I: pbuilder: network access will be disabled during build I: Current time: Tue May 21 09:18:41 +14 2024 I: pbuilder-time-stamp: 1716232721 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [isospec_2.2.1-1.dsc] I: copying [./isospec_2.2.1.orig.tar.gz] I: copying [./isospec_2.2.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Nov 15 03:13:21 2022 +14 gpgv: using RSA key B053304E17D6D419DD9B465141AB484D7694CF42 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./isospec_2.2.1-1.dsc: no acceptable signature found dpkg-source: info: extracting isospec in isospec-2.2.1 dpkg-source: info: unpacking isospec_2.2.1.orig.tar.gz dpkg-source: info: unpacking isospec_2.2.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-Ensure-the-header-files-are-found-in-the-system.patch dpkg-source: info: applying 0002-Remove-the-mtune-native-march-native.patch dpkg-source: info: applying software-version.patch dpkg-source: info: applying 0003-cmake-directive-avoid-rpath.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/44200/tmp/hooks/D01_modify_environment starting debug: Running on ionos16-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 21 09:18 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/44200/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/44200/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=cd1758f8b528410397e5e0743e771ae8 LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=44200 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ZsROVSCM/pbuilderrc_uWrW --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZsROVSCM/b2 --logfile b2/build.log --extrapackages usrmerge isospec_2.2.1-1.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Feb 13 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 21 2022 cat -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash -rwxr-xr-x 1 root root 137160 Sep 21 2022 date -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd -rwxr-xr-x 1 root root 108940 Sep 21 2022 df -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir -rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln -rwxr-xr-x 1 root root 55600 Mar 24 2023 login -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 24 2023 more -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 May 21 09:18 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty -rwsr-xr-x 1 root root 83492 Mar 24 2023 su -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync -rwxr-xr-x 1 root root 598456 Apr 7 2023 tar -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch -rwxr-xr-x 1 root root 34664 Sep 21 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/44200/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), dh-exec (>= 0.3), dpkg-dev (>= 1.18.25), graphicsmagick-imagemagick-compat, cmake (>= 3.12), d-shlibs (>= 0.48~), dh-python, python3-dev, python3-setuptools, python3-cffi, texlive-latex-base, texlive-latex-recommended, texlive-latex-extra, texlive-plain-generic, texlive-fonts-recommended, texlive-font-utils, ghostscript, doxygen, libjs-mathjax dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19604 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 dh-exec (>= 0.3); however: Package dh-exec is not installed. pbuilder-satisfydepends-dummy depends on graphicsmagick-imagemagick-compat; however: Package graphicsmagick-imagemagick-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake (>= 3.12); however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs (>= 0.48~); however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-cffi; however: Package python3-cffi is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-base; however: Package texlive-latex-base is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on texlive-plain-generic; however: Package texlive-plain-generic is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-font-utils; however: Package texlive-font-utils is not installed. pbuilder-satisfydepends-dummy depends on ghostscript; however: Package ghostscript is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-exec{a} dh-python{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lmodern{a} fonts-mathjax{a} fonts-urw-base35{a} gettext{a} gettext-base{a} ghostscript{a} graphicsmagick{a} graphicsmagick-imagemagick-compat{a} groff-base{a} intltool-debian{a} isa-support{a} libaom3{a} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbrotli1{a} libbsd0{a} libcairo2{a} libclang-cpp14{a} libclang1-14{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2{a} libcurl4{a} libdav1d6{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libglib2.0-0{a} libgraphicsmagick-q16-3{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libharfbuzz0b{a} libheif1{a} libhwy1{a} libice6{a} libicu72{a} libidn12{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} libjxl0.7{a} libkpathsea6{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm14{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libnuma1{a} libopenjp2-7{a} libpaper-utils{a} libpaper1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtexluajit2{a} libtiff6{a} libtool{a} libuchardet0{a} libuv1{a} libwebp7{a} libwebpmux3{a} libwmflite-0.2-7{a} libx11-6{a} libx11-data{a} libx265-199{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libz3-4{a} libzzip-0-13{a} m4{a} man-db{a} media-types{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python3{a} python3-cffi{a} python3-cffi-backend{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-ply{a} python3-pycparser{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sse2-support{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-font-utils{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} texlive-plain-generic{a} ucf{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus default-jre dvisvgm fonts-droid-fallback javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl lmodern lynx ps2eps psmisc publicsuffix ruby shared-mime-info tex-gyre tipa tk wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 184 newly installed, 0 to remove and 0 not upgraded. Need to get 278 MB of archives. After unpacking 1012 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 12 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 isa-support i386 15 [9692 B] Get: 14 http://deb.debian.org/debian bookworm/main i386 sse2-support i386 15 [3320 B] Get: 15 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 ucf all 3.0043+nmu1 [55.