Diff of the two buildlogs: -- --- b1/build.log 2020-10-03 00:24:02.794703523 +0000 +++ b2/build.log 2020-10-03 00:24:57.432379060 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Oct 2 12:19:20 -12 2020 -I: pbuilder-time-stamp: 1601684360 +I: Current time: Fri Nov 5 20:46:59 +14 2021 +I: pbuilder-time-stamp: 1636094819 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -18,7 +18,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Mon Oct 15 02:56:05 2018 -12 +gpgv: Signature made Tue Oct 16 04:56:05 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -30,138 +30,172 @@ dpkg-source: info: applying link_lnlopt.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2756/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/39992/tmp/hooks/D01_modify_environment starting +debug: Running on profitbricks-build16-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/39992/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/39992/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + 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=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='7d2cd42edd6a4e83aa19fad28990f2b4' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2756' - PS1='# ' - PS2='> ' + INVOCATION_ID=8c8fb1707290466b882dd14c6ce7d8f7 + 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=39992 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.WxuqNLWPxh/pbuilderrc_qmWo --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WxuqNLWPxh/b1 --logfile b1/build.log phyx_0.999+ds-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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/tmp.WxuqNLWPxh/pbuilderrc_csMj --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WxuqNLWPxh/b2 --logfile b2/build.log phyx_0.999+ds-1.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://85.184.249.68:3128 I: uname -a - Linux profitbricks-build12-i386 4.19.0-11-686-pae #1 SMP Debian 4.19.146-1 (2020-09-17) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-11-amd64 #1 SMP Debian 4.19.146-1 (2020-09-17) x86_64 GNU/Linux I: ls -l /bin - total 5488 - -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 38692 Feb 28 2019 cat - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown - -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp - -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash - -rwxr-xr-x 1 root root 120676 Feb 28 2019 date - -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd - -rwxr-xr-x 1 root root 100620 Feb 28 2019 df - -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir - -rwxr-xr-x 1 root root 79412 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 34532 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 34532 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 30112 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 206392 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 100952 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln - -rwxr-xr-x 1 root root 55400 Jul 26 2018 login - -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls - -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 42348 Jan 9 2019 more - -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount - -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 157832 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38660 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm - -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Sep 20 20:25 sh -> dash - -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty - -rwsr-xr-x 1 root root 71072 Jan 9 2019 su - -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync - -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar - -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch - -rwxr-xr-x 1 root root 34532 Feb 28 2019 true - -rwxr-xr-x 1 root root 17768 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount - -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34208 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/2756/tmp/hooks/D02_print_environment finished + total 5476 + -rwxr-xr-x 1 root root 1302248 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 38692 Mar 1 2019 cat + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 63268 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 75588 Mar 1 2019 chown + -rwxr-xr-x 1 root root 153732 Mar 1 2019 cp + -rwxr-xr-x 1 root root 132820 Jan 18 2019 dash + -rwxr-xr-x 1 root root 120676 Mar 1 2019 date + -rwxr-xr-x 1 root root 92040 Mar 1 2019 dd + -rwxr-xr-x 1 root root 100620 Mar 1 2019 df + -rwxr-xr-x 1 root root 149736 Mar 1 2019 dir + -rwxr-xr-x 1 root root 79412 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 34532 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 34532 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 67700 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 30112 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 206392 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 100952 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 21916 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 79752 Mar 1 2019 ln + -rwxr-xr-x 1 root root 55400 Jul 27 2018 login + -rwxr-xr-x 1 root root 149736 Mar 1 2019 ls + -rwxr-xr-x 1 root root 112032 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 87972 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 79748 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 46916 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 42348 Jan 10 2019 more + -rwsr-xr-x 1 root root 50592 Jan 10 2019 mount + -rwxr-xr-x 1 root root 13724 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 157832 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38660 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 46852 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 75588 Mar 1 2019 rm + -rwxr-xr-x 1 root root 42756 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 22276 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Nov 5 20:47 sh -> bash + lrwxrwxrwx 1 root root 4 Oct 25 04:48 sh.distrib -> dash + -rwxr-xr-x 1 root root 34532 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 79652 Mar 1 2019 stty + -rwsr-xr-x 1 root root 71072 Jan 10 2019 su + -rwxr-xr-x 1 root root 34564 Mar 1 2019 sync + -rwxr-xr-x 1 root root 504024 Apr 24 2019 tar + -rwxr-xr-x 1 root root 13860 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 104292 Mar 1 2019 touch + -rwxr-xr-x 1 root root 34532 Mar 1 2019 true + -rwxr-xr-x 1 root root 17768 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 30108 Jan 10 2019 umount + -rwxr-xr-x 1 root root 34532 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 149736 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34208 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/39992/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -287,7 +321,7 @@ Get: 76 http://deb.debian.org/debian buster/main i386 libnlopt-dev i386 2.4.2+dfsg-8+b1 [167 kB] Get: 77 http://deb.debian.org/debian buster/main i386 libnlopt-cxx0 i386 2.4.2+dfsg-8+b1 [172 kB] Get: 78 http://deb.debian.org/debian buster/main i386 libnlopt-cxx-dev i386 2.4.2+dfsg-8+b1 [188 kB] -Fetched 37.1 MB in 4s (8620 kB/s) +Fetched 37.1 MB in 1s (67.