I: pbuilder: network access will be disabled during build
I: Current time: Thu Jan  9 02:01:19 +14 2025
I: pbuilder-time-stamp: 1736337679
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [phast_1.7+dfsg-2.dsc]
I: copying [./phast_1.7+dfsg.orig.tar.xz]
I: copying [./phast_1.7+dfsg-2.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./phast_1.7+dfsg-2.dsc: unsupported subcommand
dpkg-source: info: extracting phast in phast-1.7+dfsg
dpkg-source: info: unpacking phast_1.7+dfsg.orig.tar.xz
dpkg-source: info: unpacking phast_1.7+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying clapack.patch
dpkg-source: info: applying do_not_install_to_opt.patch
dpkg-source: info: applying use_debian_packaged_libpcre.patch
dpkg-source: info: applying use_debian_packaged_help2man.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying pcre2.patch
dpkg-source: info: applying gcc-14.patch
dpkg-source: info: applying make.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/46343/tmp/hooks/D01_modify_environment starting
debug: Running on ionos12-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jan  8 12:01 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/46343/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/46343/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
  BASH_VERSION='5.2.37(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=i386
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=i686
  HOST_ARCH=i386
  IFS=' 	
  '
  INVOCATION_ID=b9facd3d719d4bd19c404ee8f05bda0c
  LANG=C
  LANGUAGE=de_CH:de
  LC_ALL=C
  LD_LIBRARY_PATH=/usr/lib/libeatmydata
  LD_PRELOAD=libeatmydata.so
  MACHTYPE=i686-pc-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=46343
  PS4='+ '
  PWD=/
  SHELL=/bin/bash
  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
  SHLVL=3
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.bLSPY1bU/pbuilderrc_SZpb --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.bLSPY1bU/b2 --logfile b2/build.log phast_1.7+dfsg-2.dsc'
  SUDO_GID=112
  SUDO_UID=107
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://46.16.76.132:3128
I: uname -a
  Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/46343/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), liblapack-dev | liblapack.so, libblas-dev | libblas.so, liblapacke-dev, libtmglib-dev, libpcre2-dev, help2man
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19834 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on liblapack-dev | liblapack.so; however:
  Package liblapack-dev is not installed.
  Package liblapack.so is not installed.
 pbuilder-satisfydepends-dummy depends on libblas-dev | libblas.so; however:
  Package libblas-dev is not installed.
  Package libblas.so is not installed.
 pbuilder-satisfydepends-dummy depends on liblapacke-dev; however:
  Package liblapacke-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libtmglib-dev; however:
  Package libtmglib-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libpcre2-dev; however:
  Package libpcre2-dev is not installed.
 pbuilder-satisfydepends-dummy depends on help2man; however:
  Package help2man is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas-dev{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} liblapack-dev{a} liblapack3{a} liblapacke{a} liblapacke-dev{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libtmglib-dev{a} libtmglib3{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 
0 packages upgraded, 45 newly installed, 0 to remove and 0 not upgraded.
Need to get 30.8 MB of archives. After unpacking 129 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-4 [201 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-14 [96.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-4 [723 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.23 [90.6 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 libtool all 2.5.4-2 [539 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 22 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 23 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-4 [1632 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 debhelper all 13.23 [919 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 help2man i386 1.49.3 [198 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-4 [143 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 libblas-dev i386 3.12.0-4 [155 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-12 [735 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-4 [2194 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 liblapack-dev i386 3.12.0-4 [4452 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 libtmglib3 i386 3.12.0-4 [122 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 liblapacke i386 3.12.0-4 [376 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 libtmglib-dev i386 3.12.0-4 [127 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 liblapacke-dev i386 3.12.0-4 [350 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 libpcre2-16-0 i386 10.44-5 [258 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 libpcre2-32-0 i386 10.44-5 [246 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 libpcre2-posix3 i386 10.44-5 [60.4 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 libpcre2-dev i386 10.44-5 [800 kB]
Fetched 30.8 MB in 1s (61.5 MB/s)
Preconfiguring packages ...
Selecting previously unselected package liblocale-gettext-perl.
(Reading database ... 
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(Reading database ... 10%
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(Reading database ... 25%
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(Reading database ... 100%
(Reading database ... 19834 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_i386.deb ...
Unpacking liblocale-gettext-perl (1.07-7+b1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:i386.
Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_i386.deb ...
Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.45-3+b1_i386.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.22.5-4_i386.deb ...