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 libarchive13 i386 3.6.2-1 [385 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-8 [419 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 libjsoncpp25 i386 1.9.5-4 [86.2 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 librhash0 i386 1.4.3-3 [149 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libuv1 i386 1.44.2-1 [147 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 cmake-data all 3.25.1-1 [2026 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 cmake i386 3.25.1-1 [9767 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 d-shlibs all 0.104 [18.6 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 56 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 58 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 dh-exec i386 0.27 [28.2 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-2 [131 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130 [104 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libedit2 i386 3.1-20221030-2 [97.2 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libz3-4 i386 4.8.12-3.1 [7853 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libllvm14 i386 1:14.0.6-12 [25.0 MB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libclang-cpp14 i386 1:14.0.6-12 [12.7 MB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libclang1-14 i386 1:14.0.6-12 [7086 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 doxygen i386 1.9.4-4 [4836 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 libfontenc1 i386 1:1.1.4-1 [24.5 kB] Get: 77 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-4 [410 kB] Get: 79 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 xfonts-utils i386 1:7.7+6 [95.2 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 83 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 fonts-lmodern all 2.005-1 [4540 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 libgs-common all 10.0.0~dfsg-11 [148 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 libgs10-common all 10.0.0~dfsg-11 [586 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 libavahi-common-data i386 0.8-9 [107 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 libavahi-common3 i386 0.8-9 [43.3 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 libdbus-1-3 i386 1.14.6-1 [213 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 libavahi-client3 i386 0.8-9 [47.3 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 libcups2 i386 2.4.2-3 [261 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libidn12 i386 1.41-1 [85.3 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 libijs-0.35 i386 0.35-15 [16.9 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 libjbig2dec0 i386 0.19-3 [70.0 kB] Get: 97 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB] Get: 99 http://deb.debian.org/debian bookworm/main i386 libopenjp2-7 i386 2.5.0-1+b1 [196 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 libpaper1 i386 1.1.29 [12.7 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.1 [293 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-5 [332 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 107 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 108 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 109 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2 [292 kB] Get: 110 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2 [782 kB] Get: 111 http://deb.debian.org/debian bookworm/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 112 http://deb.debian.org/debian bookworm/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 113 http://deb.debian.org/debian bookworm/main i386 libxt6 i386 1:1.2.1-1.1 [192 kB] Get: 114 http://deb.debian.org/debian bookworm/main i386 libgs10 i386 10.0.0~dfsg-11 [2606 kB] Get: 115 http://deb.debian.org/debian bookworm/main i386 ghostscript i386 10.0.0~dfsg-11 [56.7 kB] Get: 116 http://deb.debian.org/debian bookworm/main i386 libaom3 i386 3.6.0-1 [1895 kB] Get: 117 http://deb.debian.org/debian bookworm/main i386 libdav1d6 i386 1.0.0-2 [316 kB] Get: 118 http://deb.debian.org/debian bookworm/main i386 libde265-0 i386 1.0.11-1 [193 kB] Get: 119 http://deb.debian.org/debian bookworm/main i386 libnuma1 i386 2.0.16-1 [22.7 kB] Get: 120 http://deb.debian.org/debian bookworm/main i386 libx265-199 i386 3.5-2+b1 [687 kB] Get: 121 http://deb.debian.org/debian bookworm/main i386 libheif1 i386 1.15.1-1 [230 kB] Get: 122 http://deb.debian.org/debian bookworm/main i386 libhwy1 i386 1.0.3-3 [232 kB] Get: 123 http://deb.debian.org/debian bookworm/main i386 libjxl0.7 i386 0.7.0-10 [865 kB] Get: 124 http://deb.debian.org/debian bookworm/main i386 libwebpmux3 i386 1.2.4-0.1 [111 kB] Get: 125 http://deb.debian.org/debian bookworm/main i386 libwmflite-0.2-7 i386 0.2.12-5 [84.3 kB] Get: 126 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 127 http://deb.debian.org/debian bookworm/main i386 libgraphicsmagick-q16-3 i386 1.4+really1.3.40-2 [1232 kB] Get: 128 http://deb.debian.org/debian bookworm/main i386 graphicsmagick i386 1.4+really1.3.40-2 [1019 kB] Get: 129 http://deb.debian.org/debian bookworm/main i386 graphicsmagick-imagemagick-compat all 1.4+really1.3.40-2 [13.4 kB] Get: 130 http://deb.debian.org/debian bookworm/main i386 libapache-pom-java all 29-2 [5276 B] Get: 131 http://deb.debian.org/debian bookworm/main i386 libpixman-1-0 i386 0.42.2-1 [548 kB] Get: 132 http://deb.debian.org/debian bookworm/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 133 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 134 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 135 http://deb.debian.org/debian bookworm/main i386 libcairo2 i386 1.16.0-7 [627 kB] Get: 136 http://deb.debian.org/debian bookworm/main i386 libcommons-parent-java all 56-1 [10.8 kB] Get: 137 http://deb.debian.org/debian bookworm/main i386 libcommons-logging-java all 1.2-3 [62.4 kB] Get: 138 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB] Get: 139 http://deb.debian.org/debian bookworm/main i386 libfontbox-java all 1:1.8.16-2 [211 kB] Get: 140 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB] Get: 141 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 