Tue Apr 16 20:40:14 UTC 2024 I: starting to build libpal-java/trixie/i386 on jenkins on '2024-04-16 20:40' Tue Apr 16 20:40:14 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/7658/console.log Tue Apr 16 20:40:14 UTC 2024 I: Downloading source for trixie/libpal-java=1.5.1+dfsg-9 --2024-04-16 20:40:14-- http://deb.debian.org/debian/pool/main/libp/libpal-java/libpal-java_1.5.1%2bdfsg-9.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2106 (2.1K) [text/prs.lines.tag] Saving to: ‘libpal-java_1.5.1+dfsg-9.dsc’ 0K .. 100% 248M=0s 2024-04-16 20:40:14 (248 MB/s) - ‘libpal-java_1.5.1+dfsg-9.dsc’ saved [2106/2106] Tue Apr 16 20:40:14 UTC 2024 I: libpal-java_1.5.1+dfsg-9.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libpal-java Binary: libpal-java, libpal-java-doc Architecture: all Version: 1.5.1+dfsg-9 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://www.cebl.auckland.ac.nz/pal-project/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/libpal-java Vcs-Git: https://salsa.debian.org/med-team/libpal-java.git Build-Depends: debhelper-compat (= 13), javahelper, debhelper, ant Build-Depends-Indep: default-jdk Package-List: libpal-java deb java optional arch=all libpal-java-doc deb doc optional arch=all Checksums-Sha1: f7b012738189546411893daaa7dd38528ec43263 350656 libpal-java_1.5.1+dfsg.orig.tar.xz ec31cbaf015f4b0dddd17692e6b63681316fcdb2 5156 libpal-java_1.5.1+dfsg-9.debian.tar.xz Checksums-Sha256: 1e75504d897283a6a4bafbcdd89c517af26294a5c00d7386402c19ccd6f24ce1 350656 libpal-java_1.5.1+dfsg.orig.tar.xz 6cbf7aa07d8f5c0b8e6f90eeab799285253bdfb670c321d685c6563367a667e1 5156 libpal-java_1.5.1+dfsg-9.debian.tar.xz Files: 72a87fa3e629c884bc6ae8a89e5f5751 350656 libpal-java_1.5.1+dfsg.orig.tar.xz 8d209376c4d2230afd461f7ccf6cf3c8 5156 libpal-java_1.5.1+dfsg-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmSzwUQACgkQYAMWptwn dHZ2Ig/+JQGKaGwnIU+hX7DblBONoF3Tll70f0vAioX0vUFoCOmE+9ZFHiGrT05x 9izzxz/jsx4GAHr52Xo+HH232/auBViuFp3MdNlQvgDD4ehWtwEfSHC9vEfsm7sW eurd4FtjcjXkKU3bX/3UUtDOZJiCvIq14aodofXoJB/g+FLMDDyNuPoShQSSFLuA 7fnY4DcpuVMPvHxpDK7IaPdAbb4WJOIZImYqMnpEAFYckzWpqGyWuRSc4MdYidAl S0yL76aEZcp+rzApFP6v9si4cuzQar2Sx+LuJ3Rk/hmzJ0/N+trhaRnwhrJd10Cu o5QN+1wxz5dPCaO51INZNSJNy3eAzz90DYwPJ/dEdnwLrOFN87h404KyoU0LlnDU KsUlSsZqN6ZzWYJjVyYhUHaVl1cmDNR7NURNmdEwGfTyPDQwDBGIiKw78nnwcA8L SUgyE6mqEFYiy5Is/HC4CSilg8X3gG21uUEYRdVSczolQpsthctXgIsU+/Xft4fX pqGSjaHjx0e1ZrZ392wd8QcJtXOHBWavzLtbUq9IWWRMoNBzuzV9jkHLyijRIuC7 L/AGEd04MZpsi9OuRjrlnyDatOcu1Ed4BAq2MP2zDUJLWpETsUK2RVR9Nc8laPN5 m0GJWlwrDMwG97fS+LGq6Uml3Km9vAjelM/fX64x4jZ8Av28qiw= =xUG8 -----END PGP SIGNATURE----- Tue Apr 16 20:40:14 UTC 2024 I: Checking whether the package is not for us Tue Apr 16 20:40:14 UTC 2024 I: Starting 1st build on remote node ionos12-i386.debian.net. Tue Apr 16 20:40:14 UTC 2024 I: Preparing to do remote build '1' on ionos12-i386.debian.net. Tue Apr 16 20:42:15 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 16 08:40:16 -12 2024 I: pbuilder-time-stamp: 1713300016 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [libpal-java_1.5.1+dfsg-9.dsc] I: copying [./libpal-java_1.5.1+dfsg.orig.tar.xz] I: copying [./libpal-java_1.5.1+dfsg-9.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jul 16 10:07:00 2023 gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libpal-java_1.5.1+dfsg-9.dsc: no acceptable signature found dpkg-source: info: extracting libpal-java in libpal-java-1.5.1+dfsg dpkg-source: info: unpacking libpal-java_1.5.1+dfsg.orig.tar.xz dpkg-source: info: unpacking libpal-java_1.5.1+dfsg-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying TransitionProbability.patch dpkg-source: info: applying fix_encoding.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/36954/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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=11 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='210ff01cc3674ac285a47fdeacede48d' 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='36954' PS1='# ' PS2='> ' 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/r-b-build.egAw5b38/pbuilderrc_5lXl --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.egAw5b38/b1 --logfile b1/build.log libpal-java_1.5.1+dfsg-9.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' I: uname -a Linux ionos12-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 16 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/36954/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 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), javahelper, debhelper, ant, default-jdk dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19874 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 javahelper; however: Package javahelper is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on ant; however: Package ant is not installed. pbuilder-satisfydepends-dummy depends on default-jdk; however: Package default-jdk 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: adwaita-icon-theme{a} ant{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} binfmt-support{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} fastjar{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} jarwrapper{a} java-common{a} javahelper{a} libarchive-zip-perl{a} libasound2{a} libasound2-data{a} libassuan0{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbrotli1{a} libbsd0{a} libcairo2{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcups2{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdynaloader-functions-perl{a} libedit2{a} libelf1{a} libencode-locale-perl{a} libexpat1{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgif7{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libjbig0{a} libjpeg62-turbo{a} libksba8{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm17{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmodule-runtime-perl{a} libmoo-perl{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnpth0{a} libnspr4{a} libnss3{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librole-tiny-perl{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv0{a} libsub-override-perl{a} libsub-quote-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libvulkan1{a} libwebp7{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxext6{a} libxfixes3{a} libxi6{a} libxinerama1{a} libxml2{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxtst6{a} libxxf86vm1{a} libz3-4{a} m4{a} man-db{a} media-types{a} netbase{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} shared-mime-info{a} tzdata{a} wdiff{a} x11-common{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf ant-optional curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistro-info-perl libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libglib2.0-data libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libio-compress-brotli-perl libjson-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl librsvg2-common libsasl2-modules libsoap-lite-perl libstring-shellquote-perl libxstring-perl libxt-dev licensecheck lintian lynx mesa-vulkan-drivers pristine-tar python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg strace unzip wget xdg-user-dirs 0 packages upgraded, 217 newly installed, 0 to remove and 0 not upgraded. Need to get 229 MB of archives. After unpacking 692 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 binfmt-support i386 2.2.2-7 [65.8 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libpython3.11-minimal i386 3.11.8-1 [817 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.5.0-2+b2 [104 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 python3.11-minimal i386 3.11.8-1 [2087 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.11.6-1 [26.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 tzdata all 2024a-1 [255 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-3 [69.1 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libreadline8 i386 8.2-3+b1 [171 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpython3.11-stdlib i386 3.11.8-1 [1821 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 python3.11 i386 3.11.8-1 [597 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.11.6-1 [9224 B] Get: 15 http://deb.debian.org/debian trixie/main i386 python3 i386 3.11.6-1 [26.2 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 openssl i386 3.1.5-1 [1246 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20240203 [158 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-2+b1 [314 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libmagic1 i386 1:5.45-2+b1 [114 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-2+b1 [43.0 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-3 [1195 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.39.3-6 [93.3 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.0-3 [1413 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libglib2.0-0 i386 2.78.4-1 [1520 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b2 [727 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 shared-mime-info i386 2.4-1 [752 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-2+b2 [169 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libpng16-16 i386 1.6.43-1 [285 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.3.2-0.4 [107 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.3.2-0.4 [314 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libgdk-pixbuf-2.0-0 i386 2.42.10+dfsg-3+b1 [147 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 gtk-update-icon-cache i386 3.24.41-1 [46.0 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 adwaita-icon-theme all 46.0-1 [614 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 ca-certificates-java all 20240118 [11.6 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 java-common all 0.75 [6640 B] Get: 46 http://deb.debian.org/debian trixie/main i386 libavahi-common-data i386 0.8-13+b1 [111 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libavahi-common3 i386 0.8-13+b1 [45.3 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libdbus-1-3 i386 1.14.10-4 [216 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libavahi-client3 i386 0.8-13+b1 [49.2 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libcups2 i386 2.4.7-1+b1 [263 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 liblcms2-2 i386 2.14-2+b1 [165 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.2+dfsg-1+b1 [449 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libnspr4 i386 2:4.35-1.1+b1 [118 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libnss3 i386 2:3.99-1 [1523 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libasound2-data all 1.2.10-3 [20.7 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libasound2 i386 1.2.10-3 [394 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libgraphite2-3 i386 1.3.14-2 [77.7 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libharfbuzz0b i386 8.3.0-2 [2234 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libpcsclite1 i386 2.0.1-1+b1 [52.2 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 openjdk-17-jre-headless i386 17.0.10+7-1 [42.7 MB] Get: 66 http://deb.debian.org/debian trixie/main i386 default-jre-headless i386 2:1.17-75 [3068 B] Get: 67 http://deb.debian.org/debian trixie/main i386 ant all 1.10.14-1 [2162 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 at-spi2-common all 2.50.0-1 [163 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 dctrl-tools i386 2.24-3 [105 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 82 http://deb.debian.org/debian trixie/main i386 libelf1 i386 0.190-1+b1 [182 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1 [118 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 libgtk2.0-common all 2.24.33-3 [2659 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 libatk1.0-0 i386 2.50.0-1+b1 [49.7 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libpixman-1-0 i386 0.42.2-1+b1 [555 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1 [822 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libcairo2 i386 1.18.0-1+b1 [587 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 fontconfig i386 2.15.0-1.1 [462 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libfribidi0 i386 1.0.13-3+b1 [71.8 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libdatrie1 i386 0.2.13-3 [39.5 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libthai0 i386 0.1.29-2 [50.1 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libpango-1.0-0 i386 1.52.0+ds-1 [224 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libpangoft2-1.0-0 i386 1.52.0+ds-1 [51.0 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libpangocairo-1.0-0 i386 1.52.0+ds-1 [35.9 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libxcomposite1 i386 1:0.4.5-1 [16.9 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libxfixes3 i386 1:6.0.0-2 [23.0 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libxcursor1 i386 1:1.2.1-1 [42.4 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libxdamage1 i386 1:1.1.6-1 [15.3 kB] Get: 114 http://deb.debian.org/debian trixie/main i386 libxi6 i386 2:1.8.1-1 [81.0 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libxinerama1 i386 2:1.1.4-3 [18.1 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libxrandr2 i386 2:1.5.4-1 [37.7 kB] Get: 117 http://deb.debian.org/debian trixie/main i386 libgtk2.0-0 i386 2.24.33-3 [1938 kB] Get: 118 http://deb.debian.org/debian trixie/main i386 libglvnd0 i386 1.7.0-1 [43.7 kB] Get: 119 http://deb.debian.org/debian trixie/main i386 libdrm-common all 2.4.120-2 [7688 B] Get: 120 http://deb.debian.org/debian trixie/main i386 libdrm2 i386 2.4.120-2 [41.4 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libglapi-mesa i386 23.3.5-1 [35.4 kB] Get: 122 http://deb.debian.org/debian trixie/main i386 libx11-xcb1 i386 2:1.8.7-1 [232 kB] Get: 123 http://deb.debian.org/debian trixie/main i386 libxcb-dri2-0 i386 1.15-1 [107 kB] Get: 124 http://deb.debian.org/debian trixie/main i386 libxcb-dri3-0 i386 1.15-1 [107 kB] Get: 125 http://deb.debian.org/debian trixie/main i386 libxcb-glx0 i386 1.15-1 [124 kB] Get: 126 http://deb.debian.org/debian trixie/main i386 libxcb-present0 i386 1.15-1 [106 kB] Get: 127 http://deb.debian.org/debian trixie/main i386 libxcb-randr0 i386 1.15-1 [118 kB] Get: 128 http://deb.debian.org/debian trixie/main i386 libxcb-sync1 i386 1.15-1 [109 kB] Get: 129 http://deb.debian.org/debian trixie/main i386 libxcb-xfixes0 i386 1.15-1 [110 kB] Get: 130 http://deb.debian.org/debian trixie/main i386 libxshmfence1 i386 1.3-1 [8976 B] Get: 131 http://deb.debian.org/debian trixie/main i386 libxxf86vm1 i386 1:1.1.4-1+b2 [21.7 kB] Get: 132 http://deb.debian.org/debian trixie/main i386 libvulkan1 i386 1.3.275.0-1 [141 kB] Get: 133 http://deb.debian.org/debian trixie/main i386 libdrm-amdgpu1 i386 2.4.120-2 [24.4 kB] Get: 134 http://deb.debian.org/debian trixie/main i386 libpciaccess0 i386 0.17-3 [53.6 kB] Get: 135 http://deb.debian.org/debian trixie/main i386 libdrm-intel1 i386 2.4.120-2 [66.5 kB] Get: 136 http://deb.debian.org/debian trixie/main i386 libdrm-nouveau2 i386 2.4.120-2 [20.8 kB] Get: 137 http://deb.debian.org/debian trixie/main i386 libdrm-radeon1 i386 2.4.120-2 [23.0 kB] Get: 138 http://deb.debian.org/debian trixie/main i386 libedit2 i386 3.1-20230828-1 [97.5 kB] Get: 139 http://deb.debian.org/debian trixie/main i386 libz3-4 i386 4.8.12-3.1+b2 [7989 kB] Get: 140 http://deb.debian.org/debian trixie/main i386 libllvm17 i386 1:17.0.6-5 [27.7 MB] Get: 141 http://deb.debian.org/debian trixie/main i386 libsensors-config all 1:3.6.0-9 [14.6 kB] Get: 142 http://deb.debian.org/debian trixie/main i386 libsensors5 i386 1:3.6.0-9 [35.4 kB] Get: 143 http://deb.debian.org/debian trixie/main i386 libgl1-mesa-dri i386 23.3.5-1 [8327 kB] Get: 144 http://deb.debian.org/debian trixie/main i386 libglx-mesa0 i386 23.3.5-1 [157 kB] Get: 145 http://deb.debian.org/debian trixie/main i386 libglx0 i386 1.7.0-1 [37.8 kB] Get: 146 http://deb.debian.org/debian trixie/main i386 libgl1 i386 1.7.0-1 [82.0 kB] Get: 147 http://deb.debian.org/debian trixie/main i386 libgif7 i386 5.2.2-1 [45.3 kB] Get: 148 http://deb.debian.org/debian trixie/main i386 x11-common all 1:7.7+23 [252 kB] Get: 149 http://deb.debian.org/debian trixie/main i386 libxtst6 i386 2:1.2.3-1.1 [28.6 kB] Get: 150 http://deb.debian.org/debian trixie/main i386 openjdk-17-jre i386 17.0.10+7-1 [184 kB] Get: 151 http://deb.debian.org/debian trixie/main i386 default-jre i386 2:1.17-75 [1056 B] Get: 152 http://deb.debian.org/debian trixie/main i386 openjdk-17-jdk-headless i386 17.0.10+7-1 [74.0 MB] Get: 153 http://deb.debian.org/debian trixie/main i386 default-jdk-headless i386 2:1.17-75 [1108 B] Get: 154 http://deb.debian.org/debian trixie/main i386 openjdk-17-jdk i386 17.0.10+7-1 [2829 kB] Get: 155 http://deb.debian.org/debian trixie/main i386 default-jdk i386 2:1.17-75 [1068 B] Get: 156 http://deb.debian.org/debian trixie/main i386 libassuan0 i386 2.5.6-1 [51.9 kB] Get: 157 http://deb.debian.org/debian trixie/main i386 gpgconf i386 2.2.40-1.1+b1 [572 kB] Get: 158 http://deb.debian.org/debian trixie/main i386 libksba8 i386 1.6.6-1 [138 kB] Get: 159 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] Get: 160 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] Get: 161 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] Get: 162 http://deb.debian.org/debian trixie/main i386 libnpth0 i386 1.6-3+b1 [18.1 kB] Get: 163 http://deb.debian.org/debian trixie/main i386 dirmngr i386 2.2.40-1.1+b1 [820 kB] Get: 164 http://deb.debian.org/debian trixie/main i386 gnupg-l10n all 2.2.40-1.1 [1093 kB] Get: 165 http://deb.debian.org/debian trixie/main i386 gnupg-utils i386 2.2.40-1.1+b1 [973 kB] Get: 166 http://deb.debian.org/debian trixie/main i386 gpg i386 2.2.40-1.1+b1 [991 kB] Get: 167 http://deb.debian.org/debian trixie/main i386 pinentry-curses i386 1.2.1-3 [79.4 kB] Get: 168 http://deb.debian.org/debian trixie/main i386 gpg-agent i386 2.2.40-1.1+b1 [716 kB] Get: 169 http://deb.debian.org/debian trixie/main i386 gpg-wks-client i386 2.2.40-1.1+b1 [551 kB] Get: 170 http://deb.debian.org/debian trixie/main i386 gpg-wks-server i386 2.2.40-1.1+b1 [541 kB] Get: 171 http://deb.debian.org/debian trixie/main i386 gpgsm i386 2.2.40-1.1+b1 [691 kB] Get: 172 http://deb.debian.org/debian trixie/main i386 gnupg all 2.2.40-1.1 [846 kB] Get: 173 http://deb.debian.org/debian trixie/main i386 libfile-dirlist-perl all 0.05-3 [7600 B] Get: 174 http://deb.debian.org/debian trixie/main i386 libfile-which-perl all 1.27-2 [15.1 kB] Get: 175 http://deb.debian.org/debian trixie/main i386 libfile-homedir-perl all 1.006-2 [42.4 kB] Get: 176 http://deb.debian.org/debian trixie/main i386 libfile-touch-perl all 0.12-2 [8816 B] Get: 177 http://deb.debian.org/debian trixie/main i386 libio-pty-perl i386 1:1.20-1 [35.7 kB] Get: 178 http://deb.debian.org/debian trixie/main i386 libipc-run-perl all 20231003.0-2 [101 kB] Get: 179 http://deb.debian.org/debian trixie/main i386 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get: 180 http://deb.debian.org/debian trixie/main i386 libclass-xsaccessor-perl i386 1.19-4+b2 [37.7 kB] Get: 181 http://deb.debian.org/debian trixie/main i386 libb-hooks-op-check-perl i386 0.22-2+b2 [10.7 kB] Get: 182 http://deb.debian.org/debian trixie/main i386 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get: 183 http://deb.debian.org/debian trixie/main i386 libdevel-callchecker-perl i386 0.008-2+b1 [15.1 kB] Get: 184 http://deb.debian.org/debian trixie/main i386 libparams-classify-perl i386 0.015-2+b2 [23.1 kB] Get: 185 http://deb.debian.org/debian trixie/main i386 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get: 186 http://deb.debian.org/debian trixie/main i386 libimport-into-perl all 1.002005-2 [11.3 kB] Get: 187 http://deb.debian.org/debian trixie/main i386 librole-tiny-perl all 2.002004-1 [21.4 kB] Get: 188 http://deb.debian.org/debian trixie/main i386 libsub-quote-perl all 2.006008-1 [21.8 kB] Get: 189 http://deb.debian.org/debian trixie/main i386 libmoo-perl all 2.005005-1 [58.0 kB] Get: 190 http://deb.debian.org/debian trixie/main i386 libencode-locale-perl all 1.05-3 [12.9 kB] Get: 191 http://deb.debian.org/debian trixie/main i386 libtimedate-perl all 2.3300-2 [39.3 kB] Get: 192 http://deb.debian.org/debian trixie/main i386 libhttp-date-perl all 6.06-1 [10.7 kB] Get: 193 http://deb.debian.org/debian trixie/main i386 libfile-listing-perl all 6.16-1 [12.4 kB] Get: 194 http://deb.debian.org/debian trixie/main i386 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 195 http://deb.debian.org/debian trixie/main i386 liburi-perl all 5.28-1 [98.6 kB] Get: 196 http://deb.debian.org/debian trixie/main i386 libhtml-parser-perl i386 3.81-1+b1 [100 kB] Get: 197 http://deb.debian.org/debian trixie/main i386 libhtml-tree-perl all 5.07-3 [211 kB] Get: 198 http://deb.debian.org/debian trixie/main i386 libclone-perl i386 0.46-1+b1 [13.9 kB] Get: 199 http://deb.debian.org/debian trixie/main i386 libio-html-perl all 1.004-3 [16.2 kB] Get: 200 http://deb.debian.org/debian trixie/main i386 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get: 201 http://deb.debian.org/debian trixie/main i386 libhttp-message-perl all 6.45-1 [82.0 kB] Get: 202 http://deb.debian.org/debian trixie/main i386 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get: 203 http://deb.debian.org/debian trixie/main i386 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get: 204 http://deb.debian.org/debian trixie/main i386 perl-openssl-defaults i386 7+b1 [7920 B] Get: 205 http://deb.debian.org/debian trixie/main i386 libnet-ssleay-perl i386 1.94-1 [339 kB] Get: 206 http://deb.debian.org/debian trixie/main i386 libio-socket-ssl-perl all 2.085-1 [218 kB] Get: 207 http://deb.debian.org/debian trixie/main i386 libnet-http-perl all 6.23-1 [23.9 kB] Get: 208 http://deb.debian.org/debian trixie/main i386 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get: 209 http://deb.debian.org/debian trixie/main i386 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 210 http://deb.debian.org/debian trixie/main i386 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get: 211 http://deb.debian.org/debian trixie/main i386 libwww-perl all 6.77-1 [183 kB] Get: 212 http://deb.debian.org/debian trixie/main i386 patchutils i386 0.4.2-1 [79.6 kB] Get: 213 http://deb.debian.org/debian trixie/main i386 wdiff i386 1.2.2-6 [120 kB] Get: 214 http://deb.debian.org/debian trixie/main i386 devscripts all 2.23.7 [1068 kB] Get: 215 http://deb.debian.org/debian trixie/main i386 fastjar i386 2:0.98-7 [47.3 kB] Get: 216 http://deb.debian.org/debian trixie/main i386 jarwrapper all 0.79 [10.1 kB] Get: 217 http://deb.debian.org/debian trixie/main i386 javahelper all 0.79 [84.6 kB] Fetched 229 MB in 5s (47.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19874 files and directories currently installed.) Preparing to unpack .../libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... Selecting previously unselected package binfmt-support. Preparing to unpack .../binfmt-support_2.2.2-7_i386.deb ... Unpacking binfmt-support (2.2.2-7) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../libpython3.11-minimal_3.11.8-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.8-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-2+b2_i386.deb ... Unpacking libexpat1:i386 (2.5.0-2+b2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-1_i386.deb ... Unpacking python3.11-minimal (3.11.8-1) ... Setting up libpython3.11-minimal:i386 (3.11.8-1) ... Setting up libexpat1:i386 (2.5.0-2+b2) ... Setting up python3.11-minimal (3.11.8-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libdatrie1:i386 (0.2.13-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up libio-pty-perl (1:1.20-1) ... Setting up libmagic-mgc (1:5.45-2+b1) ... Setting up libclone-perl:i386 (0.46-1+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:i386 (2.78.4-1) ... No schema files found: doing nothing. Setting up libglvnd0:i386 (1.7.0-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:i386 (1.1.0-2+b3) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libtry-tiny-perl (0.31-2) ... Setting up libsensors-config (1:3.6.0-9) ... Setting up libmagic1:i386 (1:5.45-2+b1) ... Setting up libdeflate0:i386 (1.20-1) ... Setting up perl-openssl-defaults:i386 (7+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libnpth0:i386 (1.6-3+b1) ... Setting up file (1:5.45-2+b1) ... Setting up libassuan0:i386 (2.5.6-1) ... Setting up libjbig0:i386 (2.1-6.1+b1) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-4+b1) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Apr 16 20:41:17 UTC 2024. Universal Time is now: Tue Apr 16 20:41:17 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.10-3) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:i386 (4.8.12-3.1+b2) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libnspr4:i386 (2:4.35-1.1+b1) ... Setting up gnupg-l10n (2.2.40-1.1) ... Setting up libavahi-common-data:i386 (0.8-13+b1) ... Setting up libdbus-1-3:i386 (1.14.10-4) ... Setting up libfribidi0:i386 (1.0.13-3+b1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:i386 (1.6.43-1) ... Setting up libio-html-perl (1.004-3) ... Setting up autopoint (0.21-14) ... Setting up binfmt-support (2.2.2-7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libb-hooks-op-check-perl:i386 (0.22-2+b2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libipc-run-perl (20231003.0-2) ... Setting up libpcsclite1:i386 (2.0.1-1+b1) ... Setting up libsensors5:i386 (1:3.6.0-9) ... Setting up libglapi-mesa:i386 (23.3.5-1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-4+b1) ... Setting up libvulkan1:i386 (1.3.275.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:i386 (1.3.2-0.4) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libgif7:i386 (5.2.2-1) ... Setting up sensible-utils (0.0.22) ... Setting up libxshmfence1:i386 (1.3-1) ... Setting up at-spi2-common (2.50.0-1) ... Setting up libtiff6:i386 (4.5.1+git230720-4) ... Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libasound2:i386 (1.2.10-3) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b2) ... Setting up libgtk2.0-common (2.24.33-3) ... Setting up libatk1.0-0:i386 (2.50.0-1+b1) ... Setting up libfile-dirlist-perl (0.05-3) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up openssl (3.1.5-1) ... Setting up libbsd0:i386 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libelf1:i386 (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3+b2) ... Setting up liburi-perl (5.28-1) ... Setting up libfile-touch-perl (0.12-2) ... Setting up dctrl-tools (2.24-3) ... Setting up libnet-ssleay-perl:i386 (1.94-1) ... 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 pinentry-curses (1.2.1-3) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-14+b1) ... Setting up libxcb-xfixes0:i386 (1.15-1) ... Setting up libfile-listing-perl (6.16-1) ... Setting up jarwrapper (0.79) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:i386 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libxcb-glx0:i386 (1.15-1) ... Setting up libedit2:i386 (3.1-20230828-1) ... Setting up libreadline8:i386 (8.2-3+b1) ... Setting up libavahi-common3:i386 (0.8-13+b1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libnss3:i386 (2:3.99-1) ... Setting up libxcb-shm0:i386 (1.15-1) ... Setting up libdevel-callchecker-perl:i386 (0.008-2+b1) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5+b3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libxcb-present0:i386 (1.15-1) ... Setting up dh-autoreconf (20) ... Setting up patchutils (0.4.2-1) ... Setting up libthai0:i386 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libfreetype6:i386 (2.13.2+dfsg-1+b1) ... Setting up libxcb-sync1:i386 (1.15-1) ... Setting up shared-mime-info (2.4-1) ... Setting up libxcb-dri2-0:i386 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libdrm2:i386 (2.4.120-2) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libxcb-randr0:i386 (1.15-1) ... Setting up libhtml-parser-perl:i386 (3.81-1+b1) ... Setting up gpgconf (2.2.40-1.1+b1) ... Setting up libx11-6:i386 (2:1.8.7-1) ... Setting up libharfbuzz0b:i386 (8.3.0-2) ... Setting up libgdk-pixbuf-2.0-0:i386 (2.42.10+dfsg-3+b1) ... Setting up libfontconfig1:i386 (2.15.0-1.1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libllvm17:i386 (1:17.0.6-5) ... Setting up libxcomposite1:i386 (1:0.4.5-1) ... Setting up libavahi-client3:i386 (0.8-13+b1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-1.1+b1) ... Setting up gnupg-utils (2.2.40-1.1+b1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libdrm-amdgpu1:i386 (2.4.120-2) ... Setting up libxcb-dri3-0:i386 (1.15-1) ... Setting up gtk-update-icon-cache (3.24.41-1) ... Setting up libx11-xcb1:i386 (2:1.8.7-1) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up fontconfig (2.15.0-1.1) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:i386 (2.4.120-2) ... Setting up libxdamage1:i386 (1:1.1.6-1) ... Setting up gpg-agent (2.2.40-1.1+b1) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libdrm-radeon1:i386 (2.4.120-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libpython3.11-stdlib:i386 (3.11.8-1) ... Setting up libparams-classify-perl:i386 (0.015-2+b2) ... Setting up gpgsm (2.2.40-1.1+b1) ... Setting up libpango-1.0-0:i386 (1.52.0+ds-1) ... Setting up libdrm-intel1:i386 (2.4.120-2) ... Setting up libgl1-mesa-dri:i386 (23.3.5-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.18.0-1+b1) ... Setting up libxxf86vm1:i386 (1:1.1.4-1+b2) ... Setting up dirmngr (2.2.40-1.1+b1) ... Setting up adwaita-icon-theme (46.0-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libmodule-runtime-perl (0.016-2) ... Setting up libxfixes3:i386 (1:6.0.0-2) ... Setting up libxinerama1:i386 (2:1.1.4-3) ... Setting up libxrandr2:i386 (2:1.5.4-1) ... Setting up gpg-wks-server (2.2.40-1.1+b1) ... Setting up libcups2:i386 (2.4.7-1+b1) ... Setting up libpangoft2-1.0-0:i386 (1.52.0+ds-1) ... Setting up libpangocairo-1.0-0:i386 (1.52.0+ds-1) ... Setting up libpython3-stdlib:i386 (3.11.6-1) ... Setting up python3.11 (3.11.8-1) ... Setting up libglx-mesa0:i386 (23.3.5-1) ... Setting up libxi6:i386 (2:1.8.1-1) ... Setting up gpg-wks-client (2.2.40-1.1+b1) ... Setting up libglx0:i386 (1.7.0-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libxtst6:i386 (2:1.2.3-1.1) ... Setting up libmoo-perl (2.005005-1) ... Setting up libxcursor1:i386 (1:1.2.1-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.6-1) ... Setting up libgl1:i386 (1.7.0-1) ... Setting up openjdk-17-jre-headless:i386 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up gnupg (2.2.40-1.1) ... Setting up libgtk2.0-0:i386 (2.24.33-3) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.77-1) ... Setting up devscripts (2.23.7) ... Setting up javahelper (0.79) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-17-jdk-headless:i386 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up ant (1.10.14-1) ... Setting up default-jre-headless (2:1.17-75) ... Setting up openjdk-17-jre:i386 (17.0.10+7-1) ... Setting up default-jre (2:1.17-75) ... Setting up openjdk-17-jdk:i386 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-i386/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.17-75) ... Setting up default-jdk (2:1.17-75) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libpal-java-1.5.