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19234 files and directories currently installed.) @@ -629,7 +663,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/phyx-0.999+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/phyx-0.999+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package phyx dpkg-buildpackage: info: source version 0.999+ds-1 dpkg-buildpackage: info: source distribution unstable @@ -699,8 +733,8 @@ config.status: creating config.h configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking dh_auto_build -O--sourcedirectory=src - cd src && make -j10 -make[1]: Entering directory '/build/phyx-0.999+ds/src' + cd src && make -j18 +make[1]: Verzeichnis „/build/phyx-0.999+ds/src“ wird betreten g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "utils.d" -o "utils.o" "utils.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "log.d" -o "log.o" "log.cpp" g++ -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -c -fmessage-length=0 -MMD -MP -MF "node.d" -o "node.o" "node.cpp" @@ -806,8 +840,8 @@ building pxcltr g++ -o "pxcltr" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize clean_tree.o main_cltr.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxs2fa -building pxs2phy g++ -o "pxs2fa" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_s2fa.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o +building pxs2phy g++ -o "pxs2phy" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_s2phy.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxs2nex g++ -o "pxs2nex" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_s2nex.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o @@ -857,403 +891,72 @@ g++ -o "pxrls" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize relabel.o main_rls.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtscale g++ -o "pxtscale" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize tscale.o main_tscale.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o -building pxssort building pxtcol -g++ -o "pxssort" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_ssort.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o g++ -o "pxtcol" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_tcol.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxtcomb g++ -o "pxtcomb" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_tcomb.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o -building pxcolt -g++ -o "pxcolt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize collapse_tree.o main_colt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxbdfit +building pxcolt g++ -o "pxbdfit" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize bd_fit.o main_bd_fit.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo +g++ -o "pxcolt" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize collapse_tree.o main_colt.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o +building pxssort +g++ -o "pxssort" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_ssort.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o building pxstrec g++ -o "pxstrec" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_strec.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo -lnlopt_cxx -lnlopt # -lgfortran building pxseqgen g++ -o "pxseqgen" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_seqgen.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo -lnlopt_cxx -lnlopt building pxcontrates g++ -o "pxcontrates" -O3 -std=c++11 -fopenmp -DOMP -ffast-math -ftree-vectorize main_contrates.o optimize_cont_models_nlopt.o ./rate_model.o ./state_reconstructor.o ./optimize_state_reconstructor_nlopt.o ./optimize_state_reconstructor_periods_nlopt.o ./branch_segment.o ./cont_models.o ./seq_gen.o ./utils.o ./log.o ./node.o ./tree.o ./tree_reader.o ./tree_utils.o ./sequence.o ./seq_reader.o ./seq_utils.o ./seq_models.o ./pairwise_alignment.o ./superdouble.o -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -llapack -lblas -lpthread -lm -lnlopt -larmadillo -lnlopt_cxx -lnlopt -make[1]: Leaving directory '/build/phyx-0.999+ds/src' +make[1]: Verzeichnis „/build/phyx-0.999+ds/src“ wird verlassen debian/rules override_dh_auto_test -make[1]: Entering directory '/build/phyx-0.999+ds' +make[1]: Verzeichnis „/build/phyx-0.999+ds“ wird betreten cd src && python run_tests.py ================= -TESTING pxs2fa -PASSED -================= -TESTING pxrlt +TESTING pxcolt ( ( True -E E True -u u True -b b True -a a True -c c True -t t True -e e True -r r True -i i True +( ( True +T T True a a True +x x True +o o True +n n True +C C True : : True -4 4 True -2 2 True -0 0 True 0 0 True -. , False -0 ( False -0 A False -0 r False -0 c False -0 h False -0 a False -0 e False +. . True +2 2 True +5 5 True +0 , False +0 T False 0 a False +0 x False +0 o False +0 n False +0 A False 0 : False -0 3 False -0 8 False 0 0 True -0 6 False 0 . False -0 0 True -0 1 False -0 0 True 0 2 False -0 4 False -0 9 False -, 9 False -( 9 False -A 9 False -r 9 False -c 9 False -h 9 False -a 8 False -e 1 False -a 4 False -: 5 False -3 , False -8 ( False -0 ( False -6 ( False -. ( False -0 S False -1 A False -0 R False -2 : False -4 1 False -9 6 False -9 2 False -9 6 False -9 . False -9 0 False -9 4 False -9 2 False -8 7 False -1 3 False -4 1 False -4 9 False -6 9 False -3 9 False -0 9 False -8 9 False -, 9 False -( 8 False -( 8 False -( 7 False -( 2 False -S , False -A P False -R l False -: a False -1 n False -6 t False -2 : False -6 1 False -. 6 False 0 2 False -4 6 False -2 . False -7 0 False -3 2 False -1 7 False -9 6 False -9 6 False -9 7 False -9 0 False -9 0 False -9 0 False -8 0 False -8 0 False -7 0 False -1 0 False -9 6 False -3 4 False -5 9 False -5 ) False -, : False -P 7 False -l 2 False -a . False -n 3 False -t 8 False -: 0 False -1 1 True -6 8 False -2 3 False -6 9 False -. 9 False -0 9 False -2 9 False -7 9 False -6 9 False -6 9 False -7 9 False -0 9 False -0 8 False -0 5 False 0 5 False -0 , False -0 E False -0 x False -6 c False -4 a False -9 v False -4 a False -5 t False -2 a False -0 : False -) 1 False -: 6 False -7 9 False -2 8 False -. . True -3 4 False -8 2 False -0 2 False -1 9 False -8 1 False -3 5 False -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 8 False -9 6 False -8 5 False -5 ) False -5 : False -3 7 False -9 4 False -, . False -E 7 False -x 3 False -c 1 False -a 2 False -v 1 False -a 9 False -t 9 False -a 9 False -: 9 False -1 9 False -6 9 False -9 9 True -8 9 False -. 9 False -4 3 False -2 3 False -2 2 True -9 , False -1 A False -5 m False -9 o False -9 e False -9 b False -9 o False -9 z False -9 o False -9 a False -8 : False -6 1 False -5 7 False -2 7 False -4 3 False -9 . False -3 1 False -) 5 False -: 4 False -7 1 False -4 3 False -. 