142 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB] Get: 143 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 144 http://deb.debian.org/debian bookworm/main i386 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 145 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 146 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 147 http://deb.debian.org/debian bookworm/main i386 libkpathsea6 i386 2022.20220321.62855-5 [155 kB] Get: 148 http://deb.debian.org/debian bookworm/main i386 libpaper-utils i386 1.1.29 [8972 B] Get: 149 http://deb.debian.org/debian bookworm/main i386 libpdfbox-java all 1:1.8.16-2 [5205 kB] Get: 150 http://deb.debian.org/debian bookworm/main i386 libptexenc1 i386 2022.20220321.62855-5 [44.6 kB] Get: 151 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB] Get: 152 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 153 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB] Get: 154 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B] Get: 155 http://deb.debian.org/debian bookworm/main i386 libsynctex2 i386 2022.20220321.62855-5 [62.2 kB] Get: 156 http://deb.debian.org/debian bookworm/main i386 libteckit0 i386 2.5.11+ds1-1+b1 [282 kB] Get: 157 http://deb.debian.org/debian bookworm/main i386 libtexlua53-5 i386 2022.20220321.62855-5 [126 kB] Get: 158 http://deb.debian.org/debian bookworm/main i386 libtexluajit2 i386 2022.20220321.62855-5 [262 kB] Get: 159 http://deb.debian.org/debian bookworm/main i386 libxmu6 i386 2:1.1.3-3 [62.5 kB] Get: 160 http://deb.debian.org/debian bookworm/main i386 libxpm4 i386 1:3.5.12-1.1 [50.0 kB] Get: 161 http://deb.debian.org/debian bookworm/main i386 libxaw7 i386 2:1.0.14-1 [209 kB] Get: 162 http://deb.debian.org/debian bookworm/main i386 libxi6 i386 2:1.8-1+b1 [86.2 kB] Get: 163 http://deb.debian.org/debian bookworm/main i386 libzzip-0-13 i386 0.13.72+dfsg.1-1.1 [60.1 kB] Get: 164 http://deb.debian.org/debian bookworm/main i386 tex-common all 6.18 [32.5 kB] Get: 165 http://deb.debian.org/debian bookworm/main i386 preview-latex-style all 12.2-1 [201 kB] Get: 166 http://deb.debian.org/debian bookworm/main i386 python3-cffi-backend i386 1.15.1-5+b1 [88.0 kB] Get: 167 http://deb.debian.org/debian bookworm/main i386 python3-ply all 3.11-5 [65.8 kB] Get: 168 http://deb.debian.org/debian bookworm/main i386 python3-pycparser all 2.21-1 [78.8 kB] Get: 169 http://deb.debian.org/debian bookworm/main i386 python3-cffi all 1.15.1-5 [86.2 kB] Get: 170 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB] Get: 171 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB] Get: 172 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 173 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB] Get: 174 http://deb.debian.org/debian bookworm/main i386 t1utils i386 1.41-4 [62.3 kB] Get: 175 http://deb.debian.org/debian bookworm/main i386 texlive-binaries i386 2022.20220321.62855-5 [10.6 MB] Get: 176 http://deb.debian.org/debian bookworm/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 177 http://deb.debian.org/debian bookworm/main i386 texlive-base all 2022.20230122-3 [21.9 MB] Get: 178 http://deb.debian.org/debian bookworm/main i386 texlive-font-utils all 2022.20230122-3 [4130 kB] Get: 179 http://deb.debian.org/debian bookworm/main i386 texlive-fonts-recommended all 2022.20230122-3 [4988 kB] Get: 180 http://deb.debian.org/debian bookworm/main i386 texlive-latex-base all 2022.20230122-3 [1182 kB] Get: 181 http://deb.debian.org/debian bookworm/main i386 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 182 http://deb.debian.org/debian bookworm/main i386 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 183 http://deb.debian.org/debian bookworm/main i386 texlive-latex-extra all 2022.20230122-3 [19.2 MB] Get: 184 http://deb.debian.org/debian bookworm/main i386 texlive-plain-generic all 2022.20230122-3 [28.9 MB] Fetched 278 MB in 12s (23.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package poppler-data. (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 ... 19604 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.11-minimal:i386. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_i386.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:i386 (3.11.2-6) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 20454 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_i386.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20888 files and directories currently installed.) Preparing to unpack .../python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package isa-support:i386. Preparing to unpack .../isa-support_15_i386.deb ... Unpacking isa-support:i386 (15) ... Setting up isa-support:i386 (15) ... Selecting previously unselected package sse2-support. (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 ... 20928 files and directories currently installed.) Preparing to unpack .../000-sse2-support_15_i386.deb ... Unpacking sse2-support (15) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../001-libproc2-0_2%3a4.0.2-3_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.2-3_i386.deb ... Unpacking procps (2:4.0.2-3) ... 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Creating config file /etc/papersize with new version Setting up libxpm4:i386 (1:3.5.12-1.1) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up libheif1:i386 (1.15.1-1) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libclang1-14 (1:14.0.6-12) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:i386 (1.16.0-7) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libclang-cpp14 (1:14.0.6-12) ... Setting up libgraphicsmagick-q16-3 (1.4+really1.3.40-2) ... Setting up libxt6:i386 (1:1.2.1-1.1) ... Setting up libcups2:i386 (2.4.2-3) ... Setting up cmake (3.25.1-1) ... Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libxmu6:i386 (2:1.1.3-3) ... Setting up libpython3.11:i386 (3.11.2-6) ... Setting up libxi6:i386 (2:1.8-1+b1) ... Setting up graphicsmagick (1.4+really1.3.40-2) ... Setting up graphicsmagick-imagemagick-compat (1.4+really1.3.40-2) ... Setting up preview-latex-style (12.2-1) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up dh-exec (0.27) ... Setting up libxaw7:i386 (2:1.0.14-1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up doxygen (1.9.4-4) ... Setting up libpython3.11-dev:i386 (3.11.2-6) ... Setting up texlive-binaries (2022.20220321.62855-5) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up python3-lib2to3 (3.11.2-2) ... Setting up texlive-base (2022.20230122-3) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up python3-cffi-backend:i386 (1.15.1-5+b1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up libgs10-common (10.0.0~dfsg-11) ... Setting up libpython3-dev:i386 (3.11.2-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3.11-dev (3.11.2-6) ... Setting up python3-ply (3.11-5) ... Setting up texlive-plain-generic (2022.20230122-3) ... Setting up texlive-font-utils (2022.20230122-3) ... Setting up python3-pycparser (2.21-1) ... Setting up texlive-latex-base (2022.20230122-3) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up texlive-latex-recommended (2022.20230122-3) ... Setting up texlive-pictures (2022.20230122-3) ... Setting up texlive-fonts-recommended (2022.20230122-3) ... Setting up libgs10:i386 (10.0.0~dfsg-11) ... Setting up python3-cffi (1.15.1-5) ... Setting up texlive-latex-extra (2022.20230122-3) ... Setting up ghostscript (10.0.0~dfsg-11) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... 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 Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). fakeroot is already the newest version (1.31-1.2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/44200/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/44200/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/isospec-2.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../isospec_2.2.1-1_source.changes dpkg-buildpackage: info: source package isospec dpkg-buildpackage: info: source version 2.2.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Filippo Rusconi dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dpkg-query: no packages found matching r-base-dev dpkg-query: no packages found matching r-base-core dh clean --with python3 dh_auto_clean make -j15 clean make[1]: Verzeichnis „/build/isospec-2.2.1“ wird betreten rm -rf IsoSpecPy.egg-info build dist make[1]: Verzeichnis „/build/isospec-2.2.1“ wird verlassen debian/rules override_dh_clean make[1]: Verzeichnis „/build/isospec-2.2.1“ wird betreten dpkg-query: Kein Paket gefunden, das auf r-base-dev passt dpkg-query: Kein Paket gefunden, das auf r-base-core passt rm -rf obj-x86_64-linux-gnu # The setup.py script immediately creates that link which # makes the package building to stop because it finds that # the source tree has changed. So, first remove that link, # that we'll recreate when we need it later, in the # override_dh_auto_build target. rm -rf IsoSpecPy/IsoSpec++ rm -rf .pybuild/ rm -rf tmp-install/ rm -rf IsoSpec++/IsoSpec++ rm -rf IsoSpecPy/build/ rm -rf man/html/ rm -rf man/latex/ rm -rf man/man/ # Now the default target dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/libisospec\+\+-dev.substvars debian/libisospec\+\+2.substvars debian/python3-isospec.substvars debian/libisospec\+\+-doc.substvars debian/files rm -fr -- debian/libisospec\+\+-dev/ debian/tmp/ debian/libisospec\+\+2/ debian/python3-isospec/ debian/libisospec\+\+-doc/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) make[1]: Verzeichnis „/build/isospec-2.2.1“ wird verlassen debian/rules build dpkg-query: no packages found matching r-base-dev dpkg-query: no packages found matching r-base-core dh build --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Verzeichnis „/build/isospec-2.2.1“ wird betreten dpkg-query: Kein Paket gefunden, das auf r-base-dev passt dpkg-query: Kein Paket gefunden, das auf r-base-core passt dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done Configuring build for project IsoSpec -- CMAKE_CXX_COMPILER: /usr/bin/c++ -- Setting definition -Wno-unknown-pragmas. -- Setting definition -Wall. -- Setting definition -Wextra. -- Setting definition -pedantic. -- CMAKE_SOURCE_DIR: /build/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/isospec-2.2.1/obj-i686-linux-gnu UNIX non APPLE environment ~~~~~~ Instructions ~~~~~~ On UNIX/GNU-Linux, please run the configuration like this: cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE= -DCMAKE_INSTALL_PREFIX= ../development -- Starting configuration for the doc material for IsoSpec  gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. -- Finished configuration of the doc material. -- Starting configuration for the example material for IsoSpec  -- Finished configuration for the example material. The build toolchain is: Linux  -- CMAKE_BUILD_TYPE: None. -- CMAKE_INSTALL_PREFIX: /usr. "Now configuring IsoSpec++/ for IsoSpec" -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/isospec-2.2.1/obj-i686-linux-gnu dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 .. Configuring build for project IsoSpec -- CMAKE_CXX_COMPILER: /usr/bin/c++ -- Setting definition -Wno-unknown-pragmas. -- Setting definition -Wall. -- Setting definition -Wextra. -- Setting definition -pedantic. -- CMAKE_SOURCE_DIR: /build/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/isospec-2.2.1/obj-i686-linux-gnu UNIX non APPLE environment ~~~~~~ Instructions ~~~~~~ On UNIX/GNU-Linux, please run the configuration like this: cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE= -DCMAKE_INSTALL_PREFIX= ../development -- Starting configuration for the doc material for IsoSpec  gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. -- Finished configuration of the doc material. -- Starting configuration for the example material for IsoSpec  -- Finished configuration for the example material. The build toolchain is: Linux  -- CMAKE_BUILD_TYPE: None. -- CMAKE_INSTALL_PREFIX: /usr. "Now configuring IsoSpec++/ for IsoSpec" -- Configuring done -- Generating done -- Build files have been written to: /build/isospec-2.2.1/obj-i686-linux-gnu dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=. pybuild --configure -i python{version} -p 3.11 I: pybuild base:240: python3.11 setup.py config running config dh override_dh_auto_configure --with python3 make[1]: Verzeichnis „/build/isospec-2.2.1“ wird verlassen rm -f debian/libisospec\+\+-dev.debhelper.log debian/libisospec\+\+-doc.debhelper.log debian/libisospec\+\+2.debhelper.log debian/python3-isospec.debhelper.log debian/rules override_dh_auto_build