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libpal-java_1.5.1+dfsg-9_source.changes dpkg-buildpackage: info: source package libpal-java dpkg-buildpackage: info: source version 1.5.1+dfsg-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Pierre Gruet dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with javahelper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/libpal-java-1.5.1+dfsg' cd src; ant clean Buildfile: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/build.xml clean: BUILD SUCCESSFUL Total time: 0 seconds make[1]: Leaving directory '/build/reproducible-path/libpal-java-1.5.1+dfsg' jh_clean dh_clean debian/rules binary dh binary --with javahelper dh_update_autotools_config dh_autoreconf jh_linkjars debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/libpal-java-1.5.1+dfsg' ant -buildfile src/build.xml -propertyfile debian/ant.properties Buildfile: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/build.xml init: [mkdir] Created dir: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/build compile: [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/build.xml:24: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 350 source files to /build/reproducible-path/libpal-java-1.5.1+dfsg/src/build [javac] Using ant.build.javac.target 1.5 is no longer supported, switching to 7 [javac] Using ant.build.javac.target 1.5 is no longer supported, switching to 7 [javac] Using ant.build.javac.source 1.5 is no longer supported, switching to 7 [javac] warning: [options] bootstrap class path not set in conjunction with -source 7 [javac] warning: [options] source value 7 is obsolete and will be removed in a future release [javac] warning: [options] target value 7 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/LabelMapping.java:100: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] totals.put(mapping,new Integer(count)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/LabelMapping.java:115: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] counts.put(mapping,new Integer(count)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/ReadAlignment.java:340: warning: [removal] Character(char) in Character has been deprecated and marked for removal [javac] sites.addElement(new Character((char) c)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/ReadAlignment.java:354: warning: [removal] Character(char) in Character has been deprecated and marked for removal [javac] sites.addElement(new Character((char) c)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/ReadAlignmentOld.java:131: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal [javac] numSites = new Integer(tempWord.substring(6,stringSize)).intValue() ; [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/ReadAlignmentOld.java:138: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal [javac] numSeqs = new Integer(tempWord.substring(5,stringSize)).intValue() ; [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/ReadAlignmentOld.java:324: warning: [removal] Character(char) in Character has been deprecated and marked for removal [javac] sites.addElement(new Character((char) c)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/ReadAlignmentOld.java:338: warning: [removal] Character(char) in Character has been deprecated and marked for removal [javac] sites.addElement(new Character((char) c)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:172: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] intervals.addElement(new Double(finish - start)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:173: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] lineages.addElement(new Integer(numLines)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:183: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] intervals.addElement(new Double(finish - start)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:184: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] lineages.addElement(new Integer(numLines)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:215: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] childs.addElement(new Integer(node.getChildCount())); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:230: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] childs.addElement(new Integer(node.getChildCount())); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/popgen/LinkageDisequilibrium.java:125: warning: [removal] Character(char) in Character has been deprecated and marked for removal [javac] if(!stateVector[i].contains(new Character(c))) [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/popgen/LinkageDisequilibrium.java:126: warning: [removal] Character(char) in Character has been deprecated and marked for removal [javac] {stateVector[i].add(new Character(c)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/popgen/LinkageDisequilibrium.java:127: warning: [removal] Character(char) in Character has been deprecated and marked for removal [javac] S[j][i]=(byte)stateVector[i].indexOf(new Character(c)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/popgen/LinkageDisequilibrium.java:130: warning: [removal] Character(char) in Character has been deprecated and marked for removal [javac] {S[j][i]=(byte)stateVector[i].indexOf(new Character(c)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/gui/TreePainterNormal.java:164: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] att = new Double(node.getNodeHeight()); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/gui/TreePainterNormal.java:166: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] att = new Double(node.getBranchLength()); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Attribute.java:50: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal [javac] value = new Integer(val); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Attribute.java:53: warning: [removal] Double(String) in Double has been deprecated and marked for removal [javac] value = new Double(val); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Attribute.java:59: warning: [removal] Boolean(String) in Boolean has been deprecated and marked for removal [javac] value = new Boolean(val); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Attribute.java:61: warning: [removal] Integer(String) in Integer has been deprecated and marked for removal [javac] value = new Integer(val); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Attribute.java:63: warning: [removal] Double(String) in Double has been deprecated and marked for removal [javac] value = new Double(val); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Attribute.java:65: warning: [removal] Float(String) in Float has been deprecated and marked for removal [javac] value = new Float(val); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/IdGenerator.java:33: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] name = (new Integer(i)).toString(); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/SimpleIdGroup.java:48: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] indices.put(ids[i].getName(), new Integer(i)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/SimpleIdGroup.java:164: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] indices.put(id.getName(), new Integer(i)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/CladeSystem.java:133: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] tree.setAttribute(node, AttributeNode.CLADE_PROBABILITY, new Double(pr)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/RootedTreeUtils.java:266: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] tree.setAttribute(node, AttributeNode.CLADE_PROBABILITY, new Double(pr)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/RootedTreeUtils.java:269: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] tree.setAttribute(node, AttributeNode.MEAN_CLADE_HEIGHT, new Double(meanCladeHeight)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/RootedTreeUtils.java:274: warning: [removal] Double(double) in Double has been deprecated and marked for removal [javac] tree.setAttribute(node, AttributeNode.SUBTREE_PROBABILITY, new Double(pr)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/TreeUtils.java:1151: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] new Integer(support) [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/TreeUtils.java:1193: warning: [removal] Integer(int) in Integer has been deprecated and marked for removal [javac] new Integer(support) [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/xml/ElementParser.java:221: warning: [removal] Double(String) in Double has been deprecated and marked for removal [javac] freqs.addElement(new Double(token)); [javac] ^ [javac] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/xml/ElementParser.java:391: warning: [removal] Double(String) in Double has been deprecated and marked for removal [javac] Double time = new Double(timeElement.getAttribute(VALUE)); [javac] ^ [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 41 warnings dist: [mkdir] Created dir: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/lib [jar] Building jar: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/lib/pal-cvs.jar BUILD SUCCESSFUL Total time: 8 seconds ant -buildfile src/build.xml -propertyfile debian/ant.properties doc Buildfile: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/build.xml doc: [javadoc] Generating Javadoc [javadoc] Using javadoc -source 1.5 is no longer supported, switching to 7 [javadoc] Debian build on Java 9+ detected: Adding the --ignore-source-errors option [javadoc] Debian build on Java 9+ detected: Adding the -Xdoclint:none option [javadoc] Javadoc execution [javadoc] Loading source files for package pal.algorithmics... [javadoc] Loading source files for package pal.alignment... [javadoc] Loading source files for package pal.coalescent... [javadoc] Loading source files for package pal.datatype... [javadoc] Loading source files for package pal.distance... [javadoc] Loading source files for package pal.eval... [javadoc] Loading source files for package pal.gui... [javadoc] Loading source files for package pal.io... [javadoc] Loading source files for package pal.math... [javadoc] Loading source files for package pal.mep... [javadoc] Loading source files for package pal.misc... [javadoc] Loading source files for package pal.popgen... [javadoc] Loading source files for package pal.statistics... [javadoc] Loading source files for package pal.substmodel... [javadoc] Loading source files for package pal.supgma... [javadoc] Loading source files for package pal.tree... [javadoc] Loading source files for package pal.treesearch... [javadoc] Loading source files for package pal.util... [javadoc] Loading source files for package pal.xml... [javadoc] Constructing Javadoc information... [javadoc] Creating destination directory: "/build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/" [javadoc] Building index for all the packages and classes... [javadoc] Standard Doclet version 17.0.10+7-Debian-1 [javadoc] Building tree for all the packages and classes... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AbstractAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/AbstractLeafNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/AbstractParentableConstrainedNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/AbstractRateMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/AlgorithmCallback.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/AlgorithmCallback.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/Alignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentBuilder.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/AlignmentDistanceMatrix.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/distance/AlignmentDistanceMatrix.java:78: warning: @param argument "immediateCompute" is not a parameter name. [javadoc] * @param immediateCompute - signifies whether to calculate distances from within constructor [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentGenerator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentReaders.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentReaders.PhylipClustalAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentReaders.UnalignedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentReceiver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentReceiver.BucketReceiver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentReceiver.SingleReceiver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AlignmentUtils.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentUtils.java:267: warning: @param argument "alignment" is not a parameter name. [javadoc] * @param alignment the alignment represented as an array of strings [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/AlignmentUtils.java:277: warning: @param argument "alignment" is not a parameter name. [javadoc] * @param alignment the alignment represented as an array of strings [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/AmbiguousDataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/AminoAcidModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/AminoAcidModelID.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/AminoAcids.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/AnnotationAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/Assessor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Attribute.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/AttributeNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/Binomial.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/BLOSUM62.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/BootstrappedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/BootstrapStatistics.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/BoundsCheckedFunction.