Unpacking gettext-base (0.22.5-4) ...
Selecting previously unselected package libuchardet0:i386.
Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_i386.deb ...
Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../07-groff-base_1.23.0-7_i386.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../08-bsdextrautils_2.40.2-14_i386.deb ...
Unpacking bsdextrautils (2.40.2-14) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../09-libpipeline1_1.5.8-1_i386.deb ...
Unpacking libpipeline1:i386 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../10-man-db_2.13.0-1_i386.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../11-m4_1.4.19-5_i386.deb ...
Unpacking m4 (1.4.19-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../12-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../15-autopoint_0.22.5-4_all.deb ...
Unpacking autopoint (0.22.5-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../16-libdebhelper-perl_13.23_all.deb ...
Unpacking libdebhelper-perl (13.23) ...
Selecting previously unselected package libtool.
Preparing to unpack .../17-libtool_2.5.4-2_all.deb ...
Unpacking libtool (2.5.4-2) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../18-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.14.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.0-1) ...
Selecting previously unselected package libelf1t64:i386.
Preparing to unpack .../22-libelf1t64_0.192-4_i386.deb ...
Unpacking libelf1t64:i386 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1+b1_i386.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:i386.
Preparing to unpack .../24-libunistring5_1.3-1_i386.deb ...
Unpacking libunistring5:i386 (1.3-1) ...
Selecting previously unselected package libicu72:i386.
Preparing to unpack .../25-libicu72_72.1-5+b1_i386.deb ...
Unpacking libicu72:i386 (72.1-5+b1) ...
Selecting previously unselected package libxml2:i386.
Preparing to unpack .../26-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ...
Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../27-gettext_0.22.5-4_i386.deb ...
Unpacking gettext (0.22.5-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../30-debhelper_13.23_all.deb ...
Unpacking debhelper (13.23) ...
Selecting previously unselected package help2man.
Preparing to unpack .../31-help2man_1.49.3_i386.deb ...
Unpacking help2man (1.49.3) ...
Selecting previously unselected package libblas3:i386.
Preparing to unpack .../32-libblas3_3.12.0-4_i386.deb ...
Unpacking libblas3:i386 (3.12.0-4) ...
Selecting previously unselected package libblas-dev:i386.
Preparing to unpack .../33-libblas-dev_3.12.0-4_i386.deb ...
Unpacking libblas-dev:i386 (3.12.0-4) ...
Selecting previously unselected package libgfortran5:i386.
Preparing to unpack .../34-libgfortran5_14.2.0-12_i386.deb ...
Unpacking libgfortran5:i386 (14.2.0-12) ...
Selecting previously unselected package liblapack3:i386.
Preparing to unpack .../35-liblapack3_3.12.0-4_i386.deb ...
Unpacking liblapack3:i386 (3.12.0-4) ...
Selecting previously unselected package liblapack-dev:i386.
Preparing to unpack .../36-liblapack-dev_3.12.0-4_i386.deb ...
Unpacking liblapack-dev:i386 (3.12.0-4) ...
Selecting previously unselected package libtmglib3:i386.
Preparing to unpack .../37-libtmglib3_3.12.0-4_i386.deb ...
Unpacking libtmglib3:i386 (3.12.0-4) ...
Selecting previously unselected package liblapacke:i386.
Preparing to unpack .../38-liblapacke_3.12.0-4_i386.deb ...
Unpacking liblapacke:i386 (3.12.0-4) ...
Selecting previously unselected package libtmglib-dev:i386.
Preparing to unpack .../39-libtmglib-dev_3.12.0-4_i386.deb ...
Unpacking libtmglib-dev:i386 (3.12.0-4) ...
Selecting previously unselected package liblapacke-dev:i386.
Preparing to unpack .../40-liblapacke-dev_3.12.0-4_i386.deb ...
Unpacking liblapacke-dev:i386 (3.12.0-4) ...
Selecting previously unselected package libpcre2-16-0:i386.
Preparing to unpack .../41-libpcre2-16-0_10.44-5_i386.deb ...
Unpacking libpcre2-16-0:i386 (10.44-5) ...
Selecting previously unselected package libpcre2-32-0:i386.
Preparing to unpack .../42-libpcre2-32-0_10.44-5_i386.deb ...
Unpacking libpcre2-32-0:i386 (10.44-5) ...
Selecting previously unselected package libpcre2-posix3:i386.