make[1]: Verzeichnis „/build/isospec-2.2.1“ wird betreten dpkg-query: Kein Paket gefunden, das auf r-base-dev passt dpkg-query: Kein Paket gefunden, das auf r-base-core passt dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=. pybuild --configure -i python{version} -p 3.11 I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=cmake -O--system=distutils --sourcedirectory=. cd obj-i686-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles /build/isospec-2.2.1/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/depend make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/depend make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake --color= make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/DependInfo.cmake --color= make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten [ 25%] Building CXX object IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o cd /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ && /usr/bin/c++ -DIsoSpec___shared_EXPORTS -I/build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ -I/build/isospec-2.2.1/IsoSpec++ -g -O2 -ffile-prefix-map=/build/isospec-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wno-unknown-pragmas -Wall -Wextra -pedantic -std=gnu++17 -MD -MT IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o -MF CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o.d -o CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o -c /build/isospec-2.2.1/IsoSpec++/unity-build.cpp [ 50%] Building CXX object IsoSpec++/CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o cd /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ && /usr/bin/c++ -I/build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ -I/build/isospec-2.2.1/IsoSpec++ -g -O2 -ffile-prefix-map=/build/isospec-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -Wall -Wextra -pedantic -std=gnu++17 -MD -MT IsoSpec++/CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o -MF CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o.d -o CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o -c /build/isospec-2.2.1/IsoSpec++/unity-build.cpp [ 75%] Linking CXX static library libIsoSpec++.a cd /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ && /usr/bin/cmake -P CMakeFiles/IsoSpec++-static.dir/cmake_clean_target.cmake cd /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/IsoSpec++-static.dir/link.txt --verbose=1 /usr/bin/ar qc libIsoSpec++.a "CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o" /usr/bin/ranlib libIsoSpec++.a [100%] Linking CXX shared library libIsoSpec++.so cd /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/IsoSpec++-shared.dir/link.txt --verbose=1 make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/isospec-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libIsoSpec++.so.2 -o libIsoSpec++.so.2.2.1 "CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o" [100%] Built target IsoSpec++-static cd /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ && /usr/bin/cmake -E cmake_symlink_library libIsoSpec++.so.2.2.1 libIsoSpec++.so.2 libIsoSpec++.so make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen [100%] Built target IsoSpec++-shared make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 .. Configuring build for project IsoSpec -- CMAKE_CXX_COMPILER: /usr/bin/c++ -- Setting definition -Wno-unknown-pragmas. -- Setting definition -Wall. -- Setting definition -Wextra. -- Setting definition -pedantic. -- CMAKE_SOURCE_DIR: /build/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/isospec-2.2.1/obj-i686-linux-gnu UNIX non APPLE environment ~~~~~~ Instructions ~~~~~~ On UNIX/GNU-Linux, please run the configuration like this: cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE= -DCMAKE_INSTALL_PREFIX= ../development -- Starting configuration for the doc material for IsoSpec  gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. -- Finished configuration of the doc material. -- Starting configuration for the example material for IsoSpec  -- Finished configuration for the example material. The build toolchain is: Linux  -- CMAKE_BUILD_TYPE: None. -- CMAKE_INSTALL_PREFIX: /usr. "Now configuring IsoSpec++/ for IsoSpec" -- Configuring done -- Generating done -- Build files have been written to: /build/isospec-2.2.1/obj-i686-linux-gnu dh_auto_build -O--buildsystem=cmake cd obj-i686-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles /build/isospec-2.2.1/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/depend make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/depend make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake --color= make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/DependInfo.cmake --color= Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o.d" is newer than depends file "/build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/compiler_depend.internal". Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o.d" is newer than depends file "/build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target IsoSpec++-shared Consolidate compiler generated dependencies of target IsoSpec++-static make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make[4]: Für das Ziel „IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build“ ist nichts zu tun. make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make[4]: Für das Ziel „IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build“ ist nichts zu tun. make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen [ 50%] Built target IsoSpec++-shared [100%] Built target IsoSpec++-static make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 .. Configuring build for project IsoSpec -- CMAKE_CXX_COMPILER: /usr/bin/c++ -- Setting definition -Wno-unknown-pragmas. -- Setting definition -Wall. -- Setting definition -Wextra. -- Setting definition -pedantic. -- CMAKE_SOURCE_DIR: /build/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/isospec-2.2.1/obj-i686-linux-gnu UNIX non APPLE environment ~~~~~~ Instructions ~~~~~~ On UNIX/GNU-Linux, please run the configuration like this: cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE= -DCMAKE_INSTALL_PREFIX= ../development -- Starting configuration for the doc material for IsoSpec  gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. -- Finished