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/math/BoundsCheckedFunction.java:27: warning: @param argument "minArg" is not a parameter name. [javadoc] * @param minArg lower constraint [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/math/BoundsCheckedFunction.java:28: warning: @param argument "maxArg" is not a parameter name. [javadoc] * @param maxArg upper constraint [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/BranchAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/BranchAccess.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/BranchLimits.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/CachedRateMatrix.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/substmodel/CachedRateMatrix.java:44: warning: @param argument "model" is not a parameter name. [javadoc] * @param model the underlying substitution model [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/substmodel/CachedRateMatrix.java:55: warning: @param argument "model" is not a parameter name. [javadoc] * @param model the underlying substitution model [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/substmodel/CachedRateMatrix.java:62: warning: Tag @return cannot be used in constructor documentation. It can only be used in the following types of documentation: method, inline text. [javadoc] * @return a clone of this cached model. [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/substmodel/CachedRateMatrix.java:63: warning: @param argument "model" is not a parameter name. [javadoc] * @param model the previous cached model. [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/CharacterAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ChiSquareDistribution.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/ChiSquareDistribution.java:63: warning: @param argument "x" is not a parameter name. [javadoc] * @param x argument [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ChiSquareTest.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/ChiSquareValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/CircularGraphics.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/CladeSystem.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/CladeSystem.java:176: warning: @param argument "boolean" is not a parameter name. [javadoc] * @param boolean[] clade [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/ClassDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/ClockTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/ClusterTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/ClusterTree.ClusteringMethod.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/CoalescentException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/CoalescentIntervals.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/CoalescentIntervals.java:254: warning: invalid input: '<' [javadoc] * Returns a list stating which of the intervals are <= minSize [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/CoalescentIntervals.java:254: warning: invalid input: '<' [javadoc] * Returns a list stating which of the intervals are <= minSize [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/CoalescentIntervals.java:327: warning: invalid input: '<' [javadoc] * small intervals (<= minSize) are pooled with the next non-small interval [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/CoalescentSimulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/CoalescentTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/CodonModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/Codons.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/datatype/Codons.java:112: warning: @param argument "residue" is not a parameter name. [javadoc] * @param residue states an array of states corresponding to states of this datatype [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/datatype/Codons.java:240: warning: @param argument "startingPosition" is not a parameter name. [javadoc] * @param startingPosition an offset into the array to start examining [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/datatype/Codons.java:287: warning: @param argument "index" is not a parameter name. [javadoc] * @param index the codon index [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/CodonTable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/CodonTableFactory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/CodonTableUtils.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/datatype/CodonTableUtils.java:36: warning: @param argument "starting" is not a parameter name. [javadoc] * @param starting position - the starting position to begin reading from [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/Comparable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/ComparableDouble.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/Comparator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/ConcatenatedAlignment.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/ConcatenatedAlignment.java:28: warning: @param argument "Alignment" is not a parameter name. [javadoc] * @param Alignment array with alignment to concatenate [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/ConcatenatedAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/ConditionalProbabilityStore.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/ConditionalProbabilityStore.ExtraProcessor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/ConjugateDirectionSearch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/ConjugateGradientSearch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/ConstantIndependentSingleSplitDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/ConstantMutationRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/ConstantPopulation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/Constants.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/ConstExpConst.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/ConstExpGrowth.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/ConstExpGrowth.java:253: warning: @param argument "parameterization" is not a parameter name. [javadoc] * @param parameterization is a combination of bits representing the parameterization. Valid values are:
[javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/ConstrainedInternalNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/ConstrainedLeafNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/ConstrainedNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/ConstrainedNode.HeightAdjustment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/ConstraintModel.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/treesearch/ConstraintModel.java:23: warning: @param argument "leafLabel" is not a parameter name. [javadoc] * @param leafLabel the label of the leaf [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/ConstraintModel.GroupManager.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ContigencyTable.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/ContigencyTable.java:52: warning: @param argument "contig" is not a parameter name. [javadoc] * @param contig is the array of integers with observed states [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/ContigencyTable.java:202: warning: @param argument "reps" is not a parameter name. [javadoc] * @param reps is the number of permutations used to the probability [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/CPREV.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/DataTranslator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/DataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/DataType.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/DataTypeTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/Dayhoff.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/DefaultCache.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/DeltaModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/DeltaModel.Instance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/DeltaModel.Utils.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/mep/DeltaModel.java:59: warning: @param argument "initialDeltas" is not a parameter name. [javadoc] * @param initialDeltas, if not of required length (for given tocd) uses subset (or sets remainder to zero) [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/DemographicClockTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/DemographicLikelihoodValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/DemographicModel.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/DemographicModel.java:183: warning: @param argument "model" is not a parameter name. [javadoc] * @param model the demographic model to test. [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/DemographicTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/DemographicValue.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/DemographicValue.java:66: warning: @param argument "t" is not a parameter name. [javadoc] * @param t tree [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/DifferentialEvolution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/DiscreteStatistics.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/DiscreteStatistics.java:218: warning: invalid input: '<' [javadoc] * compute the cumulative probability Pr(x <= z) for a given z [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/DiscreteStatistics.java:197: warning: invalid input: '<' [javadoc] * compute the cumulative probability Pr(x <= z) for a given z [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/DiscreteStatistics.java:159: warning: invalid input: '<' [javadoc] * @param q quantile (0 < q <= 1) [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/DiscreteStatistics.java:159: warning: invalid input: '<' [javadoc] * @param q quantile (0 < q <= 1) [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/DiscreteStatistics.java:183: warning: invalid input: '<' [javadoc] * @param q quantile (0 <= q <= 1) [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/DiscreteStatistics.java:183: warning: invalid input: '<' [javadoc] * @param q quantile (0 <= q <= 1) [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/DiscreteStatistics.java:197: warning: invalid input: '<' [javadoc] * compute the cumulative probability Pr(x <= z) for a given z [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/statistics/DiscreteStatistics.java:218: warning: invalid input: '<' [javadoc] * compute the cumulative probability Pr(x <= z) for a given z [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/DistanceMatrix.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/distance/DistanceMatrix.java:280: warning: @param argument "exlcusion" is not a parameter name. [javadoc] * @param exlcusion indexes of things that should not be considered, may be null [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/distance/DistanceMatrix.java:307: warning: @param argument "exlcusion" is not a parameter name. [javadoc] * @param exlcusion indexes of things that should not be considered, may be null [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/DistanceMatrixAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/DistanceMatrixAccess.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/DistanceMatrixGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/DistanceMatrixGenerator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/DistanceMatrixUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/DistanceParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/DistanceTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/DoubleKey.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/DoubleKeyCache.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/ElementFactory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/ElementParser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/ErrorFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/EvaluationCounter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/ExpandingPopulation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ExponentialDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/ExponentialGrowth.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/ExternalParameterListener.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/F81.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/F84.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/FastFourStateLHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/FastLikelihoodCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/FisherExact.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/FixedBSRDTGlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/FixedSRDTGlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/FormattedInput.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/io/FormattedInput.java:143: warning: @param argument "input" is not a parameter name. [javadoc] * @param input stream [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/FormattedOutput.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/io/FormattedOutput.java:166: warning: @param argument "output" is not a parameter name. [javadoc] * @param output stream [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/FreeBranch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/FreeInternalNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/FreeLeafNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/FreeNode.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/treesearch/FreeNode.java:36: warning: @return tag cannot be used in method with void return type. [javadoc] public void getAllComponents(ArrayList store, Class componentType, FreeBranch connection); [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/GammaDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/GammaFunction.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/math/GammaFunction.java:33: warning: @param argument "function" is not a parameter name. [javadoc] * @param function value [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/math/GammaFunction.java:98: warning: @param argument "double" is not a parameter name. [javadoc] * @param double lnGammaA precomputed lnGamma(a) [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/GammaRates.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/GapBalanced.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/GapBalancedAlignment.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/GapBalancedAlignment.java:58: warning: @param argument "Alignment" is not a parameter name. [javadoc] * @param Alignment on which to based this gap balanced alignment [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/GapBalancedAlignment.java:59: warning: @param argument "the" is not a parameter name. [javadoc] * @param the estimated startingCodonPosition of the alignment [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/GapBalancedAlignment.java:67: warning: @param argument "Alignment" is not a parameter name. [javadoc] * @param Alignment on which to based this gap balanced alignment [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/alignment/GapBalancedAlignment.java:79: warning: @param argument "Alignment" is not a parameter name. [javadoc] * @param Alignment on which to based this gap balanced alignment [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/GeneralConstraintGroupManager.