Preparing to unpack .../43-libpcre2-posix3_10.44-5_i386.deb ...
Unpacking libpcre2-posix3:i386 (10.44-5) ...
Selecting previously unselected package libpcre2-dev:i386.
Preparing to unpack .../44-libpcre2-dev_10.44-5_i386.deb ...
Unpacking libpcre2-dev:i386 (10.44-5) ...
Setting up libpipeline1:i386 (1.5.8-1) ...
Setting up libicu72:i386 (72.1-5+b1) ...
Setting up bsdextrautils (2.40.2-14) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.23) ...
Setting up libmagic1t64:i386 (1:5.45-3+b1) ...
Setting up gettext-base (0.22.5-4) ...
Setting up m4 (1.4.19-5) ...
Setting up file (1:5.45-3+b1) ...
Setting up libpcre2-16-0:i386 (10.44-5) ...
Setting up libelf1t64:i386 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libpcre2-32-0:i386 (10.44-5) ...
Setting up libblas3:i386 (3.12.0-4) ...
update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode
Setting up libunistring5:i386 (1.3-1) ...
Setting up autopoint (0.22.5-4) ...
Setting up libgfortran5:i386 (14.2.0-12) ...
Setting up autoconf (2.72-3) ...
Setting up libpcre2-posix3:i386 (10.44-5) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:i386 (0.0.8-1+b2) ...
Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up liblocale-gettext-perl (1.07-7+b1) ...
Setting up libblas-dev:i386 (3.12.0-4) ...
update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) 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 (1.14.0-1) ...
Setting up liblapack3:i386 (3.12.0-4) ...
update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode
Setting up gettext (0.22.5-4) ...
Setting up libpcre2-dev:i386 (10.44-5) ...
Setting up libtool (2.5.4-2) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up help2man (1.49.3) ...
Setting up dh-autoreconf (20) ...
Setting up libtmglib3:i386 (3.12.0-4) ...
Setting up liblapack-dev:i386 (3.12.0-4) ...
update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-7) ...
Setting up liblapacke:i386 (3.12.0-4) ...
Setting up libtmglib-dev:i386 (3.12.0-4) ...
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Setting up liblapacke-dev:i386 (3.12.0-4) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
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Processing triggers for libc-bin (2.40-5) ...
Reading package lists...
Building dependency tree...
Reading state information...
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Initializing package states...
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Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/46343/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/46343/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/phast-1.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../phast_1.7+dfsg-2_source.changes
dpkg-buildpackage: info: source package phast
dpkg-buildpackage: info: source version 1.7+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg'
dh_auto_clean
cd src && /usr/bin/make clean
make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib'
cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/../version: No such file or directory
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.7+dfsg/src/lib/$dir && /usr/bin/make clean ; done
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base'
cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../version: No such file or directory
rm -f *.o 
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa'
cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../version: No such file or directory
rm -f *.o 
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature'
cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../version: No such file or directory
rm -f *.o 
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm'
cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../version: No such file or directory
rm -f *.o 
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo'
cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../version: No such file or directory
rm -f *.o 
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm'
cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../version: No such file or directory
rm -f *.o 
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif'
cat: /build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../version: No such file or directory
rm -f *.o 
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif'
rm -f /build/reproducible-path/phast-1.7+dfsg/src/lib/../../lib/*
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/dless'
cat: /build/reproducible-path/phast-1.7+dfsg/src/dless/../version: No such file or directory
rm -f *.o dless.help dlessP.help /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dless /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dlessP 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/dless'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy'
cat: /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../version: No such file or directory
rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../bin/exoniphy 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons'
cat: /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../version: No such file or directory
rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../bin/phastCons phastCons.help
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds'
cat: /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../version: No such file or directory
rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../bin/phastOdds 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif'
cat: /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../version: No such file or directory
rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../bin/phastMotif 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit'
cat: /build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../version: No such file or directory
rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.help
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot'
cat: /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../version: No such file or directory
rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../bin/phyloBoot 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP'
cat: /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../version: No such file or directory
rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../bin/phyloP phyloP.help
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel'
cat: /build/reproducible-path/phast-1.7+dfsg/src/prequel/../version: No such file or directory
rm -f *.o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsDecode /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsEncode /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsScoreMatrix /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsTrain /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/prequel pbsDecode.help pbsEncode.help pbsScoreMatrix.help pbsTrain.help prequel.help
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/util'
cat: /build/reproducible-path/phast-1.7+dfsg/src/util/../version: No such file or directory
rm -f *.o *.help /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/clean_genes /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/consEntropy /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/display_rate_matrix /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/eval_predictions /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_train /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_tweak /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_view /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelFit /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelHistory /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/maf_parse /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/makeHKY /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/modFreqs /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_diff /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_split /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_view /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phast /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phastBias /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/refeature /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/stringiphy /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/treeGen /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/tree_doctor 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/util'
rm -rf ../bin ../lib ../doc
make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src'
make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg'
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
   dh_auto_build
	make -j10 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg'
Type "make package" to create a tarball reflecting the current state of the CVS tree.