configuration of the doc material. -- Starting configuration for the example material for IsoSpec  -- Finished configuration for the example material. The build toolchain is: Linux  -- CMAKE_BUILD_TYPE: None. -- CMAKE_INSTALL_PREFIX: /usr. "Now configuring IsoSpec++/ for IsoSpec" -- Configuring done -- Generating done -- Build files have been written to: /build/isospec-2.2.1/obj-i686-linux-gnu # Generate the dev-doc in the man/hml and man/latex directories #doxygen man/doxyfile dh_auto_build -O--buildsyste=cmake -- html_doc cd obj-i686-linux-gnu && make -j15 "INSTALL=install --strip-program=true" html_doc VERBOSE=1 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 html_doc make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 1 make -f CMakeFiles/Makefile2 man/CMakeFiles/html_doc.dir/all make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/depend make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/man /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/man /build/isospec-2.2.1/obj-i686-linux-gnu/man/CMakeFiles/html_doc.dir/DependInfo.cmake --color= make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/build make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten [100%] Doxygen-based developer html documentation generation cd /build/isospec-2.2.1/man && doxygen doxyfile warning: Tag 'TCL_SUBST' at line 248 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: ignoring unsupported tag 'CLANG_COMPILATION_DATABASE_PATH' at line 1102, file doxyfile warning: Tag 'COLS_IN_ALPHA_INDEX' at line 1120 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1833 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'RTF_SOURCE_CODE' at line 1915 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOCBOOK_PROGRAMLISTING' at line 2013 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 2193 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 2206 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 2215 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Doxygen version used: 1.9.4 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/isospec-2.2.1/IsoSpec++ Reading and parsing tag files Parsing files Preprocessing /build/isospec-2.2.1/IsoSpec++/allocator.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/allocator.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/allocator.h... Parsing file /build/isospec-2.2.1/IsoSpec++/allocator.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/btrd.h... Parsing file /build/isospec-2.2.1/IsoSpec++/btrd.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/conf.h... Parsing file /build/isospec-2.2.1/IsoSpec++/conf.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/cwrapper.h... Parsing file /build/isospec-2.2.1/IsoSpec++/cwrapper.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Parsing file /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/element_tables.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/element_tables.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/element_tables.h... Parsing file /build/isospec-2.2.1/IsoSpec++/element_tables.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/fasta.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/fasta.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/fasta.h... Parsing file /build/isospec-2.2.1/IsoSpec++/fasta.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Parsing file /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/isoMath.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/isoMath.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/isoMath.h... Parsing file /build/isospec-2.2.1/IsoSpec++/isoMath.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/isoSpec++.h... Parsing file /build/isospec-2.2.1/IsoSpec++/isoSpec++.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Parsing file /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/misc.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/misc.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/misc.h... Parsing file /build/isospec-2.2.1/IsoSpec++/misc.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/mman.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/mman.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/mman.h... Parsing file /build/isospec-2.2.1/IsoSpec++/mman.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/operators.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/operators.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/operators.h... Parsing file /build/isospec-2.2.1/IsoSpec++/operators.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/platform.h... Parsing file /build/isospec-2.2.1/IsoSpec++/platform.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/platform_incl.h... Parsing file /build/isospec-2.2.1/IsoSpec++/platform_incl.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/pod_vector.h... Parsing file /build/isospec-2.2.1/IsoSpec++/pod_vector.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/python-build.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/python-build.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/summator.h... Parsing file /build/isospec-2.2.1/I/build/isospec-2.2.1/IsoSpec++/allocator.h:33: warning: Compound IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:53: warning: Compound IsoSpec::ConfEqual is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:75: warning: Compound IsoSpec::ConfOrder is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:87: warning: Compound IsoSpec::ConfOrderMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:102: warning: Compound IsoSpec::ConfOrderMarginalDescending is not documented. /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:25: warning: Compound IsoSpec::DirtyAllocator is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:40: warning: Compound IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:439: warning: Compound IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:542: warning: Compound IsoSpec::IsoStochasticGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:28: warning: Compound IsoSpec::KeyHasher is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:141: warning: Compound IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:24: warning: Compound IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:117: warning: Compound IsoSpec::ReverseOrder is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:26: warning: Compound IsoSpec::SSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:76: warning: Compound IsoSpec::Summator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:99: warning: Compound IsoSpec::TSummator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:124: warning: Compound IsoSpec::TableOrder is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:32: warning: Compound pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/cwrapper.h:146: warning: Compound ws_match_res is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command soSpec++/summator.