6 False -7 0 False -3 0 False -1 0 False -2 0 False -1 0 False -9 0 False -9 1 False -9 0 False -9 7 False -9 7 False -9 ) False -9 : False -9 7 False -9 . False -3 9 False -3 3 True -1 7 False -9 5 False -7 3 False -6 4 False -, 9 False -A 9 False -m 9 False -o 9 False -e 9 False -b 9 False -o 9 False -z 9 False -o 9 False -a 5 False -: 6 False -1 3 False -7 2 False -7 , False -3 ( False -. A False -1 n False -5 i False -4 m False -1 a False -3 l False -6 : False -0 1 False -0 2 False -0 9 False -0 5 False -0 . False -0 7 False -1 1 True -0 7 False -7 5 False -7 4 False -4 4 True -2 0 False -3 0 False -8 0 False -) 0 False -: 0 False -7 0 False -. 0 False -9 8 False -3 9 False -7 , False -5 F False -3 u False -4 n False -9 g False -9 i False -9 : False -9 1 False -9 2 False -9 9 True -9 5 False -9 . False -9 7 False -5 0 False -6 3 False -3 3 True -1 6 False -6 1 False -, 0 False -( 0 False -A 0 False -n 0 False -i 0 False -m 0 False -a 0 False -l 8 False -: 6 False -1 3 False -2 ) False -9 : False -5 4 False -. 8 False -7 5 False -1 . False -7 3 False -5 8 False -4 0 False -4 0 False -0 6 False -0 0 True 0 0 True 0 0 True 0 0 True 0 0 True 0 0 True -8 0 False -8 0 False -9 1 False -9 4 False -9 5 False -5 ) False -1 : False -, 2 False -F 0 False -u 2 False -n 4 False -g . False -i 9 False -: 2 False -1 0 False -2 0 False -9 0 False -5 0 False -. 0 False -7 0 False +, 0 False +T 0 False +a 0 False +x 0 False +o 0 False +n 0 False +A 0 False +: 0 False 0 0 True -3 0 False -3 0 False -6 0 False -1 0 False -0 7 False -0 2 False -0 8 False -0 ) False -0 : False -0 3 False -0 9 False -8 4 False -6 ) False -2 ; False -7 -False -FAILED -intended output: (Eubacteria:4200,(Archaea:3806.0102499999998145,((((SAR:1626.0427319999998872,Plant:1626.0276670000000649):72.380183999999999855,Excavata:1698.4229159999999865):74.73121999999999332,Amoebozoa:1773.1541360000001077):7.9375349999999995632,(Animal:1295.717544000000089,Fungi:1295.7033610000000863):485.3800600000000145):2024.9200000000000728):394); - -your output: (Eubacteria:4200.00000000000000000000,(Archaea:3806.01024999999981446308,((((SAR:1626.04273199999988719355,Plant:1626.02766700000006494520):72.38018399999999985539,Excavata:1698.42291599999998652493):74.73character: 0 -character: 1 -character: 2 -121999999999331976,Amoebozoa:1773.15413600000010774238):7.93753499999999956316,(Animal:1295.71754400000008899951,Fungi:1295.70336100000008627831):485.38006000000001449735):2024.92000000000007275958):394.00000000000000000000); - -================= -TESTING pxssort -PASSED -================= -TESTING pxtscale -( ( True -( ( True -( ( True -T T True -a a True -x x True -o o True -n n True -A A True -: : True -1 1 True -. , False +. 5 False +2 5 False +2 5 False +5 , False 0 T False 0 a False 0 x False @@ -1263,163 +966,160 @@ 0 : False 0 0 True 0 . False -0 2 False -0 9 False -0 9 False -0 9 False -0 9 False -0 9 False -0 9 False -0 9 False -0 9 False +0 1 False +0 5 False +0 4 False 0 9 False 0 9 False +5 9 False +5 9 False +5 9 False , 9 False T 9 False a 9 False x 9 False o 9 False -n 8 False -B 8 False +n 9 False +B 9 False : 9 False -0 ) False -. : False -2 1 False +0 9 False +. 8 False +1 8 False +5 9 False +4 ) False +9 1 False 9 . False -9 2 False -9 5 False -9 , False -9 T False -9 a False -9 x False -9 o False -9 n False -9 C False +9 0 False 9 : False -9 2 False +9 0 False 9 . False -9 5 False -9 ) False -8 : False -8 4 False -9 , False +9 4 False +9 0 False +9 0 False +9 0 False +9 0 False +9 0 False +9 0 False +9 0 False +8 0 False +8 0 False +9 0 False +) 0 False +1 0 False +. 0 False +0 0 True +: 0 False +0 2 False +. 2 False +4 2 False +0 , False 0 ( False -) T False -: a False -1 x False -. o False -2 n False -5 D False +0 T False +0 a False +0 x False +0 o False +0 n False +0 D False 0 : False -0 2 False +0 0 True 0 . False +0 2 False 0 3 False 0 0 True 0 0 True +2 0 False +2 0 False +2 0 False 0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -, 2 False -T 6 False -a 6 False -x 5 False -o , False -n T False -C a False -: x False -2 o False -. n False -5 E False +, 0 False +( 0 False +T 0 False +a 0 False +x 0 False +o 0 False +n 0 False +D 0 False +: 0 False +0 9 False +. 9 False +2 9 False +3 , False +0 T False +0 a False +0 x False +0 o False +0 n False +0 E False 0 : False -0 1 False +0 0 True 0 . False +0 1 False 0 6 False 0 0 True 0 0 True 0 0 True 0 0 True +9 0 False +9 0 False +9 0 False +, 0 False +T 0 False +a 0 False +x 0 False +o 0 False +n 0 False +E 0 False +: 0 False +0 3 False +. 3 False +1 3 False +6 ) False 0 0 True +0 . False +0 9 False +0 4 False +0 : False 0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -) 8 False +0 . False +0 2 False +0 9 False +0 9 False +0 9 False +0 9 False +0 9 False +0 9 False +0 9 False +3 9 False +3 9 False +3 9 False +) 9 False +0 9 False +. 9 False +9 9 True +4 9 False : 8 False -4 8 False -. ) False -0 : False -0 3 False -0 ) False -0 ; False -0 +0 8 False +. 9 False +2 ) False +9 ; False +9 False FAILED -intended output: (((TaxonA:1,TaxonB:0.2999999999999999889):1.25,TaxonC:2.5):4,(TaxonD:2.3000000000000002665,TaxonE:1.6000000000000000888):3); +intended output: ((TaxonC:0.25,TaxonA:0.22500000000000000555,TaxonB:0.15499999999999999889)1.0:0.4000000000000000222,(TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333)0.94:0.2999999999999999889); -your output: (((TaxonA:1.00000000000000000000,TaxonB:0.29999999999999998890):1.25000000000000000000,TaxonC:2.50000000000000000000):4.00000000000000000000,(TaxonD:2.30000000000000026645,TaxonE:1.60000000000000008882):3.00000000000000000000); +your output: ((TaxonC:0.25000000000000000000,TaxonA:0.22500000000000000555,TaxonB:0.15499999999999999889)1.0:0.40000000000000002220,(TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333)0.94:0.29999999999999998890); ================= -TESTING pxvcf2fa -PASSED -================= -TESTING pxlog -PASSED -================= -TESTING pxtcol -no test for pxtcol -================= -TESTING pxseqgen -PASSED -================= -TESTING pxclsq -PASSED -================= -TESTING pxs2nex -PASSED -================= -TESTING pxsw -PASSED -================= -TESTING pxrevcomp -PASSED -================= -TESTING pxrecode +TESTING pxcat PASSED ================= TESTING pxrls PASSED ================= -TESTING pxcontrates -PASSED -================= -TESTING pxrms -PASSED -================= -TESTING pxfqfilt -PASSED -================= -TESTING pxbdfit -PASSED -================= -TESTING pxlssq +TESTING pxs2fa PASSED ================= -TESTING pxsstat +TESTING pxconsq PASSED ================= TESTING pxrmt @@ -1583,19 +1283,528 @@ your output: ((TaxonC:0.25000000000000000000,TaxonB:0.15499999999999999889):0.40000000000000002220,(TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333):0.29999999999999998890); ================= -TESTING pxstrec -n 0 False -a . False -n 3 False - 1 False - -6 False +TESTING pxrmk +( ( True +( ( True +( ( True +( ( True +( ( True +s s True +4 4 True +: : True +0 0 True +. . True +1 1 True +1 1 True +9 9 True +0 0 True +3 3 True +3 3 True +2 2 True +1 1 True +9 9 True +1 1 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +3 3 True +9 9 True +4 4 True +, , True +s s True +5 5 True +: : True +0 0 True +. . True +1 1 True +1 1 True +9 9 True +0 0 True +3 3 True +3 3 True +2 2 True +1 1 True +9 9 True +1 1 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +3 3 True +9 9 True +4 4 True +) ) True +C C True +: : True +0 0 True +. . True +0 0 True +2 2 True +5 5 True +4 4 True +4 4 True +1 1 True +7 7 True +1 1 True +7 7 True +4 4 True +5 5 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +0 0 True +1 0 False +, 7 False +s , False +6 s False +: 6 False +0 : False +. 