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/GeneralConstraintGroupManager.LikelihoodScoreAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/GeneralConstraintGroupManager.Store.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/GeneralConstructionTool.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/treesearch/GeneralConstructionTool.java:48: warning: @param argument "numberOfStates" is not a parameter name. [javadoc] * @param numberOfStates the number of states [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/treesearch/GeneralConstructionTool.java:49: warning: @param argument "numberOfCategories" is not a parameter name. [javadoc] * @param numberOfCategories the number of model classes [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/treesearch/GeneralConstructionTool.java:50: warning: @param argument "freeCalculatorGenerator" is not a parameter name. [javadoc] * @param freeCalculatorGenerator The generator for free calculation (may be null if no free components) [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/treesearch/GeneralConstructionTool.java:51: warning: @param argument "constrainedCalcGenerator" is not a parameter name. [javadoc] * @param constrainedCalcGenerator The generator for constrained calculation (assuming a Molecular Clock, and may be null if no constrained components) [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/GeneralizedDEOptimizer.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/GeneralLikelihoodCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/GeneralLikelihoodSearcher.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/GeneralObjectState.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/GeneralOptimisable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/GeneralPoissonRateMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/GeneralRateDistributionSubstitutionModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/GeneralREVRateMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/GeneralTopologyPool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/GeneralTreeComponent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/Genotype.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/GlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/GroupLeader.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/GTR.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/HeapSort.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/HeightInformationUser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/HKY.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Identifier.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Identifier.java:95: warning: @param argument "toIgnoreIndex" is not a parameter name. [javadoc] * @param toIgnoreIndex the index of an idetifier to ignore, if <0 no element is ignored [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Identifier.java:95: warning: invalid input: '<' [javadoc] * @param toIgnoreIndex the index of an idetifier to ignore, if <0 no element is ignored [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Identifier.java:143: warning: @param argument "toIgnoreIndex" is not a parameter name. [javadoc] * @param toIgnoreIndex the index of an idetifier to ignore, if <0 no element is ignored [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Identifier.java:143: warning: invalid input: '<' [javadoc] * @param toIgnoreIndex the index of an idetifier to ignore, if <0 no element is ignored [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/Identifier.java:162: warning: @param argument "toIgnoreIndex" is not a parameter name. [javadoc] * @param toIgnoreIndex the indexes of an idetifier to ignore, does not need to be sorted */ [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/IdGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/IdGroup.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/IdGroup.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/IndelAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/IndelAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/IndividualParameterHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/IndividualParameterHandler.Listener.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/IndividualParameterHandler.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/InputSource.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/IntervalsExtractor.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/coalescent/IntervalsExtractor.java:41: warning: invalid input: '<' [javadoc] * height zero. Starting at time zero, small (<= minSize) intervals are pooled [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/InvariableSites.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/IUPACNucleotides.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/datatype/IUPACNucleotides.java:300: warning: @param argument "staringIndex" is not a parameter name. [javadoc] * @param staringIndex amount to skip at beginning of input array [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/IUPACPenaltyTable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/JTT.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/JukesCantorDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/JumbledAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/KishinoHasegawaTest.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/LabelDisplayer.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/LabelDisplayer.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/LabelMapping.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/LabelMapping.java:57: warning: @param argument "names" is not a parameter name. [javadoc] * @param names Names [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/LabelMapping.java:58: warning: @param argument "colours" is not a parameter name. [javadoc] * @param colours associated colours [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/LabelMapping.Relabeller.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/LayoutTracker.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LHCalculator.AbstractExternal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LHCalculator.External.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:121: warning: @param argument "conditionalProbabilities" is not a parameter name. [javadoc] * @param conditionalProbabilities The conditionals [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:132: warning: @param argument "leftConditionalProbabilities" is not a parameter name. [javadoc] * @param leftConditionalProbabilities [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:133: warning: @param argument "rightConditionalProbabilities" is not a parameter name. [javadoc] * @param rightConditionalProbabilities [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:134: warning: @param argument "categoryPatternLogLikelihoodStore" is not a parameter name. [javadoc] * @param categoryPatternLogLikelihoodStore after call will hold a matrix of values in the form [cat][pattern], where [cat][pattern] represents the site probability under a particular category/class, *not* multiplied by the category probability or pattern weights [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:147: warning: @param argument "leftConditionalProbabilities" is not a parameter name. [javadoc] * @param leftConditionalProbabilities [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:148: warning: @param argument "rightConditionalProbabilities" is not a parameter name. [javadoc] * @param rightConditionalProbabilities [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:149: warning: @param argument "categoryPatternLogLikelihoodStore" is not a parameter name. [javadoc] * @param categoryPatternLogLikelihoodStore after call will hold a matrix of values in the form [cat][pattern], where [cat][pattern] represents the site probability under a particular category/class, *not* multiplied by the category probability or pattern weights [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LHCalculator.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LHCalculator.Generator.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/LHCalculator.java:248: warning: @param argument "parentGenerator" is not a parameter name. [javadoc] * @param parentGenerator A reference to an encompasing generator (that may for example [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LHCalculator.Internal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LHCalculator.Leaf.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LikelihoodCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/LikelihoodEvaluator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/LikelihoodEvaluator.MLResult.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/LikelihoodEvaluator.SimpleMLResult.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/LikelihoodEvaluator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LikelihoodOptimiser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/LikelihoodRatioTest.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LikelihoodSummary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LikelihoodTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/LikelihoodValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/LineFunction.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/math/LineFunction.java:20: warning: @param argument "start" is not a parameter name. [javadoc] * @param start start point [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/math/LineFunction.java:21: warning: @param argument "dir" is not a parameter name. [javadoc] * @param dir direction vector [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/math/LineFunction.java:163: warning: @param argument "list" is not a parameter name. [javadoc] * @param list of active variables (on return) [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/popgen/LinkageDisequilibrium.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/LinkageDisequilibriumComponent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/LMSSolver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/LMSSolver.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/Local.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/Local.java:42: warning: @param argument "scale" is not a parameter name. [javadoc] * @param scale determines whether or not the backbone is scaled [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/Log.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/Logger.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/LogParameterizedTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/MachineAccuracy.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/Markable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/MathUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/Matrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/MatrixExponential.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/substmodel/MatrixExponential.java:59: warning: @param argument "r" is not a parameter name. [javadoc] * @param r rate matrix [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/MersenneTwisterFast.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/MFWithGradient.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/MinimiserMonitor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/MinimiserMonitor.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/ModelParameters.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ModelSupport.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/MolecularClockLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/MolecularClockLikelihoodModel.External.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:52: warning: @param argument "distance" is not a parameter name. [javadoc] * @param distance [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:53: warning: @param argument "model" is not a parameter name. [javadoc] * @param model [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:54: warning: @param argument "patternLookup" is not a parameter name. [javadoc] * @param patternLookup [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:55: warning: @param argument "numberOfPatterns" is not a parameter name. [javadoc] * @param numberOfPatterns [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:56: warning: @param argument "leftConditionalProbabilityProbabilties" is not a parameter name. [javadoc] * @param leftConditionalProbabilityProbabilties Implementations must not overwrite or change [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:57: warning: @param argument "rightConditionalProbabilityProbabilties" is not a parameter name. [javadoc] * @param rightConditionalProbabilityProbabilties Implementations must not overwrite or change [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:62: warning: @return tag cannot be used in method with void return type. [javadoc] public void calculateExtendedConditionals( double topBaseHeight, double bottomBaseHeight, [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:72: warning: @param argument "leftConditionalProbabilities" is not a parameter name. [javadoc] * @param leftConditionalProbabilities Assumed to be extended to the rootHeight [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:73: warning: @param argument "rightConditionalProbabilities" is not a parameter name. [javadoc] * @param rightConditionalProbabilities Assumed to be extended to the rootHeight [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:83: warning: @param argument "centerPatter" is not a parameter name. [javadoc] * @param centerPatter assumed left is ascendent component, right is descendent [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:84: warning: @param argument "ascendentConditionalProbabilities" is not a parameter name. [javadoc] * @param ascendentConditionalProbabilities Assumed to be extended (downwards) to the nodeHeight [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:85: warning: @param argument "descendentConditionalProbabilities" is not a parameter name. [javadoc] * @param descendentConditionalProbabilities Assumed to be extended (upwards) to the nodeHeight [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/MolecularClockLikelihoodModel.HeightConverter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/MolecularClockLikelihoodModel.Instance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/MolecularClockLikelihoodModel.Internal.