(cd src; make DESTDIR= CLAPACKPATH=/usr/lib )
make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src'
mkdir -p ../bin ../lib
for dir in lib dless exoniphy phastCons phastOdds phastMotif phyloFit phyloBoot phyloP prequel util  ; do cd /build/reproducible-path/phast-1.7+dfsg/src/$dir && make ; done	
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib'
for dir in base msa feature hmm phylo phylo_hmm motif; do cd /build/reproducible-path/phast-1.7+dfsg/src/lib/$dir && make ; done
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_matrix.c -o phast_complex_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_complex_vector.c -o phast_complex_vector.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_eigen.c -o phast_eigen.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_hashtable.c -o phast_hashtable.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_list_of_lists.c -o phast_list_of_lists.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_lists.c -o phast_lists.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_markov_matrix.c -o phast_markov_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_matrix.c -o phast_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_memory_handler.c -o phast_memory_handler.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_misc.c -o phast_misc.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_misc.c: In function 'make_name_hash':
phast_misc.c:673:46: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
  673 |   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:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_numerical_opt.c -o phast_numerical_opt.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_matrix.c -o phast_prob_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_prob_vector.c -o phast_prob_vector.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_stringsplus.c -o phast_stringsplus.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_stringsplus.c: In function 'str_re_match_sub':
phast_stringsplus.c:501:25: warning: pointer targets in passing argument 2 of 'pcre2_match_8' differ in signedness [-Wpointer-sign]
  501 |   rc = pcre2_match(re, s->chars, s->length, offset, 0, match_data, NULL);
      |                        ~^~~~~~~
      |                         |
      |                         char *
In file included from phast_stringsplus.c:16:
/usr/include/pcre2.h:952:1: note: expected 'PCRE2_SPTR8' {aka 'const unsigned char *'} but argument is of type 'char *'
  952 | PCRE2_TYPES_STRUCTURES_AND_FUNCTIONS
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../..\" -fno-strict-aliasing -c phast_vector.c -o phast_vector.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar: creating /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/base/../../../lib/libphast.a phast_complex_matrix.o phast_complex_vector.o phast_eigen.o phast_hashtable.o phast_list_of_lists.o phast_lists.o phast_markov_matrix.o phast_matrix.o phast_memory_handler.o phast_misc.o phast_numerical_opt.o phast_prob_matrix.o phast_prob_vector.o phast_stringsplus.o phast_vector.o
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/base'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_local_alignment.c -o phast_local_alignment.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_local_alignment.c: In function 'la_read_lav':
phast_local_alignment.c:50:55: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
   50 |   pcre2_compile_context *stanza_start_re = str_re_new("^([dshaxm])[[:space:]]*{");
      |                                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                       |
      |                                                       char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/local_alignment.h:36,
                 from phast_local_alignment.c:32:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf.c -o phast_maf.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_maf.c: In function 'maf_read_cats_subset':
phast_maf.c:29:41: warning: variable 'block_no' set but not used [-Wunused-but-set-variable]
   29 |   int i, start_idx, length, max_tuples, block_no,
      |                                         ^~~~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_maf_block.c -o phast_maf_block.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_msa.c -o phast_msa.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_msa.c: In function 'msa_read_fasta':
phast_msa.c:264:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
  264 |     descrip_re = str_re_new("[[:space:]]*>[[:space:]]*([^[:space:]]+)");
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                             |
      |                             char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/msa.h:19,
                 from phast_msa.c:39:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_multi_msa.c -o phast_multi_msa.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_multi_msa.c: In function 'multimsa_new_from_files':
phast_multi_msa.c:54:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
   54 |   pcre2_compile_context *blocks_re = str_re_new("#[[:space:]]*BLOCKS[[:space:]]*=[[:space:]]*([0-9]+)");
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                 |
      |                                                 char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/msa.h:19,
                 from phast_multi_msa.c:37:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../..\" -fno-strict-aliasing -c phast_sufficient_stats.c -o phast_sufficient_stats.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_sufficient_stats.c: In function 'ss_from_msas':
phast_sufficient_stats.c:140:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation]
  140 |     else
      |     ^~~~
phast_sufficient_stats.c:142:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else'
  142 |       max_tuples = pow_bounded(strlen(msa->alphabet) + (int)strlen(msa->missing) + 1,
      |       ^~~~~~~~~~
phast_sufficient_stats.c: In function 'ss_read':
phast_sufficient_stats.c:661:25: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
  661 |   nseqs_re = str_re_new("NSEQS[[:space:]]*=[[:space:]]*([0-9]+)");
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                         |