0 False +1 . False +4 1 False +4 4 True +4 4 True +7 4 False +4 7 False +9 4 False +3 9 False +6 3 False +5 6 False +9 5 False +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +2 9 False +3 2 False +8 3 False +) 8 False +D ) False +: D False +0 : False +. 0 False +7 . False +6 7 False +4 6 False +7 4 False +6 7 False +4 6 False +0 4 False +0 0 True +1 0 False +9 1 False +0 9 False +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +4 0 False +5 4 False +5 5 True +3 5 False +, 3 False +s , False +7 s False +: 7 False +0 : False +. 0 False +9 . False +0 9 False +9 0 False +2 9 False +3 2 False +8 3 False +9 8 False +3 9 False +8 3 False +5 8 False +0 5 False +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +3 0 False +7 3 False +9 7 False +1 9 False +) 1 False +E ) False +: E False +0 : False +. 0 False +7 . False +6 7 False +8 6 False +7 8 False +4 7 False +9 4 False +3 9 False +4 3 False +9 4 False +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +7 9 False +9 7 False +6 9 False +, 6 False +( , False +s ( False +3 s False +: 3 False +1 : False +. 1 False +2 . False +5 2 False +7 5 False +2 7 False +3 2 False +3 3 True +6 3 False +2 6 False +8 2 False +9 8 False +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +0 9 False +8 0 False +1 8 False +6 2 False +, , True +( ( True +s s True +1 1 True +: : True +0 0 True +. . True +3 3 True +6 6 True +0 0 True +3 3 True +5 5 True +5 5 True +3 3 True +4 4 True +3 3 True +1 1 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +2 2 True +9 9 True +1 1 True +, , True +s s True +2 2 True +: : True +0 0 True +. . True +3 3 True +6 6 True +0 0 True +3 3 True +5 5 True +5 5 True +3 3 True +4 4 True +3 3 True +1 1 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +2 2 True +9 9 True +1 1 True +) ) True +A A True +: : True +1 1 True +. . True +1 1 True +9 9 True +6 6 True +8 8 True +7 7 True +8 8 True +2 2 True +8 8 True +6 6 True +2 2 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +2 3 False +9 ) False +9 B False +9 : False +) 0 False +B . False +: 5 False +0 2 False +. 0 False +5 7 False +2 5 False +0 4 False +7 6 False +5 5 True +4 9 False +6 1 False +5 9 False +9 9 True +1 9 False +9 9 True +9 9 True +9 9 True +9 6 False +9 9 True +9 6 False +6 7 False +9 ) False +6 F False +7 : False +) 0 False +F . False +: 0 False +0 6 False +. 3 False +0 4 False +6 9 False +3 1 False +4 5 False +9 8 False +1 8 False +5 9 False +8 1 False +8 9 False +9 9 True +1 9 False +9 9 True +9 9 True +9 9 True +9 4 False +9 4 False +9 3 False +4 4 True +4 , False +3 ( False +, ( False +( s False +( 8 False +s : False +8 0 False +: . False +0 3 False +. 1 False +3 0 False +1 6 False +0 8 False +6 8 False +8 9 False +8 2 False +9 6 False +2 5 False +6 0 False +5 0 False +0 0 True +0 0 True +0 0 True +0 0 True +0 1 False +0 7 False +1 7 False +7 6 False +7 , False +6 s False +, 9 False +s : False +9 0 False +: . False +0 3 False +. 1 False +3 0 False +1 6 False +0 8 False +6 8 False +8 9 False +8 2 False +9 6 False +2 5 False +6 0 False +5 0 False +0 0 True +0 0 True +0 0 True +0 0 True +0 1 False +0 7 False +1 7 False +7 6 False +7 ) False +6 G False +) : False +G 0 False +: . False +0 1 False +. 0 False +1 3 False +0 1 False +3 5 False +1 0 False +5 8 False +0 2 False +8 4 False +2 8 False +4 9 False +8 9 False +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 3 False +9 2 False +3 7 False +2 , False +7 s False +, 1 False +s 0 False +1 : False +0 0 True +: . False +0 4 False +. 1 False +4 3 False +1 8 False +3 3 True +8 9 False +3 7 False +9 5 False +7 1 False +5 4 False +1 0 False +4 0 False +0 0 True +0 0 True +0 0 True +0 0 True +0 1 False +0 1 False +1 0 False +1 3 False +0 ) False +3 H False +) : False +H 1 False +: . False +1 3 False +. 2 False +3 7 False +2 6 False +7 4 False +6 0 False +4 1 False +0 2 False +1 5 False +2 9 False +5 9 False +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 2 False +9 0 False +2 5 False +0 ) False +4 ; False +8 +False FAILED -intended output: 0.316161 +intended output: (((((s4:0.11903321910000000394,s5:0.11903321910000000394)C:0.025441717459999999007,s6:0.14447493659999999238)D:0.76476400190000004553,s7:0.90923893850000003791)E:0.76874934999999999796,(s3:1.2572336289999999082,(s1:0.36035534310000000291,s2:0.36035534310000000291)A:1.19687828620000003)B:0.52075465919999996967)F:0.063491588919999994434,((s8:0.31068892650000001776,s9:0.31068892650000001776)G:0.10315082489999999327,s10:0.41383975140000001103)H:1.3276401259999999205); -your output: nan +your output: (((((s4:0.11903321910000000394,s5:0.11903321910000000394)C:0.02544171745999999901,s6:0.14447493659999999238)D:0.76476400190000004553,s7:0.90923893850000003791)E:0.76874934999999999796,(s3:1.25723362899999990816,(s1:0.36035534310000000291,s2:0.36035534310000000291)A:1.19687828620000002999)B:0.52075465919999996967)F:0.06349158891999999443,((s8:0.31068892650000001776,s9:0.31068892650000001776)G:0.10315082489999999327,s10:0.41383975140000001103)H:1.32764012599999992048); ================= +TESTING pxs2nex +PASSED +================= +TESTING pxboot +PASSED +================= +TESTING pxrevcomp +PASSED +================= +TESTING pxnw +PASSED +================= +TESTING pxvcf2fa +PASSED +================= +TESTING pxbp +PASSED +================= +TESTING pxssort +PASSED +================= +TESTING pxupgma +PASSED +================= +TESTING pxmrca +PASSED +================= +TESTING pxrecode +PASSED +================= +TESTING pxlssq +PASSED +================= +TESTING pxsw +PASSED +================= +TESTING pxtcomb +no test for pxtcomb +================= +TESTING pxbdsim +PASSED +================= +TESTING pxfqfilt +PASSED +================= TESTING pxmrcacut ( ( True ( ( True @@ -4665,16 +4874,8 @@ (s19:8.91922949699999989548,s21:8.91922949399999964726); ================= -TESTING pxtcomb -no test for pxtcomb -================= -TESTING pxtlate -PASSED -================= -TESTING pxupgma -PASSED -================= -TESTING pxcolt +TESTING pxtscale +( ( True ( ( True ( ( True T T True @@ -4682,43 +4883,10 @@ x x True o o True n n True -C C True +A A True : : True -0 0 True -. . True -2 2 True -5 5 True -0 , False -0 T False -0 a False -0 x False -0 o False -0 n False -0 A False -0 : False -0 0 True -0 . False -0 2 False -0 2 False -0 5 False -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -, 0 False -T 0 False -a 0 False -x 0 False -o 0 False -n 0 False -A 0 False -: 0 False -0 0 True -. 