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:112: warning: @param argument "patternLookup" is not a parameter name. [javadoc] * @param patternLookup [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:113: warning: @param argument "numberOfPatterns" is not a parameter name. [javadoc] * @param numberOfPatterns [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:125: warning: @param argument "patternLookup" is not a parameter name. [javadoc] * @param patternLookup [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/eval/MolecularClockLikelihoodModel.java:126: warning: @param argument "numberOfPatterns" is not a parameter name. [javadoc] * @param numberOfPatterns [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/MolecularClockLikelihoodModel.Leaf.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/MolecularClockLikelihoodModel.Simulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/MolecularDataType.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/datatype/MolecularDataType.java:27: warning: @param argument "the" is not a parameter name. [javadoc] * @param the IUPAC nucleotidestates [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/datatype/MolecularDataType.java:32: warning: @param argument "the" is not a parameter name. [javadoc] * @param the Simple nucleotide states (eg 0,1,2,3 or A,C,G,T) [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/MolecularDataType.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/MRDTGlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/MTREV24.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/MultiLocusAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/MultiParameterized.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/MultiParameterized.ParameterAccessWatcher.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/MultiRateMatrixHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/MultivariateFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/MultivariateMinimum.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/MultivariateMinimum.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/MutableDouble.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/MutationRateModel.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/mep/MutationRateModel.java:157: warning: @param argument "the" is not a parameter name. [javadoc] * @param the maximumMutationRate that is allowable, given the units. This needs to be given intelligently. [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/MutationRateModel.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/MutationRateModelTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Nameable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/NameColouriser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/NamedParameterized.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/NeighborJoiningTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/NeoParameterized.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/NeoParameterized.java:41: warning: @param argument "parameters" is not a parameter name. [javadoc] * @param parameters the array holding the parameters [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/misc/NeoParameterized.java:70: warning: @return tag cannot be used in method with void return type. [javadoc] public void getDefaultValues(double[] store, int startIndex); [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/NeoRateMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/NeutralSelectionRateMatrixGroup.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/NexusParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/NexusTokenizer.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/io/NexusTokenizer.java:443: warning: invalid input: '&' [javadoc] * tokenType == WHITESPACE_TOKEN && [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/io/NexusTokenizer.java:443: warning: invalid input: '&' [javadoc] * tokenType == WHITESPACE_TOKEN && [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/io/NexusTokenizer.java:480: warning: invalid input: '&' [javadoc] * token is whitespace && [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/io/NexusTokenizer.java:480: warning: invalid input: '&' [javadoc] * token is whitespace && [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/Node.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/NodeAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/NodeFactory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/NodeUtils.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/NodeUtils.java:113: warning: Tag @see: reference not found: getMaxNodeDepth() [javadoc] * @see getMaxNodeDepth() [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/tree/NodeUtils.java:357: warning: @param argument "node" is not a parameter name. [javadoc] * @param node child node to be removed [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/NormalDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/NucleotideModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/NucleotideModelID.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/Nucleotides.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/NumericalDerivative.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/NumericDataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/ObjectState.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/OrderEnumerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/OrderEnumerator.OEFactory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/OrderEnumerator.Utils.html... [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/math/OrderEnumerator.java:71: warning: @param argument "secondar" is not a parameter name. [javadoc] * @param secondar The primary OrderEnumerator, the entire sequence of a secondary enumerator is taken for every single index from the primary enumerator [javadoc] ^ [javadoc] /build/reproducible-path/libpal-java-1.5.1+dfsg/src/pal/math/OrderEnumerator.java:80: warning: @param argument "secondar" is not a parameter name. [javadoc] * @param secondar The primary OrderEnumerator [javadoc] ^ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/OrthogonalHints.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/OrthogonalHints.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/OrthogonalLineFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/OrthogonalSearch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/OrthogonalSearch.RoundOptimiser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/OutputTarget.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/Painter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/PairwiseDistance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/PalEventMulticaster.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/PalObjectEvent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/PalObjectListener.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/PalObjectListener.EventGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/ParameterEvent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Parameterized.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Parameterized.Null.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Parameterized.ParameterizedBase.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Parameterized.ParameterizedUser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Parameterized.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/ParameterizedDoubleBundle.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/ParameterizedNeoWrapper.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/ParameterizedTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/ParameterizedTree.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/ParameterizedTree.ParameterizedTreeBase.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/ParentableConstrainedNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ParetoDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/PatternInfo.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/PenalizedLikelihood.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/PivotNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/PositionedNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/PositiveSelectionRateMatrixGroup.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/ProbabilityIterator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/ProbabilityIterator.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/ProbabilityIterator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/Ranker.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/RateDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/RateHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/RateHandler.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/RateMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/RateMatrixGroup.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/RateMatrixHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/RateMatrixUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/ReadAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/ReadAlignmentOld.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/ReadDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/ReadTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/ReleaseInfo.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/RELLTopologyPool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ReplicateLikelihoodEvaluator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ReplicateLikelihoodEvaluator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Report.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/RootAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/RootedTreeInterface.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/RootedTreeInterface.Instructee.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/RootedTreeInterface.RBranch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/RootedTreeInterface.RNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/RootedTreeInterface.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/RootedTreeUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/SampleInformation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/SampleInformation.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/SaturatedSingleSplitDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/SearchEngine.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/SearcherUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/SearchMonitor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/SearchMonitor.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/SequencePairLikelihood.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/SequenceSimulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/SerialCoalescentGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/SerialCoalescentGenerator.Results.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/SerialCoalescentSimulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ShimodairaHasegawaStatistics.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/ShimodairaHasegawaTest.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/SimpleAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/SimpleAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/SimpleCharacterAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/SimpleDataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/SimpleIdGroup.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SimpleLeafCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SimpleLHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SimpleLikelihoodCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SimpleModelFastFourStateLHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SimpleMolecularClockLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/SimpleNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/SimpleRateMatrixGroup.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/SimpleSummarizable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/SimpleTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SimpleUnconstrainedLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SimpleUnconstrainedLikelihoodModel.InternalImpl.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SimpleUnconstrainedLikelihoodModel.LeafImpl.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/SimulatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/SimulatedAlignment.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/SingleClassSubstitutionModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/SingleSplitDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SingleSplitMolecularClockLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SiteDetails.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/SiteDetails.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/SitePattern.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/SkylinePlot.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/SpecificAminoAcids.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/SplitSystem.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/SplitUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/SRDTGlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/StateProvider.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/StateRemover.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/SteppedMutationRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/StoppingCriteria.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/StoppingCriteria.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/StoppingCriteria.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/StrippedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/StrippedAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/SubstitutionModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/SubstitutionModel.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/SubstitutionTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Summarizable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/SUPGMABase.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/SUPGMABase.CISummary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/SUPGMABase.PopulationParameters.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/SUPGMADistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/SUPGMATree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/TableReport.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/TemporalModelChange.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/TemporalModelChange.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/ThetaHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/ThetaHandler.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/ThreeNumberSort.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/TimeOrderCharacterData.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/TimeStamp.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/TN.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/TOCDSampleInformation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/TopologyTestEngine.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/TopologyTestEngine.StatisticsHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/TopologyTestEngine.TestResult.