBoot/../../lib -o /<<PKGBUILDDIR>>/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phyloBoot'
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/phyloP'
../munge-help.sh phyloP.help_src > phyloP.help
gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/phyloP/../../lib -o /<<PKGBUILDDIR>>/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/phyloP'
make[3]: Entering directory '/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/src/prequel/../../bin/pbsDecode'. Stop.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/prequel'
make[3]: Entering directory '/<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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 /<<PKGBUILDDIR>>/src/../include/phast/gff.h:21,
from /<<PKGBUILDDIR>>/src/../include/phast/msa.h:19,
from msa_view.c:14:
/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -O3 -Wall -I/<<PKGBUILDDIR>>/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/src/..\" -fno-strict-aliasing -O3 -Wall -I/<<PKGBUILDDIR>>/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/<<PKGBUILDDIR>>/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
tree_doctor.c: In function ‘main’:
tree_doctor.c:348:19: warning: the comparison will always evaluate as ‘true’ for the address of ‘name’ will never be NULL [-Waddress]
348 | if (n->name != NULL && n->name[0] != '\0' &&
| ^~
In file included from /<<PKGBUILDDIR>>/src/../include/phast/tree_model.h:26,
from tree_doctor.c:14:
/<<PKGBUILDDIR>>/src/../include/phast/trees.h:47:8: note: ‘name’ declared here
47 | char name [STR_MED_LEN]; /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */
| ^~~~
gcc -L/<<PKGBUILDDIR>>/src/util/../../lib -o /<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd test && PATH=/<<PKGBUILDDIR>>/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games make msa_view
make[2]: Entering directory '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/test'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
(cd src; make install DESTDIR=/<<PKGBUILDDIR>>/debian/phast )
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
mkdir -p /<<PKGBUILDDIR>>/debian/phast/usr/bin/
mkdir -p /<<PKGBUILDDIR>>/debian/phast/usr/share/phast/data/
mkdir -p /<<PKGBUILDDIR>>/debian/phast/usr/share/man/man1/
cp ../bin/* /<<PKGBUILDDIR>>/debian/phast/usr/bin/
cp -R ../data/* /<<PKGBUILDDIR>>/debian/phast/usr/share/phast/data/
cp -R ../doc/man/* /<<PKGBUILDDIR>>/debian/phast/usr/share/man/man1/
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installexamples
find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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/clean_genes debian/phast/usr/bin/treeGen debian/phast/usr/bin/hmm_tweak debian/phast/usr/bin/indelFit debian/phast/usr/bin/consEntropy debian/phast/usr/bin/makeHKY debian/phast/usr/bin/stringiphy debian/phast/usr/bin/chooseLines debian/phast/usr/bin/phastOdds debian/phast/usr/bin/hmm_view debian/phast/usr/bin/phyloFit debian/phast/usr/bin/convert_coords debian/phast/usr/bin/eval_predictions debian/phast/usr/bin/exoniphy debian/phast/usr/bin/phastBias debian/phast/usr/bin/indelHistory debian/phast/usr/bin/phastMotif debian/phast/usr/bin/tree_doctor debian/phast/usr/bin/hmm_train debian/phast/usr/bin/msa_split debian/phast/usr/bin/phyloP debian/phast/usr/bin/modFreqs debian/phast/usr/bin/msa_diff debian/phast/usr/bin/base_evolve debian/phast/usr/bin/phyloBoot debian/phast/usr/bin/maf_parse debian/phast/usr/bin/phastCons debian/phast/usr/bin/all_dists debian/phast/usr/bin/msa_view debian/phast/usr/bin/refeature debian/phast/usr/bin/display_rate_matrix debian/phast/usr/bin/draw_tree 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-4_armhf.deb'.
dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.6+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any -O../phast_1.6+dfsg-4_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../phast_1.6+dfsg-4_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 2023-12-25T11:21:30Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
phast_1.6+dfsg-4_armhf.changes:
-------------------------------
Format: 1.8
Date: Wed, 29 Nov 2023 10:25:18 +0100
Source: phast
Binary: phast phast-dbgsym
Architecture: armhf
Version: 1.6+dfsg-4
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
phast - phylogenetic analysis with space/time models
Closes: 1056681
Changes:
phast (1.6+dfsg-4) unstable; urgency=medium
.
[ Andreas Tille ]
* s/libatlas-base-dev/liblapacke-dev/ in Build-Depends to use LAPACKE
instead of clapack
* Provide alternative Build-Depends to liblapack-dev and libblas-dev
* Standards-Version: 4.6.2 (routine-update)
* Upstream email removed from d/copyright since its bouncing
.