5 False -2 5 False -2 5 False -5 , False +1 1 True +. , False 0 T False 0 a False 0 x False @@ -4728,172 +4896,130 @@ 0 : False 0 0 True 0 . False -0 1 False -0 5 False -0 4 False +0 2 False +0 9 False +0 9 False +0 9 False +0 9 False +0 9 False +0 9 False +0 9 False +0 9 False 0 9 False 0 9 False -5 9 False -5 9 False -5 9 False , 9 False T 9 False a 9 False x 9 False o 9 False -n 9 False -B 9 False +n 8 False +B 8 False : 9 False -0 9 False -. 8 False -1 8 False -5 9 False -4 ) False -9 1 False +0 ) False +. : False +2 1 False 9 . False -9 0 False +9 2 False +9 5 False +9 , False +9 T False +9 a False +9 x False +9 o False +9 n False +9 C False 9 : False -9 0 False +9 2 False 9 . False -9 4 False -9 0 False -9 0 False -9 0 False -9 0 False -9 0 False -9 0 False -9 0 False -8 0 False -8 0 False -9 0 False -) 0 False -1 0 False -. 0 False -0 0 True -: 0 False -0 2 False -. 2 False -4 2 False -0 , False +9 5 False +9 ) False +8 : False +8 4 False +9 , False 0 ( False -0 T False -0 a False -0 x False -0 o False -0 n False -0 D False +) T False +: a False +1 x False +. o False +2 n False +5 D False 0 : False -0 0 True -0 . False 0 2 False +0 . False 0 3 False 0 0 True 0 0 True -2 0 False -2 0 False -2 0 False 0 0 True -, 0 False -( 0 False -T 0 False -a 0 False -x 0 False -o 0 False -n 0 False -D 0 False -: 0 False -0 9 False -. 9 False -2 9 False -3 , False -0 T False -0 a False -0 x False -0 o False -0 n False -0 E False -0 : False 0 0 True -0 . False +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +, 2 False +T 6 False +a 6 False +x 5 False +o , False +n T False +C a False +: x False +2 o False +. n False +5 E False +0 : False 0 1 False +0 . False 0 6 False 0 0 True 0 0 True 0 0 True 0 0 True -9 0 False -9 0 False -9 0 False -, 0 False -T 0 False -a 0 False -x 0 False -o 0 False -n 0 False -E 0 False -: 0 False -0 3 False -. 3 False -1 3 False -6 ) False 0 0 True -0 . False -0 9 False -0 4 False -0 : False 0 0 True -0 . False -0 2 False -0 9 False -0 9 False -0 9 False -0 9 False -0 9 False -0 9 False -0 9 False -3 9 False -3 9 False -3 9 False -) 9 False -0 9 False -. 9 False -9 9 True -4 9 False +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +0 0 True +) 8 False : 8 False -0 8 False -. 9 False -2 ) False -9 ; False -9 +4 8 False +. ) False +0 : False +0 3 False +0 ) False +0 ; False +0 False FAILED -intended output: ((TaxonC:0.25,TaxonA:0.22500000000000000555,TaxonB:0.15499999999999999889)1.0:0.4000000000000000222,(TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333)0.94:0.2999999999999999889); +intended output: (((TaxonA:1,TaxonB:0.2999999999999999889):1.25,TaxonC:2.5):4,(TaxonD:2.3000000000000002665,TaxonE:1.6000000000000000888):3); -your output: ((TaxonC:0.25000000000000000000,TaxonA:0.22500000000000000555,TaxonB:0.15499999999999999889)1.0:0.40000000000000002220,(TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333)0.94:0.29999999999999998890); +your output: (((TaxonA:1.00000000000000000000,TaxonB:0.29999999999999998890):1.25000000000000000000,TaxonC:2.50000000000000000000):4.00000000000000000000,(TaxonD:2.30000000000000026645,TaxonE:1.60000000000000008882):3.00000000000000000000); ================= -TESTING pxmrca -PASSED -================= -TESTING pxbdsim -PASSED -================= -TESTING pxaa2cdn +TESTING pxlstr PASSED ================= TESTING pxnj PASSED ================= -TESTING pxcltr -no test for pxcltr -================= -TESTING pxlstr +TESTING pxs2phy PASSED ================= -TESTING pxconsq +TESTING pxaa2cdn PASSED ================= -TESTING pxs2phy +TESTING pxrms PASSED ================= TESTING pxrr @@ -5099,56 +5225,390 @@ your output: (TaxonA:0.05000000000000000278,(TaxonB:0.02999999999999999889,((TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333):0.69999999999999995559,TaxonC:0.25000000000000000000):0.12500000000000000000):0.05000000000000000278); ================= -TESTING pxboot -PASSED -================= -TESTING pxrmk -( ( True -( ( True -( ( True -( ( True +TESTING pxrlt ( ( True -s s True -4 4 True +E E True +u u True +b b True +a a True +c c True +t t True +e e True +r r True +i i True +a a True : : True +4 4 True +2 2 True 0 0 True -. . True -1 1 True +0 0 True +. , False +0 ( False +0 A False +0 r False +0 c False +0 h False +0 a False +0 e False +0 a False +0 : False +0 3 False +0 8 False +0 0 True +0 6 False +0 . False +0 0 True +0 1 False +0 0 True +0 2 False +0 4 False +0 9 False +, 9 False +( 9 False +A 9 False +r 9 False +c 9 False +h 9 False +a 8 False +e 1 False +a 4 False +: 5 False +3 , False +8 ( False +0 ( False +6 ( False +. ( False +0 S False +1 A False +0 R False +2 : False +4 1 False +9 6 False +9 2 False +9 6 False +9 . False +9 0 False +9 4 False +9 2 False +8 7 False +1 3 False +4 1 False +4 9 False +6 9 False +3 9 False +0 9 False +8 9 False +, 9 False +( 8 False +( 8 False +( 7 False +( 2 False +S , False +A P False +R l False +: a False +1 n False +6 t False +2 : False +6 1 False +. 6 False +0 2 False +4 6 False +2 . False +7 0 False +3 2 False +1 7 False +9 6 False +9 6 False +9 7 False +9 0 False +9 0 False +9 0 False +8 0 False +8 0 False +7 0 False +1 0 False +9 6 False +3 4 False +5 9 False +5 ) False +, : False +P 7 False +l 2 False +a . False +n 3 False +t 8 False +: 0 False 1 1 True +6 8 False +2 3 False +6 9 False +. 9 False +0 9 False +2 9 False +7 9 False +6 9 False +6 9 False +7 9 False +0 9 False +0 8 False +0 5 False +0 5 False +0 , False +0 E False +0 x False +6 c False +4 a False +9 v False +4 a False +5 t False +2 a False +0 : False +) 1 False +: 6 False +7 9 False +2 8 False +. . True +3 4 False +8 2 False +0 2 False +1 9 False +8 1 False +3 5 False 9 9 True -0 0 True -3 3 True -3 3 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 9 True +9 8 False +9 6 False +8 5 False +5 ) False +5 : False +3 7 False +9 4 False +, . False +E 7 False +x 3 False +c 1 False +a 2 False +v 1 False +a 9 False +t 9 False +a 9 False +: 9 False +1 9 False +6 9 False +9 9 True +8 9 False +. 9 False +4 3 False +2 3 False 2 2 True +9 , False +1 A False +5 m False +9 o False +9 e False +9 b False +9 o False +9 z False +9 o False +9 a False +8 : False +6 1 False +5 7 False +2 7 False +4 3 False +9 . False +3 1 False +) 5 False +: 4 False +7 1 False +4 3 False +. 6 False +7 0 False +3 0 False +1 0 False +2 0 False +1 0 False +9 0 False +9 1 False +9 0 False +9 7 False +9 7 False +9 ) False +9 : False +9 7 False +9 . False +3 9 False +3 3 True +1 7 False +9 5 False +7 3 False +6 4 False +, 9 False +A 9 False +m 9 False +o 9 False +e 9 False +b 9 False +o 9 False +z 9 False +o 9 False +a 5 False +: 6 False +1 3 False +7 2 False +7 , False +3 ( False +. A False +1 n False +5 i False +4 m False +1 a False +3 l False +6 : False +0 1 False +0 2 False +0 9 False +0 5 False +0 . False +0 7 False 1 1 True +0 7 False +7 5 False +7 4 False +4 4 True +2 0 False +3 0 False +8 0 False +) 0 False +: 0 False +7 0 False +. 0 False +9 8 False +3 9 False +7 , False +5 F False +3 u False +4 n False +9 g False +9 i False +9 : False +9 1 False +9 2 False 9 9 True -1 1 True +9 5 False +9 . False +9 7 False +5 0 False +6 3 False +3 3 True +1 6 False +6 1 False +, 0 False +( 0 False +A 0 False +n 0 False +i 0 False +m 0 False +a 0 False +l 8 False +: 6 False +1 3 False +2 ) False +9 : False +5 4 False +. 