      |                         char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/msa.h:19,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/sufficient_stats.h:20,
                 from phast_sufficient_stats.c:11:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/msa/../../../lib/libphast.a phast_local_alignment.o phast_maf.o phast_maf_block.o phast_msa.o phast_multi_msa.o phast_sufficient_stats.o
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/msa'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_bed.c -o phast_bed.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_bed.c: In function 'gff_print_bed':
phast_bed.c:143:52: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
  143 |     pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)");
      |                                                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                    |
      |                                                    char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
                 from phast_bed.c:15:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_category_map.c -o phast_category_map.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_category_map.c: In function 'cm_read':
phast_category_map.c:39:31: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
   39 |     cat_range_re = str_re_new("^[[:space:]]*([^[:space:]]+)[[:space:]]+([[:digit:]]+)(-([[:digit:]]+))?([[:space:]]+([[:digit:]].*))?");
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                               |
      |                               char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/category_map.h:92,
                 from phast_category_map.c:10:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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:]]*(.*)$");
      |                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                           |
      |                           char *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_category_map.c:43:28: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
   43 |     extend_re = str_re_new("^[[:space:]]*FEATURE_EXTEND[[:space:]]*:[[:space:]]*(.+)[[:space:]]*\\((.+)\\)$");
      |                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                            |
      |                            char *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_genepred.c -o phast_genepred.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_gff.c -o phast_gff.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_gff.c: In function 'gff_read_set':
phast_gff.c:56:38: 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 /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
                 from phast_gff.c:13:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../..\" -fno-strict-aliasing -c phast_wig.c -o phast_wig.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/feature/../../../lib/libphast.a phast_bed.o phast_category_map.o phast_genepred.o phast_gff.o phast_wig.o
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/feature'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_em.c -o phast_em.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../..\" -fno-strict-aliasing -c phast_hmm.c -o phast_hmm.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/hmm/../../../lib/libphast.a phast_em.o phast_hmm.o
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/hmm'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_bgc_hmm.c -o phast_bgc_hmm.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_cons.c -o phast_cons.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_dgamma.c -o phast_dgamma.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_column.c -o phast_fit_column.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_em.c -o phast_fit_em.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_fit_feature.c -o phast_fit_feature.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_history.c -o phast_indel_history.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_indel_mod.c -o phast_indel_mod.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_fit.c -o phast_phylo_fit.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p.c -o phast_phylo_p.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_phylo_p_print.c -o phast_phylo_p_print.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_phylo_p_print.c: In function 'print_feats_generic':
phast_phylo_p_print.c:752:50: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
  752 |   pcre2_compile_context *tag_val_re = str_re_new("[[:alnum:]_.]+[[:space:]]+(\"[^\"]*\"|[^[:space:]]+)");
      |                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                  |
      |                                                  char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/msa.h:19,
                 from phast_phylo_p_print.c:17:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_distrib.c -o phast_subst_distrib.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_subst_mods.c -o phast_subst_mods.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_likelihoods.c -o phast_tree_likelihoods.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_tree_model.c -o phast_tree_model.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../..\" -fno-strict-aliasing -c phast_trees.c -o phast_trees.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo/../../../lib/libphast.a phast_bgc_hmm.o phast_cons.o phast_dgamma.o phast_fit_column.o phast_fit_em.o phast_fit_feature.o phast_indel_history.o phast_indel_mod.o phast_phylo_fit.o phast_phylo_p.o phast_phylo_p_print.o phast_subst_distrib.o phast_subst_mods.o phast_tree_likelihoods.o phast_tree_model.o phast_trees.o
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_gap_patterns.c -o phast_gap_patterns.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../..\" -fno-strict-aliasing -c phast_phylo_hmm.c -o phast_phylo_hmm.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm/../../../lib/libphast.a phast_gap_patterns.o phast_phylo_hmm.o
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/phylo_hmm'
make[4]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_motif.c -o phast_motif.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_motif.c: In function 'mtf_print':