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/TopologyTestEngine.TopologyPool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/TransitionPenaltyTable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/TransitionProbability.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/Tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/Tree.TreeBase.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/TreeComponent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeGenerator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeIterator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeManipulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeManipulator.BranchAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeManipulator.PALBranchWrapper.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeManipulator.PALNodeWrapper.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeOperation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeOperation.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/TreePainter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/TreePainterCircular.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/TreePainterNormal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeRestricter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/TreeSearchTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/TreeUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/TwoStateModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/TwoStates.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/UnconstrainedLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/UnconstrainedLikelihoodModel.External.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/UnconstrainedLikelihoodModel.Instance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/UnconstrainedLikelihoodModel.Internal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/UnconstrainedLikelihoodModel.Leaf.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/UnconstrainedModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/UnconstrainedTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/UndoableAction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/UndoableAction.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/UniformRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Units.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/UnitsProvider.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/UnivariateFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/UnivariateMinimum.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/UnrootedMLSearcher.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/UnrootedMLSearcher.StateObject.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/UnrootedTreeInterface.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/UnrootedTreeInterface.BaseBranch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/UnrootedTreeInterface.GeneralBranch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/UnrootedTreeInterface.Instructee.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/UnrootedTreeInterface.UBranch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/UnrootedTreeInterface.UNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/UnrootedTreeInterface.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/UPGMATree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/UrnModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/VariableIndependentSingleSplitDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/Version.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/VT.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/WAG.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/WindowedMutationRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/XMLConstants.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/XmlParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/YangCodonModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/YangCodonModel.SimpleNeutralSelection.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/YangCodonModel.SimplePositiveSelection.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/YangCodonModel.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/popgen/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/popgen/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/package-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/package-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/constant-values.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/serialized-form.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/ProbabilityIterator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/ProbabilityIterator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/ProbabilityIterator.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/GeneralObjectState.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StoppingCriteria.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StoppingCriteria.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StoppingCriteria.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/SearchEngine.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/Assessor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StateProvider.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/Markable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/Ranker.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/ObjectState.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/UndoableAction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/UndoableAction.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ConcatenatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/StrippedAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/IndelAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SitePattern.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/BootstrappedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SimpleCharacterAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/MultiLocusAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/JumbledAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentBuilder.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReceiver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReceiver.BucketReceiver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReceiver.SingleReceiver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/IndelAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/Alignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AnnotationAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ReadAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/DataTranslator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/GapBalancedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ReadAlignmentOld.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ConcatenatedAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AbstractAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/CharacterAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SimpleAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SimpleAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/Genotype.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/StrippedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReaders.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReaders.PhylipClustalAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReaders.UnalignedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentGenerator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ExpandingPopulation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ConstExpGrowth.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ConstantPopulation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ConstExpConst.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentSimulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ExponentialGrowth.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/DemographicTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/DemographicClockTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/IntervalsExtractor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentIntervals.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SerialCoalescentGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SerialCoalescentGenerator.Results.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/DemographicModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SkylinePlot.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SerialCoalescentSimulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/CodonTableFactory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/IUPACPenaltyTable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/Nucleotides.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/NumericDataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/TransitionPenaltyTable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/StateRemover.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/DataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/DataType.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/SpecificAminoAcids.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/GapBalanced.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/CodonTable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/TwoStates.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/AminoAcids.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/Codons.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/MolecularDataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/MolecularDataType.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/DataTypeTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/IUPACNucleotides.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/SimpleDataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/CodonTableUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/AmbiguousDataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/PairwiseDistance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixGenerator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/JukesCantorDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/SequencePairLikelihood.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixAccess.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/ReadDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/AlignmentDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleUnconstrainedLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleUnconstrainedLikelihoodModel.LeafImpl.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleUnconstrainedLikelihoodModel.InternalImpl.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleMolecularClockLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/ConditionalProbabilityStore.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/ConditionalProbabilityStore.ExtraProcessor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleLikelihoodCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.AbstractExternal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.Generator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.Leaf.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.Internal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.External.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleLeafCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/ChiSquareValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.Instance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.Leaf.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.Internal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.External.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SiteDetails.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SiteDetails.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SingleSplitMolecularClockLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodOptimiser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/GeneralLikelihoodCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/FastLikelihoodCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodSummary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/DemographicValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/ModelParameters.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleLHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/DemographicLikelihoodValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleModelFastFourStateLHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/FastFourStateLHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/PatternInfo.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.Instance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.HeightConverter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.Simulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.Leaf.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.Internal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.External.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/LinkageDisequilibriumComponent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/Painter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreeComponent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreePainter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/NameColouriser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/PositionedNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/LayoutTracker.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreePainterNormal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/CircularGraphics.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreePainterCircular.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/LabelDisplayer.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/LabelDisplayer.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/FormattedOutput.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/FormattedInput.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/NexusParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/NexusTokenizer.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/OutputTarget.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/InputSource.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MersenneTwisterFast.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/LineFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MinimiserMonitor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MinimiserMonitor.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/GeneralizedDEOptimizer.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/ErrorFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalSearch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalSearch.RoundOptimiser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MachineAccuracy.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MFWithGradient.