8 False +7 5 False +1 . False +7 3 False +5 8 False +4 0 False +4 0 False +0 6 False 0 0 True 0 0 True 0 0 True 0 0 True 0 0 True 0 0 True +8 0 False +8 0 False +9 1 False +9 4 False +9 5 False +5 ) False +1 : False +, 2 False +F 0 False +u 2 False +n 4 False +g . False +i 9 False +: 2 False +1 0 False +2 0 False +9 0 False +5 0 False +. 0 False +7 0 False 0 0 True -3 3 True -9 9 True -4 4 True -, , True -s s True -5 5 True +3 0 False +3 0 False +6 0 False +1 0 False +0 7 False +0 2 False +0 8 False +0 ) False +0 : False +0 3 False +0 9 False +8 4 False +6 ) False +2 ; False +7 +False +FAILED +intended output: (Eubacteria:4200,(Archaea:3806.0102499999998145,((((SAR:1626.0427319999998872,Plant:1626.0276670000000649):72.380183999999999855,Excavata:1698.4229159999999865):74.73121999999999332,Amoebozoa:1773.1541360000001077):7.9375349999999995632,(Animal:1295.717544000000089,Fungi:1295.7033610000000863):485.3800600000000145):2024.9200000000000728):394); + +your output: (Eubacteria:4200.00000000000000000000,(Archaea:3806.01024999999981446308,((((SAR:1626.04273199999988719355,Plant:1626.02766700000006494520):72.38018399999999985539,Excavata:1698.42291599999998652493):74.73121999999999331976,Amoebozoa:1773.15413600000010774238):7.93753499999999956316,(Animal:1295.71754400000008899951,Fungi:1295.70336100000008627831):485.38006000000001449735):2024.92000000000007275958):394.00000000000000000000); + +================= +TESTING pxbdfit +PASSED +================= +TESTING pxseqgen +PASSED +================= +TESTING pxclsq +PASSED +================= +TESTING pxsstat +PASSED +================= +TESTING pxtlate +PASSED +================= +TESTING pxt2new +( ( True +( ( True +( ( True +T T True +a a True +x x True +o o True +n n True +A A True : : True 0 0 True . . True 1 1 True -1 1 True -9 9 True 0 0 True -3 3 True -3 3 True -2 2 True -1 1 True -9 9 True -1 1 True 0 0 True 0 0 True 0 0 True @@ -5156,125 +5616,29 @@ 0 0 True 0 0 True 0 0 True -3 3 True -9 9 True -4 4 True -) ) True -C C True -: : True 0 0 True -. . True -0 0 True -2 2 True -5 5 True -4 4 True -4 4 True -1 1 True -7 7 True -1 1 True -7 7 True -4 4 True -5 5 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True 0 0 True -1 0 False -, 7 False -s , False -6 s False -: 6 False -0 : False -. 0 False -1 . False -4 1 False -4 4 True -4 4 True -7 4 False -4 7 False -9 4 False -3 9 False -6 3 False -5 6 False -9 5 False -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -2 9 False -3 2 False -8 3 False -) 8 False -D ) False -: D False -0 : False -. 0 False -7 . False -6 7 False -4 6 False -7 4 False -6 7 False -4 6 False -0 4 False 0 0 True -1 0 False -9 1 False -0 9 False 0 0 True 0 0 True 0 0 True 0 0 True 0 0 True -4 0 False -5 4 False 5 5 True -3 5 False -, 3 False -s , False -7 s False -: 7 False -0 : False -. 0 False -9 . False -0 9 False -9 0 False -2 9 False -3 2 False -8 3 False -9 8 False -3 9 False -8 3 False -5 8 False -0 5 False -0 0 True -0 0 True -0 0 True +5 5 True +5 5 True +, , True +T T True +a a True +x x True +o o True +n n True +B B True +: : True 0 0 True +. . True 0 0 True -3 0 False -7 3 False -9 7 False -1 9 False -) 1 False -E ) False -: E False -0 : False -. 0 False -7 . False -6 7 False -8 6 False -7 8 False -4 7 False -9 4 False -3 9 False -4 3 False -9 4 False +2 2 True 9 9 True 9 9 True 9 9 True @@ -5283,305 +5647,164 @@ 9 9 True 9 9 True 9 9 True -7 9 False -9 7 False -6 9 False -, 6 False -( , False -s ( False -3 s False -: 3 False -1 : False -. 1 False -2 . False -5 2 False -7 5 False -2 7 False -3 2 False -3 3 True -6 3 False -2 6 False -8 2 False -9 8 False 9 9 True 9 9 True 9 9 True 9 9 True 9 9 True 9 9 True -0 9 False -8 0 False -1 8 False -6 2 False -, , True -( ( True -s s True -1 1 True +9 9 True +8 8 True +8 8 True +9 9 True +) ) True : : True 0 0 True . . True -3 3 True -6 6 True -0 0 True -3 3 True -5 5 True -5 5 True -3 3 True -4 4 True -3 3 True 1 1 True +2 2 True +5 5 True +0 , False +0 T False +0 a False +0 x False +0 o False +0 n False +0 C False +0 : False 0 0 True +0 . False +0 2 False +0 5 False +0 ) False +0 : False 0 0 True +0 . False +0 4 False +, 0 False +T 0 False +a 0 False +x 0 False +o 0 False +n 0 False +C 0 False +: 0 False 0 0 True +. 0 False +2 0 False +5 0 False 0 0 True 0 0 True 0 0 True +0 2 False +0 2 False +0 2 False +0 , False +0 ( False +0 T False +0 a False +0 x False +0 o False +0 n False +0 D False +0 : False 0 0 True -2 2 True -9 9 True -1 1 True -, , True -s s True -2 2 True -: : True -0 0 True -. . True -3 3 True -6 6 True -0 0 True -3 3 True -5 5 True -5 5 True -3 3 True -4 4 True -3 3 True -1 1 True -0 0 True +0 . False +0 2 False +) 3 False +: 0 False 0 0 True +. 0 False +4 0 False 0 0 True 0 0 True 0 0 True 0 0 True 0 0 True -2 2 True -9 9 True -1 1 True -) ) True -A A True -: : True -1 1 True -. . True -1 1 True -9 9 True -6 6 True -8 8 True -7 7 True -8 8 True -2 2 True -8 8 True -6 6 True -2 2 True 0 0 True 0 0 True 0 0 True 0 0 True 0 0 True 0 0 True -2 3 False -9 ) False -9 B False -9 : False -) 0 False -B . False -: 5 False -0 2 False -. 0 False -5 7 False -2 5 False -0 4 False -7 6 False -5 5 True -4 9 False -6 1 False -5 9 False -9 9 True -1 9 False -9 9 True -9 9 True -9 9 True -9 6 False -9 9 True -9 6 False -6 7 False -9 ) False -6 F False -7 : False -) 0 False -F . False +0 9 False +0 9 False +0 9 False +0 , False +2 T False +2 a False +2 x False +0 o False +character: 0 +character: 1 +character: 2 +, n False +( E False +T : False +a 0 False +x . False +o 1 False +n 6 False +D 0 False : 0 False -0 6 False -. 3 False -0 4 False -6 9 False -3 1 False -4 5 False -9 8 False -1 8 False -5 9 False -8 1 False -8 9 False -9 9 True -1 9 False -9 9 True -9 9 True -9 9 True -9 4 False -9 4 False -9 3 False -4 4 True -4 , False -3 ( False -, ( False -( s False -( 8 False -s : False -8 0 False -: . False -0 3 False -. 1 False -3 0 False -1 6 False -0 8 False -6 8 False -8 9 False -8 2 False -9 6 False -2 5 False -6 0 False -5 0 False -0 0 True 0 0 True -0 0 True -0 0 True -0 1 False -0 7 False -1 7 False -7 6 False -7 , False -6 s False -, 9 False -s : False -9 0 False -: . False -0 3 False -. 1 False +. 0 False +2 0 False 3 0 False -1 6 False -0 8 False -6 8 False -8 9 False -8 2 False -9 6 False -2 5 False -6 0 False -5 0 False 0 0 True 0 0 True 0 0 True 0 0 True -0 1 False -0 7 False -1 7 False -7 6 False -7 ) False -6 G False -) : False -G 0 False -: . False -0 1 False -. 0 False -1 3 False -0 1 False -3 5 False -1 0 False -5 8 False -0 2 False -8 4 False -2 8 False -4 9 False -8 9 False -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 3 False -9 2 False -3 7 False -2 , False -7 s False -, 1 False -s 0 False -1 : False 0 0 True -: . False -0 4 False -. 1 False -4 3 False -1 8 False -3 3 True -8 9 False -3 7 False -9 5 False -7 1 False -5 4 False -1 0 False -4 0 False 0 0 True 0 0 True 0 0 True 0 0 True -0 1 False -0 1 False -1 0 False -1 3 False +0 3 False +0 3 False +0 3 False 0 ) False -3 H False -) : False -H 1 False -: . False -1 3 False -. 