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/unity-build.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/unity-build.cpp... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file /build/isospec-2.2.1/IsoSpec++/allocator.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/allocator.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/btrd.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/conf.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/cwrapper.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/element_tables.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/element_tables.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/fasta.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/fasta.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/isoMath.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/isoMath.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/isoSpec++.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/misc.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/misc.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/mman.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/mman.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/operators.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/operators.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/platform.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/platform_incl.h... Generating code for file /build/isospec-2.2.1/I/build/isospec-2.2.1/IsoSpec++/pod_vector.h:194: warning: Member iterator (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:195: warning: Member const_iterator (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:196: warning: Member value_type (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:197: warning: Member size_type (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:198: warning: Member reference (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:199: warning: Member const_reference (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:39: warning: Member pod_vector(size_t initial_size=16) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:54: warning: Member operator=(pod_vector< T > &&other) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:64: warning: Member pod_vector(pod_vector< T > &&other) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:74: warning: Member pod_vector(unsafe_pod_vector< T > &&other) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:82: warning: Member fast_reserve(size_t n) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:94: warning: Member reserve(size_t n) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:100: warning: Member resize(size_t new_size) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:114: warning: Member resize_and_wipe(size_t new_size) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:122: warning: Member nocheck_push_back(const T &val) noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:129: warning: Member push_back(const T &val) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:137: warning: Member operator[](size_t n) noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:143: warning: Member operator[](size_t n) const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:149: warning: Member size() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:154: warning: Member capacity() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:159: warning: Member data() noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:164: warning: Member data() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:169: warning: Member empty() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:174: warning: Member back() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:180: warning: Member pop_back() noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:187: warning: Member swap(pod_vector< T > &other) noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:201: warning: Member begin() noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:202: warning: Member begin() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:203: warning: Member cbegin() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:204: warning: Member end() noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:205: warning: Member end() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:206: warning: Member cend() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:208: warning: Member front() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:214: warning: Member clear() (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:372: warning: Member iterator (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:373: warning: Member const_iterator (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:374: warning: Member value_type (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:375: warning: Member size_type (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:376: warning: Member reference (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:377: warning: Member const_reference (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:234: warning: Member init() (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:242: warning: Member init(size_t initial_size) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:261: warning: Member fast_reserve(size_t n) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:272: warning: Member reserve(size_t n) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:278: warning: Member