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MultivariateFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/BoundsCheckedFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/DifferentialEvolution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/ConjugateGradientSearch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrderEnumerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrderEnumerator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrderEnumerator.OEFactory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/Binomial.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/UnivariateMinimum.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/GammaFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalLineFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/EvaluationCounter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MultivariateMinimum.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MultivariateMinimum.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/UrnModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/UnivariateFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/NumericalDerivative.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/LMSSolver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/LMSSolver.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/ConjugateDirectionSearch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/Matrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MathUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalHints.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalHints.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/ConstantMutationRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/SteppedMutationRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/MutationRateModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/MutationRateModel.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/WindowedMutationRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/DeltaModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/DeltaModel.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/DeltaModel.Instance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ReleaseInfo.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/UnitsProvider.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/LabelMapping.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/LabelMapping.Relabeller.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/BranchLimits.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IdGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TimeStamp.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Report.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ParameterEvent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalObjectEvent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TimeOrderCharacterData.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ParameterizedDoubleBundle.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.Null.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.ParameterizedBase.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.ParameterizedUser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TOCDSampleInformation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalObjectListener.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalObjectListener.EventGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SimpleSummarizable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SampleInformation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SampleInformation.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Identifier.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/MultiParameterized.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/MultiParameterized.ParameterAccessWatcher.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/NeoParameterized.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ExternalParameterListener.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalEventMulticaster.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IndividualParameterHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IndividualParameterHandler.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IndividualParameterHandler.Listener.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Units.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ParameterizedNeoWrapper.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Attribute.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/NamedParameterized.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SimpleIdGroup.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Nameable.html... 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[javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/NeighborJoiningTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/LogParameterizedTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ClockTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.RBranch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.RNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.Instructee.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ParameterizedTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ParameterizedTree.ParameterizedTreeBase.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ParameterizedTree.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeOperation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeOperation.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SimulatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SimulatedAlignment.Factory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SplitUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SimpleTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/AttributeNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeIterator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeGenerator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/NodeFactory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/NodeUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ReadTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/CladeSystem.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralLikelihoodSearcher.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/TreeSearchTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/NodeAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/BranchAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/BranchAccess.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/AbstractParentableConstrainedNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GroupLeader.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SearchMonitor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SearchMonitor.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/UnconstrainedModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeBranch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/MRDTGlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FixedSRDTGlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/PivotNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralTreeComponent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedInternalNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeLeafNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ParentableConstrainedNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/AbstractLeafNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralConstructionTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedLeafNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/UnrootedMLSearcher.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/UnrootedMLSearcher.StateObject.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralOptimisable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SRDTGlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/HeightInformationUser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/Constants.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralConstraintGroupManager.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralConstraintGroupManager.LikelihoodScoreAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralConstraintGroupManager.Store.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstraintModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstraintModel.GroupManager.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeInternalNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FixedBSRDTGlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedNode.HeightAdjustment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/RootAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SearcherUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Log.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Version.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/XMLConstants.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Comparator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/DefaultCache.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/ThreeNumberSort.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Logger.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/DoubleKeyCache.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Comparable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/DoubleKey.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/AlgorithmCallback.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/AlgorithmCallback.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/ComparableDouble.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/HeapSort.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/class-use/ElementParser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/class-use/XmlParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/class-use/ElementFactory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/popgen/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/overview-tree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/deprecated-list.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/index.html... [javadoc] Building index for all classes... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/allclasses-index.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/allpackages-index.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/index-all.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/overview-summary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/help-doc.html... [javadoc] 100 warnings BUILD SUCCESSFUL Total time: 13 seconds make[1]: Leaving directory '/build/reproducible-path/libpal-java-1.5.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_install jh_installjavadoc debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/libpal-java-1.5.1+dfsg' dh_installdocs sed -i 's?/debian/[^/]\+/usr?/usr?' `find debian -name doc-base -type d`/* make[1]: Leaving directory '/build/reproducible-path/libpal-java-1.5.1+dfsg' dh_installchangelogs dh_lintian dh_perl dh_link jh_installlibs jh_classpath jh_manifest jh_depends dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libpal-java' in '../libpal-java_1.5.1+dfsg-9_all.deb'. dpkg-deb: building package 'libpal-java-doc' in '../libpal-java-doc_1.5.1+dfsg-9_all.deb'. dpkg-genbuildinfo --build=binary -O../libpal-java_1.5.1+dfsg-9_i386.buildinfo dpkg-genchanges --build=binary -O../libpal-java_1.5.1+dfsg-9_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: 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/36954 and its subdirectories I: Current time: Tue Apr 16 08:42:14 -12 2024 I: pbuilder-time-stamp: 1713300134 Tue Apr 16 20:42:15 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos16-i386.debian.net. Tue Apr 16 20:42:15 UTC 2024 I: Preparing to do remote build '2' on ionos16-i386.debian.net. Tue Apr 16 20:43:31 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. Tue Apr 16 20:43:32 UTC 2024 I: libpal-java_1.5.1+dfsg-9_i386.changes: Format: 1.8 Date: Sun, 16 Jul 2023 11:54:51 +0200 Source: libpal-java Binary: libpal-java libpal-java-doc Architecture: all Version: 1.5.1+dfsg-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Pierre Gruet Description: libpal-java - Phylogenetic Analysis Library libpal-java-doc - Phylogenetic Analysis Library - documentation Changes: libpal-java (1.5.1+dfsg-9) unstable; urgency=medium . * Team upload * Moving ant from B-D-I to B-D to build source package correctly * Raising Standards version to 4.6.2 (no change) * Adding Repository* entries in d/u/metadata * Adding a Lintian override for the embedded JS in the -doc package Checksums-Sha1: 52c6242d87f001b5adbfeaf9c6c88ef95be22960 616552 libpal-java-doc_1.5.1+dfsg-9_all.deb e1797487f884083b406f963af03a357f818d4eb4 697536 libpal-java_1.5.1+dfsg-9_all.deb 53f12a247c27dc44e8cdf03141b0a872b6a43411 11467 libpal-java_1.5.1+dfsg-9_i386.buildinfo Checksums-Sha256: 15b5edadf8847c28a530764041d55563054114f8702996016e1346f3ead0b3c9 616552 libpal-java-doc_1.5.1+dfsg-9_all.deb f8446b9500ba2401fec3466a35e1fd0f4594ef606312ab00a1262bc34bb7dc65 697536 libpal-java_1.5.1+dfsg-9_all.deb cb499e2024d66dd3d73e8a017cbbe5ff5722cda17f2c12ace1a37bcdaf239cd8 11467 libpal-java_1.5.1+dfsg-9_i386.buildinfo Files: 9d8175b231e807056c15556cc580bf7e 616552 doc optional libpal-java-doc_1.5.1+dfsg-9_all.deb ca4b5f7ae378a7e04680b4cebb27ec05 697536 java optional libpal-java_1.5.1+dfsg-9_all.deb 3b7b63b3f50b4a3f24c0426d1f58fbb3 11467 java optional libpal-java_1.5.1+dfsg-9_i386.buildinfo Tue Apr 16 20:43:33 UTC 2024 I: diffoscope 264 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_12-7658.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.egAw5b38/libpal-java_1.5.1+dfsg-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.egAw5b38/libpal-java_1.5.1+dfsg-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.egAw5b38/libpal-java_1.5.1+dfsg-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.egAw5b38/b1/libpal-java_1.5.1+dfsg-9_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.egAw5b38/b2/libpal-java_1.5.1+dfsg-9_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.441s) 0.441s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.037s) 0.037s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 825ms CPU time consumed: 824ms Tue Apr 16 20:43:34 UTC 2024 I: diffoscope 264 found no differences in the changes files, and a .buildinfo file also exists. Tue Apr 16 20:43:34 UTC 2024 I: libpal-java from trixie built successfully and reproducibly on i386. Tue Apr 16 20:43:36 UTC 2024 I: Submitting .buildinfo files to external archives: Tue Apr 16 20:43:36 UTC 2024 I: Submitting 16K b1/libpal-java_1.5.1+dfsg-9_i386.buildinfo.asc Tue Apr 16 20:43:37 UTC 2024 I: Submitting 16K b2/libpal-java_1.5.1+dfsg-9_i386.buildinfo.asc Tue Apr 16 20:43:38 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Apr 16 20:43:38 UTC 2024 I: Done submitting .buildinfo files. Tue Apr 16 20:43:38 UTC 2024 I: Removing signed libpal-java_1.5.1+dfsg-9_i386.buildinfo.asc files: removed './b1/libpal-java_1.5.1+dfsg-9_i386.buildinfo.asc' removed './b2/libpal-java_1.5.1+dfsg-9_i386.buildinfo.asc'