2 False -3 7 False -2 6 False -7 4 False -6 0 False -4 1 False -0 2 False -1 5 False -2 9 False -5 9 False -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True +0 : False +0 0 True +9 . False 9 2 False -9 0 False -2 5 False +9 9 True +, 9 False +T 9 False +a 9 False +x 9 False +o 9 False +n 9 False +E 9 False +: 9 False +0 9 False +. 9 False +1 9 False +6 9 False +0 9 False +0 9 False +0 8 False +0 8 False +0 9 False 0 ) False -4 ; False -8 +0 ; False +0 False FAILED -intended output: (((((s4:0.11903321910000000394,s5:0.11903321910000000394)C:0.025441717459999999007,s6:0.14447493659999999238)D:0.76476400190000004553,s7:0.90923893850000003791)E:0.76874934999999999796,(s3:1.2572336289999999082,(s1:0.36035534310000000291,s2:0.36035534310000000291)A:1.19687828620000003)B:0.52075465919999996967)F:0.063491588919999994434,((s8:0.31068892650000001776,s9:0.31068892650000001776)G:0.10315082489999999327,s10:0.41383975140000001103)H:1.3276401259999999205); +intended output: (((TaxonA:0.10000000000000000555,TaxonB:0.02999999999999999889):0.125,TaxonC:0.25):0.4000000000000000222,(TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333):0.2999999999999999889); -your output: (((((s4:0.11903321910000000394,s5:0.11903321910000000394)C:0.02544171745999999901,s6:0.14447493659999999238)D:0.76476400190000004553,s7:0.90923893850000003791)E:0.76874934999999999796,(s3:1.25723362899999990816,(s1:0.36035534310000000291,s2:0.36035534310000000291)A:1.19687828620000002999)B:0.52075465919999996967)F:0.06349158891999999443,((s8:0.31068892650000001776,s9:0.31068892650000001776)G:0.10315082489999999327,s10:0.41383975140000001103)H:1.32764012599999992048); +your output: (((TaxonA:0.10000000000000000555,TaxonB:0.02999999999999999889):0.12500000000000000000,TaxonC:0.25000000000000000000):0.40000000000000002220,(TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333):0.29999999999999998890); ================= -TESTING pxnw +TESTING pxtrt +no test for pxtrt +================= +TESTING pxcontrates PASSED ================= +TESTING pxtcol +no test for pxtcol +================= TESTING pxmrcaname ( ( True ( ( True @@ -10643,233 +10866,44 @@ your output: (((((s19:8.91922949699999989548,s21:8.91922949399999964726)THURSTON:19.95224960999999908040,(((s28:1.94609224399999991562,(s29:1.08757619099999991441,(s30:0.89291712800000000438,s31:0.89291712800000000438):0.19465906280000000450):0.85851605259999996811):8.39712090000000088708,s32:10.34321315000000041096):11.09543256999999982781,((s33:7.22630480499999983124,((s34:2.67034968199999989125,s35:2.67034968199999989125):2.22293397799999992159,s36:4.89328365999999981284):2.33302114500000001840):7.19287123500000014076,((s38:0.64219284539999998973,s39:0.64219284539999998973):0.02637422409999999953,s40:0.66856706949999999967):13.75060897000000004198):7.01946968200000043225):7.43283338899999979077):9.42184913400000034756,(((s46:12.20104111999999929594,s49:12.20104111999999929594):6.60475515400000023902,(s51:5.41523838400000023796,s52:5.41523838400000023796):13.39055789000000018518):7.97370739499999992006,s56:26.77950367000000042594):11.51382457999999964215):38.80946141999999809968,(((((s87:3.69084388899999993328,s88:3.69084388899999993328):11.45073370999999973208,(((s90:4.72011729300000038023,(s91:3.99756842200000006571,s92:3.99756842200000006571):0.72254887099999998146):1.54594791999999991994,(s93:2.19818455100000020863,s94:2.19818455100000020863):4.06788066300000039632):0.40424694570000002658,s95:6.67031215699999968649):8.47126543999999981338):12.39306906000000019219,((s98:5.07441544599999971865,s100:5.07441544599999971865):14.97270317000000083851,s104:20.04711861999999911177):7.48752803699999969211):20.73365370000000140749,s126:48.26830034999999696765):16.54193838999999854877,((((s133:19.19452408000000076527,(s135:5.45862787400000026850,(s136:0.50068692680000004280,s137:0.50068692680000004280):4.95794094499999982162):13.73589620999999993955):8.33506465600000012728,s140:27.52958874000000122351):2.28617424699999993720,((s151:16.86265352999999933559,((s153:3.92943149300000005297,s154:3.92943149300000005297):0.58952085890000005541,(s155:4.47746336600000027772,(s156:2.71233320000000022176,s157:2.71233320000000022176):1.76513016600000005596):0.04148898641999999859):12.34370116999999922314):11.43773361000000043930,s162:28.30038714000000155124):1.51537584899999999699):2.62772215900000016831,((s169:7.84093514100000010814,s170:7.84093514100000010814):7.59463757500000014034,(s172:13.32986005999999967742,(s173:6.72141497800000031759,((s174:0.30807071029999999467,s175:0.30807071029999999467):4.10743366300000012359,s177:4.41550437300000009344):2.30591060300000005867):6.60844508699999977352):2.10571265700000020971):17.00791243000000108054):32.36675360000000267746):12.29255092000000004759)KIM:22.89721033000000005586,((((((((s213:0.20297418419999999073,s214:0.20297418419999999073):12.71610281000000064466,((s216:5.61642962300000014864,(s218:3.71339409700000011583,s219:3.71339409700000011583):1.90303552699999989350):3.11496870899999978022,(s221:4.94108935900000023622,s222:4.94108936100000040170):3.79030897300000013672):4.18767866199999971855):2.78117196399999988543,s224:15.70024895999999969831):8.11364114300000061064,(s228:16.40398771999999993909,s229:16.40398771999999993909):7.40990237699999987342):20.19393189000000177202,(((s235:1.16476196099999995681,s237:1.16476196099999995681):30.92897798999999992020,(((s239:11.80920341000000028941,(s240:1.14519345399999994406,s241:1.14519345399999994406):10.66400995999999956609):6.47606072399999987965,(s243:5.36632866400000008156,s244:5.36632866400000008156):12.91893548000000002673):0.58795460539999999661,((s246:1.02138545400000002594,s247:1.02138545400000002594):2.27899297200000017227,s248:3.30037842499999989343):15.57284031999999918128):13.22052120999999935691):1.94229831400000008124,((((s252:0.89098380509999997034,s253:0.89098380509999997034):1.44607787299999990260,(s254:0.53647671720000000839,s255:0.53647671720000000839):1.80058496099999998385):0.53514565960000004541,s256:2.87220733799999994318):1.87232111099999998238,s257:4.74452844899999970352):29.29150981000000086851):9.97178372299999971062):17.83929795999999967648,(s266:27.92939399000000122442,(s268:4.23473174699999965753,s269:4.23473174699999965753):23.69466223999999954231):33.91772595999999850847):17.52852757000000138987,(((((((s283:0.49950781950000000542,s284:0.49950781950000000542):2.37665857899999988234,s285:2.87616639900000015118):13.27575009999999977595,s286:16.15191649000000140290):14.55523323000000068816,(s288:9.13060098300000078098,(s289:5.33950376399999981913,s290:5.33950376399999981913):3.79109721799999999092):21.57654873999999978196):2.47138813500000020795,((s292:0.10949029849999999953,s293:0.10949029849999999953):21.11008483999999896241,s296:21.21957513999999989096):11.95896272000000060132):12.97210001000000012539,s307:46.15063786999999706495)LEE:9.35151650599999939573,(s325:1.57582506099999997140,s326:1.57582506099999997140):53.92632932000000067774):23.87349314000000077840):10.77139891000000027077,(((s340:9.94055052300000063781,s341:9.94055052300000063781):21.02957736999999838190,((s345:9.06912267499999913412,s347:9.06912267699999929960):1.96826656199999994179,(s348:7.19787381899999978430,s350:7.19787381899999978430):3.83951541799999995774):19.93273865999999827636):45.33019167999999865515,(s381:4.52614791999999965810,s382:4.52614791999999965810):71.77417165999999326687):13.84672684999999958677):9.85295356199999972091); ================= -TESTING