phast_motif.c:1411:21: 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/../..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../..\" -fno-strict-aliasing -c phast_tfbs.c -o phast_tfbs.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_tfbs.c: In function 'pwm_read':
phast_tfbs.c:147:24: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
  147 |   pssm_re = str_re_new("^letter-probability matrix: alength= ([0-9]+) w= ([0-9]+)");
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                        |
      |                        char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/msa.h:19,
                 from phast_tfbs.c:16:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
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 /build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o
ar rs /build/reproducible-path/phast-1.7+dfsg/src/lib/motif/../../../lib/libphast.a phast_motif.o phast_tfbs.o
make[4]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib/motif'
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/lib'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/dless'
../munge-help.sh dless.help_src > dless.help
../munge-help.sh dlessP.help_src > dlessP.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/dless/../..\" -fno-strict-aliasing -c dless.c -o dless.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/dless/../..\" -fno-strict-aliasing -c phast_bd_phylo_hmm.c -o phast_bd_phylo_hmm.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/dless/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/dless/../..\" -fno-strict-aliasing -c dlessP.c -o dlessP.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<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
dlessP.c: In function 'do_p_values':
dlessP.c:199:45: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
  199 |   pcre2_compile_context *id_re = str_re_new(".*id \"([^\"]*)\"");
      |                                             ^~~~~~~~~~~~~~~~~~~
      |                                             |
      |                                             char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/trees.h:25,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/tree_model.h:26,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/bd_phylo_hmm.h:22,
                 from dlessP.c:17:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dless dless.o phast_bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/dless/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/dless/../../bin/dlessP dlessP.o phast_bd_phylo_hmm.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/dless'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy'
../munge-help.sh exoniphy.help_src > exoniphy.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../..\" -fno-strict-aliasing -c exoniphy.c -o exoniphy.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/exoniphy/../../bin/exoniphy exoniphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/exoniphy'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons'
../munge-help.sh phastCons.help_src > phastCons.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phastCons/../..\" -fno-strict-aliasing -c phastCons.c -o phastCons.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/phastCons/../../bin/phastCons phastCons.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastCons'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds'
../munge-help.sh phastOdds.help_src > phastOdds.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../..\" -fno-strict-aliasing -c phastOdds.c -o phastOdds.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/phastOdds/../../bin/phastOdds phastOdds.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastOdds'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif'
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../..\" -fno-strict-aliasing -c phastMotif.c -o phastMotif.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phastMotif.c: In function 'main':
phastMotif.c:131:13: warning: variable 'separate_backgd' set but not used [-Wunused-but-set-variable]
  131 |   int i, j, separate_backgd = 0,
      |             ^~~~~~~~~~~~~~~
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/phastMotif/../../bin/phastMotif phastMotif.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phastMotif'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit'
../munge-help.sh phyloFit.help_src > phyloFit.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../..\" -fno-strict-aliasing -c phyloFit.c -o phyloFit.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/phyloFit/../../bin/phyloFit phyloFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloFit'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot'
../munge-help.sh phyloBoot.help_src > phyloBoot.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../..\" -fno-strict-aliasing -c phyloBoot.c -o phyloBoot.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/phyloBoot/../../bin/phyloBoot phyloBoot.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloBoot'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP'
../munge-help.sh phyloP.help_src > phyloP.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/phyloP/../..\" -fno-strict-aliasing -c phyloP.c -o phyloP.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/phyloP/../../bin/phyloP phyloP.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/phyloP'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel'
../munge-help.sh pbsDecode.help_src > pbsDecode.help
../munge-help.sh pbsEncode.help_src > pbsEncode.help
../munge-help.sh pbsScoreMatrix.help_src > pbsScoreMatrix.help
../munge-help.sh pbsTrain.help_src > pbsTrain.help
../munge-help.sh prequel.help_src > prequel.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsDecode.c -o pbsDecode.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c phast_simplex_grid.c -o phast_simplex_grid.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c phast_pbs_code.c -o phast_pbs_code.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<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
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o 
<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
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
phast_pbs_code.c: In function 'pbs_new_from_file':
phast_pbs_code.c:88:48: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