[ Sébastien Villemot ]
* Complete migration away from ATLAS
Closes: #1056681
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Files:
365529b5af025894634c5b7b654eba16 25076956 debug optional phast-dbgsym_1.6+dfsg-4_armhf.deb
2ef17e9efc5ace35963bb0aad9ab99ff 5593 science optional phast_1.6+dfsg-4_armhf.buildinfo
98ff7ce17dbec8721fca7d397c3dd8e3 2427516 science optional phast_1.6+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: phast
Binary: phast phast-dbgsym
Architecture: armhf
Version: 1.6+dfsg-4
Checksums-Md5:
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Checksums-Sha1:
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Checksums-Sha256:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Mon, 25 Dec 2023 11:21:30 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.3),
bash (= 5.2.21-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.3-2),
bsdutils (= 1:2.39.3-2),
build-essential (= 12.10),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-13+rpi1),
cpp-13 (= 13.2.0-7+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.9),
debianutils (= 5.14),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-7+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-13+rpi1),
gcc-12-base (= 12.3.0-13+rpi1),
gcc-13 (= 13.2.0-7+rpi1),
gcc-13-base (= 13.2.0-7+rpi1),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
grep (= 3.11-3),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
help2man (= 1.49.3),
hostname (= 3.23+nmu1),
init-system-helpers (= 1.66),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-7+rpi1),
libatomic1 (= 13.2.0-7+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.2-1),
libaudit1 (= 1:3.1.2-1),
libbinutils (= 2.41-6+rpi1),
libblas-dev (= 3.11.0-2),
libblas3 (= 3.11.0-2),
libblkid1 (= 2.39.3-2),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.37-12+rpi2),
libc-dev-bin (= 2.37-12+rpi2),
libc6 (= 2.37-12+rpi2),
libc6-dev (= 2.37-12+rpi2),
libcap-ng0 (= 0.8.3-3),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-7+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libdb5.3 (= 5.3.28+dfsg2-4),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.11.9),
libdpkg-perl (= 1.22.1+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libfile-find-rule-perl (= 0.34-3),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.3.0-13+rpi1),
libgcc-13-dev (= 13.2.0-7+rpi1),
libgcc-s1 (= 13.2.0-7+rpi1),
libgcrypt20 (= 1.10.3-2),
libgdbm-compat4 (= 1.23-5),
libgdbm6 (= 1.23-5),
libgfortran5 (= 13.2.0-7+rpi1),
libgmp10 (= 2:6.3.0+dfsg-2),
libgomp1 (= 13.2.0-7+rpi1),
libgpg-error0 (= 1.47-3),
libgssapi-krb5-2 (= 1.20.1-5),
libicu72 (= 72.1-4),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libk5crypto3 (= 1.20.1-5),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-5),
libkrb5support0 (= 1.20.1-5),
liblapack-dev (= 3.11.0-2),
liblapack3 (= 3.11.0-2),
liblocale-gettext-perl (= 1.07-6),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma5 (= 5.4.5-0.1),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-1),
libmount1 (= 2.39.3-2),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libnsl-dev (= 1.3.0-3),
libnsl2 (= 1.3.0-3),
libnumber-compare-perl (= 0.03-3),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-16-0 (= 10.42-4),
libpcre2-32-0 (= 10.42-4),
libpcre2-8-0 (= 10.42-4),
libpcre2-dev (= 10.42-4),
libpcre2-posix3 (= 10.42-4),
libperl5.36 (= 5.36.0-10),
libpipeline1 (= 1.5.7-1),
libseccomp2 (= 2.5.4-2+rpi1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsmartcols1 (= 2.39.3-2),
libssl3 (= 3.1.4-2),
libstdc++-13-dev (= 13.2.0-7+rpi1),
libstdc++6 (= 13.2.0-7+rpi1),
libsub-override-perl (= 0.10-1),
libsystemd0 (= 254.5-1+rpi1),
libtext-glob-perl (= 0.11-3),
libtinfo6 (= 6.4+20231209-1),
libtirpc-common (= 1.3.4+ds-1),
libtirpc-dev (= 1.3.4+ds-1),
libtirpc3 (= 1.3.4+ds-1),
libtmglib-dev (= 3.11.0-2),
libtmglib3 (= 3.11.0-2),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-7+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.3-2),
libxml2 (= 2.9.14+dfsg-1.3),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-1),
mawk (= 1.3.4.20231126-1),
ncurses-base (= 6.4+20231209-1),
ncurses-bin (= 6.4+20231209-1),
patch (= 2.7.6-7),
perl (= 5.36.0-10),
perl-base (= 5.36.0-10),
perl-modules-5.36 (= 5.36.0-10),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-5),
tar (= 1.34+dfsg-1.3),
usr-is-merged (= 38),
usrmerge (= 38),
util-linux (= 2.39.3-2),
xz-utils (= 5.4.5-0.1),
zlib1g (= 1:1.2.13.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1701249918"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
phast-dbgsym_1.6+dfsg-4_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 25076956 bytes: control archive=2096 bytes.
1682 bytes, 12 lines control
3583 bytes, 34 lines md5sums
Package: phast-dbgsym
Source: phast
Version: 1.6+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 26845
Depends: phast (= 1.6+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for phast
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lrwxrwxrwx root/root 0 2023-11-29 09:25 ./usr/share/doc/phast-dbgsym -> phast
phast_1.6+dfsg-4_armhf.deb
--------------------------
new Debian package, version 2.0.
size 2427516 bytes: control archive=5524 bytes.
1112 bytes, 22 lines control
14785 bytes, 195 lines md5sums
Package: phast
Version: 1.6+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 21094
Depends: libc6 (>= 2.34), 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 2023-11-29 09:25 ./usr/share/phast/data/phastCons/
-rw-r--r-- root/root 103302 2023-11-29 09:25 ./usr/share/phast/data/phastCons/simple-coding-indels.hmm
-rw-r--r-- root/root 584 2023-11-29 09:25 ./usr/share/phast/data/phastCons/simple-coding.hmm
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 184548
Build-Time: 101
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 26
Job: phast_1.6+dfsg-4
Machine Architecture: arm64
Package: phast
Package-Time: 136
Source-Version: 1.6+dfsg-4
Space: 184548
Status: successful
Version: 1.6+dfsg-4
--------------------------------------------------------------------------------
Finished at 2023-12-25T11:21:30Z
Build needed 00:02:16, 184548k disk space