pxbp +TESTING pxlog PASSED ================= -TESTING pxt2new -( ( True -( ( True -( ( True -T T True -a a True -x x True -o o True -n n True -A A True -: : True -0 0 True -. . True -1 1 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -5 5 True -5 5 True -5 5 True -, , True -T T True -a a True -x x True -o o True -n n True -B B True -: : True -0 0 True -. . True -0 0 True -2 2 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -9 9 True -8 8 True -8 8 True -9 9 True -) ) True -: : True -0 0 True -. . True -1 1 True -2 2 True -5 5 True -0 , False -0 T False -0 a False -0 x False -0 o False -0 n False -0 C False -0 : False -0 0 True -0 . False -0 2 False -0 5 False -0 ) False -0 : False -0 0 True -0 . False -0 4 False -, 0 False -T 0 False -a 0 False -x 0 False -o 0 False +TESTING pxstrec n 0 False -C 0 False -: 0 False -0 0 True -. 0 False -2 0 False -5 0 False -0 0 True -0 0 True -0 0 True -0 2 False -0 2 False -0 2 False -0 , False -0 ( False -0 T False -0 a False -0 x False -0 o False -0 n False -0 D False -0 : False -0 0 True -0 . False -0 2 False -) 3 False -: 0 False -0 0 True -. 0 False -4 0 False -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 9 False -0 9 False -0 9 False -0 , False -2 T False -2 a False -2 x False -0 o False -, n False -( E False -T : False -a 0 False -x . False -o 1 False -n 6 False -D 0 False -: 0 False -0 0 True -. 0 False -2 0 False -3 0 False -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 0 True -0 3 False -0 3 False -0 3 False -0 ) False -0 : False -0 0 True -9 . False -9 2 False -9 9 True -, 9 False -T 9 False -a 9 False -x 9 False -o 9 False -n 9 False -E 9 False -: 9 False -0 9 False -. 9 False -1 9 False -6 9 False -0 9 False -0 9 False -0 8 False -0 8 False -0 9 False -0 ) False -0 ; False -0 -False +a . False +n 3 False + 1 False + +6 False FAILED -intended output: (((TaxonA:0.10000000000000000555,TaxonB:0.02999999999999999889):0.125,TaxonC:0.25):0.4000000000000000222,(TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333):0.2999999999999999889); +intended output: 0.316161 -your output: (((TaxonA:0.10000000000000000555,TaxonB:0.02999999999999999889):0.12500000000000000000,TaxonC:0.25000000000000000000):0.40000000000000002220,(TaxonD:0.23000000000000000999,TaxonE:0.16000000000000000333):0.29999999999999998890); +your output: nan ================= -TESTING pxcat -PASSED -================= -TESTING pxtrt -no test for pxtrt +TESTING pxcltr +no test for pxcltr ================= PASSED TESTS: 30 FAILED TESTS: 10 These failed: - pxrlt,pxtscale,pxrmt,pxstrec,pxmrcacut,pxcolt,pxrr,pxrmk,pxmrcaname,pxt2new -make[1]: Leaving directory '/build/phyx-0.999+ds' + pxcolt,pxrmt,pxrmk,pxmrcacut,pxtscale,pxrr,pxrlt,pxt2new,pxmrcaname,pxstrec +make[1]: Verzeichnis „/build/phyx-0.999+ds“ wird verlassen create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --sourcedirectory=src dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src debian/rules override_dh_auto_install -make[1]: Entering directory '/build/phyx-0.999+ds' +make[1]: Verzeichnis „/build/phyx-0.999+ds“ wird betreten mkdir -p /build/phyx-0.999+ds/debian/phyx/usr/bin dh_auto_install -- prefix=/build/phyx-0.999+ds/debian/phyx/usr - cd src && make -j10 install DESTDIR=/build/phyx-0.999\+ds/debian/phyx AM_UPDATE_INFO_DIR=no prefix=/build/phyx-0.999\+ds/debian/phyx/usr -make[2]: Entering directory '/build/phyx-0.999+ds/src' + cd src && make -j18 install DESTDIR=/build/phyx-0.999\+ds/debian/phyx AM_UPDATE_INFO_DIR=no prefix=/build/phyx-0.999\+ds/debian/phyx/usr +make[2]: Verzeichnis „/build/phyx-0.999+ds/src“ wird betreten install -m 0755 px* /build/phyx-0.999+ds/debian/phyx/usr/bin -make[2]: Leaving directory '/build/phyx-0.999+ds/src' -make[1]: Leaving directory '/build/phyx-0.999+ds' +make[2]: Verzeichnis „/build/phyx-0.999+ds/src“ wird verlassen +make[1]: Verzeichnis „/build/phyx-0.999+ds“ wird verlassen dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installexamples -O--sourcedirectory=src @@ -10879,35 +10913,37 @@ dh_link -O--sourcedirectory=src dh_strip_nondeterminism -O--sourcedirectory=src debian/rules override_dh_compress -make[1]: Entering directory '/build/phyx-0.999+ds' +make[1]: Verzeichnis „/build/phyx-0.999+ds“ wird betreten dh_compress --exclude=.pdf -make[1]: Leaving directory '/build/phyx-0.999+ds' +make[1]: Verzeichnis „/build/phyx-0.999+ds“ wird verlassen dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_strip -O--sourcedirectory=src dh_makeshlibs -O--sourcedirectory=src dh_shlibdeps -O--sourcedirectory=src -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phyx/usr/bin/pxcontrates debian/phyx/usr/bin/pxseqgen debian/phyx/usr/bin/pxstrec were not linked against libnlopt_cxx.so.0 (they use none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phyx/usr/bin/pxbdfit debian/phyx/usr/bin/pxcontrates debian/phyx/usr/bin/pxseqgen debian/phyx/usr/bin/pxstrec were not linked against libblas.so.3 (they use none of the library's symbols) -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phyx/usr/bin/pxbdfit debian/phyx/usr/bin/pxcontrates debian/phyx/usr/bin/pxseqgen debian/phyx/usr/bin/pxstrec were not linked against liblapack.so.3 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phyx/usr/bin/pxseqgen debian/phyx/usr/bin/pxbdfit debian/phyx/usr/bin/pxstrec debian/phyx/usr/bin/pxcontrates were not linked against liblapack.so.3 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phyx/usr/bin/pxseqgen debian/phyx/usr/bin/pxstrec debian/phyx/usr/bin/pxcontrates were not linked against libnlopt_cxx.so.0 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/phyx/usr/bin/pxseqgen debian/phyx/usr/bin/pxbdfit debian/phyx/usr/bin/pxstrec debian/phyx/usr/bin/pxcontrates were not linked against libblas.so.3 (they use none of the library's symbols) dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src -dpkg-deb: building package 'phyx-dbgsym' in '../phyx-dbgsym_0.999+ds-1_i386.deb'. -dpkg-deb: building package 'phyx' in '../phyx_0.999+ds-1_i386.deb'. +dpkg-deb: Paket »phyx« wird in »../phyx_0.999+ds-1_i386.deb« gebaut. +dpkg-deb: Paket »phyx-dbgsym« wird in »../phyx-dbgsym_0.999+ds-1_i386.deb« gebaut. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../phyx_0.999+ds-1_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) I: copying local configuration +I: user script /srv/workspace/pbuilder/39992/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/39992/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/2756 and its subdirectories -I: Current time: Fri Oct 2 12:24:02 -12 2020 -I: pbuilder-time-stamp: 1601684642 +I: removing directory /srv/workspace/pbuilder/39992 and its subdirectories +I: Current time: Fri Nov 5 20:47:52 +14 2021 +I: pbuilder-time-stamp: 1636094872