   88 |   pcre2_compile_context *nrows_re = str_re_new("##NROWS[[:space:]]*=[[:space:]]*([0-9]+)"),
      |                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                |
      |                                                char *
In file included from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/pbs_code.h:8,
                 from phast_pbs_code.c:14:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_pbs_code.c:89:32: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
   89 |     *dimension_re = str_re_new("##DIMENSION[[:space:]]*=[[:space:]]*([0-9]+)"),
      |                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                |
      |                                char *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_pbs_code.c:90:29: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
   90 |     *nbytes_re = str_re_new("##NBYTES[[:space:]]*=[[:space:]]*([0-9]+)"),
      |                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                             |
      |                             char *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
phast_pbs_code.c:91:31: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
   91 |     *codesize_re = str_re_new("##CODESIZE[[:space:]]*=[[:space:]]*([0-9]+)");
      |                               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                               |
      |                               char *
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
prequel.c: In function 'main':
prequel.c:285:32: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 255 [-Wformat-overflow=]
  285 |       sprintf(out_fname, "%s.%s.bin", out_root, n->name);
      |                                ^~~~
In file included from /usr/include/stdio.h:970,
                 from prequel.c:11:
In function 'sprintf',
    inlined from 'main' at prequel.c:285:7:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 6 or more bytes (assuming 261) into a destination of size 256
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
prequel.c: In function 'main':
prequel.c:253:32: warning: '.fa' directive writing 3 bytes into a region of size between 0 and 255 [-Wformat-overflow=]
  253 |       sprintf(out_fname, "%s.%s.fa", out_root, n->name);
      |                                ^~~
In function 'sprintf',
    inlined from 'main' at prequel.c:253:7:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 5 or more bytes (assuming 260) into a destination of size 256
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
prequel.c: In function 'main':
prequel.c:203:32: warning: '.probs' directive writing 6 bytes into a region of size between 0 and 255 [-Wformat-overflow=]
  203 |       sprintf(out_fname, "%s.%s.probs", out_root, n->name);
      |                                ^~~~~~
In function 'sprintf',
    inlined from 'main' at prequel.c:203:7:
/usr/include/i386-linux-gnu/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 8 or more bytes (assuming 263) into a destination of size 256
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsDecode pbsDecode.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsEncode pbsEncode.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsScoreMatrix pbsScoreMatrix.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/pbsTrain pbsTrain.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc  -L/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../lib  -o /build/reproducible-path/phast-1.7+dfsg/src/prequel/../../bin/prequel prequel.o phast_simplex_grid.o phast_pbs_code.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/prequel'
make[3]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src/util'
../munge-help.sh base_evolve.help_src > base_evolve.help
../munge-help.sh clean_genes.help_src > clean_genes.help
../munge-help.sh consEntropy.help_src > consEntropy.help
../munge-help.sh indelFit.help_src > indelFit.help
../munge-help.sh indelHistory.help_src > indelHistory.help
../munge-help.sh makeHKY.help_src > makeHKY.help
../munge-help.sh modFreqs.help_src > modFreqs.help
../munge-help.sh msa_diff.help_src > msa_diff.help
../munge-help.sh phast.help_src > phast.help
../munge-help.sh phastBias.help_src > phastBias.help
../munge-help.sh treeGen.help_src > treeGen.help
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c all_dists.c -o all_dists.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c base_evolve.c -o base_evolve.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<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
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<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
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 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o 
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o 
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 /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/gff.h:21,
                 from /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/msa.h:19,
                 from msa_view.c:14:
/build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
  386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
      |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o 
<command-line>: warning: "PHAST_HOME" redefined
<command-line>: note: this is the location of the previous definition
gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
<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 /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/tree_model.h:26,
                 from tree_doctor.c:14:
/build/reproducible-path/phast-1.7+dfsg/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/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
make[3]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src/util'
mkdir -p ../doc/man/
Generating man pages...
USAGE: convert_coords -m <msa_fname> -f <feature_fname> [-s <src_frame>] [-d <dest_frame>] [-p] [-n] [-i PHYLIP|FASTA|MPM]

DESCRIPTION:
Converts coordinates of features in a GFF file according to a multiple
alignment.  Will map from the coordinate system of any sequence to any
other sequence; can also map to or from the coordinate system of the
entire alignment.  In addition, supports translation of coordinates by
specified offset.

OPTIONS:
    -m <msa_fname>  (required) Name of file in which alignment is defined.
    -f <gff_fname>  (required) Name of file in which features are defined (GFF). 
    -s <src_frame>  Index of frame of reference for feature coordinates, as 
                    defined in the GFF file.  Use an integer 1-N (if N seqs) 
                    or 0 to indicate the coordinate system of the alignment 
                    as a whole.  Default behavior is to match features with 
                    alignment sequences by name (feature by feature).
    -d <dest_frame> Index of destination frame of reference.  Default is 0
                    (whole MSA).
    -p <coord_off>  Positive coordinate offset.  This value will be
                    added to all coordinates.  Useful when 
                    the alignment (or sequence) for which the coordinates 
                    are specified is a sub-alignment of yours. 
    -n <coord_off>  Negative coordinate offset.  This value will be
                    subtracted from all coordinates.  Useful when your
                    alignment is a sub-alignment of the alignment (or 
                    sequence) for which the coordinates are specified.
    -i FASTA|PHYLIP|MPM|SS
                    Alignment format.  Default is to guess format from file
                    contents


PROGRAM:        draw_tree
DESCRIPTION:    Produces a simple postscript rendering of a tree.
USAGE:          draw_tree [-dbvs] <tree.nh>|<tree.mod>

OPTIONS:
    <tree_fname>    (Required) File name of tree (expected to be in 
                    Newick format, unless filename ends with '.mod', in
                    which case expected to be a tree model file).
    -d              Print "diagonal" branches, instead of "right-angle" or 
                    "square" ones (produces a "cladogram", as opposed to a 
                    "phenogram").  This option implies -s.
    -b              Suppress branch lengths.
    -v              Vertical layout.
    -s              Don't draw branches to scale.

Done.
make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src'
make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg'
cd test && PATH=/build/reproducible-path/phast-1.7+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path /usr/bin/make msa_view
make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/test'
*** Testing msa_view ***
msa_view hmrc.ss -i SS --end 10000 > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o PHYLIP > hmrc.ph
msa_view hmrc.ph -i PHYLIP > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm
msa_view hmrc.mpm --in-format MPM > hmrc.fa
if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa -o SS > hmrc_short_a.ss
msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss
if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi
msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa
msa_view --seqs human,cow hmrc.fa > hm_b.fa
if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa
msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa
if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa
msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa
if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa
msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa
if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
msa_view hmrc.ss --summary -i SS > hmrc_summary
if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi
Passed all tests.

make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/test'
make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install --destdir=debian/phast/
	make -j10 install DESTDIR=/build/reproducible-path/phast-1.7\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg'
(cd src; make install DESTDIR=/build/reproducible-path/phast-1.7+dfsg/debian/phast )
make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src'
mkdir -p /build/reproducible-path/phast-1.7+dfsg/debian/phast/usr/bin/
mkdir -p /build/reproducible-path/phast-1.7+dfsg/debian/phast/usr/share/phast/data/
mkdir -p /build/reproducible-path/phast-1.7+dfsg/debian/phast/usr/share/man/man1/
cp ../bin/* /build/reproducible-path/phast-1.7+dfsg/debian/phast/usr/bin/
cp -R ../data/* /build/reproducible-path/phast-1.7+dfsg/debian/phast/usr/share/phast/data/
cp -R ../doc/man/* /build/reproducible-path/phast-1.7+dfsg/debian/phast/usr/share/man/man1/
make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/src'
make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg'
   dh_installdocs
   dh_installchangelogs
   debian/rules override_dh_installexamples
make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg'
dh_installexamples
find debian/*/usr/share/doc/*/examples -type f -size +1k -exec xz \{\} \;
make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg'
   dh_installman
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'phast' in '../phast_1.7+dfsg-2_i386.deb'.
dpkg-deb: building package 'phast-dbgsym' in '../phast-dbgsym_1.7+dfsg-2_i386.deb'.
 dpkg-genbuildinfo --build=binary -O../phast_1.7+dfsg-2_i386.buildinfo
 dpkg-genchanges --build=binary -O../phast_1.7+dfsg-2_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/46343/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/46343/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/46343 and its subdirectories
I: Current time: Thu Jan  9 02:04:41 +14 2025
I: pbuilder-time-stamp: 1736337881