resize(size_t new_size) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:292: warning: Member resize_and_wipe(size_t new_size) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:300: warning: Member nocheck_push_back(const T &val) noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:307: warning: Member push_back(const T &val) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:315: warning: Member operator[](size_t n) noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:321: warning: Member operator[](size_t n) const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:327: warning: Member size() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:332: warning: Member capacity() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:337: warning: Member data() noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:342: warning: Member data() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:347: warning: Member empty() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:352: warning: Member back() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:358: warning: Member pop_back() noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:365: warning: Member swap(pod_vector< T > &other) noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:379: warning: Member begin() noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:380: warning: Member begin() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:381: warning: Member cbegin() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:382: warning: Member end() noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:383: warning: Member end() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:384: warning: Member cend() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:386: warning: Member front() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:392: warning: Member clear() (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/cwrapper.h:147: warning: Member res1 (variable) of struct ws_match_res is not documented. /build/isospec-2.2.1/IsoSpec++/cwrapper.h:148: warning: Member res2 (variable) of struct ws_match_res is not documented. /build/isospec-2.2.1/IsoSpec++/cwrapper.h:149: warning: Member flow (variable) of struct ws_match_res is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:27: warning: Member RealType (typedef) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:28: warning: Member IntType (typedef) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:22: warning: Member Conf (typedef) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/allocator.h:26: warning: Member copyConf(const T *source, T *destination, int dim) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:77: warning: Member btrd(IntType _t, RealType p, IntType m, std::mt19937 &urng=random_gen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:160: warning: Member invert(IntType t, RealType p, std::mt19937 &urng=random_gen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:189: warning: Member boost_binomial_distribution_variate(IntType t_arg, RealType p_arg, std::mt19937 &urng=random_gen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.h:33: warning: Member parse_fasta(const char *fasta, int atomCounts[6]) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp:134: warning: Member reorder_array(T *arr, size_t *order, size_t size, bool can_destroy=false) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:37: warning: Member AbyssalWassersteinDistanceGrad(FixedEnvelope *const *envelopes, const double *scales, double *ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:23: warning: Member release_g_lfact_table() (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:32: warning: Member alloc_lfact_table() (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:47: warning: Member RationalApproximation(double t) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:57: warning: Member NormalCDFInverse(double p) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:65: warning: Member NormalCDFInverse(double p, double mean, double stdev) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:70: warning: Member NormalCDF(double x, double mean, double stdev) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:95: warning: Member NormalPDF(double x, double mean, double stdev) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:104: warning: Member LowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:131: warning: Member InverseLowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:150: warning: Member random_gen(random_dev()) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:151: warning: Member stdunif(0.0, 1.0) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:153: warning: Member rdvariate_binom(size_t tries, double succ_prob, std::mt19937 &rgen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:68: warning: Member InverseChiSquareCDF2(int k, double x) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:76: warning: Member rdvariate_beta_1_b(double b, std::mt19937 &rgen=random_gen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.cpp:355: warning: Member parse_formula(const char *formula, std::vector< double > &isotope_masses, std::vector< double > &isotope_probabilities, int **isotopeNumbers, int **atomCounts, unsigned int *confSize, bool use_nominal_masses) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:149: warning: Member get_loggamma_nominator(int x) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:156: warning: Member verify_atom_cnt(int atomCnt) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.cpp:28: warning: Member quickselect(void **array, int n, int start, int end) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:29: warning: Member combinedSum(const int *conf, const std::vector< double > **valuesContainer, int dimNumber) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:38: warning: Member combinedSum(const int *conf, const pod_vector< double > **valuesContainer, int dimNumber) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:47: warning: Member getConf(void *conf) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:54: warning: Member getLProb(void *conf) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:61: warning: Member unnormalized_logProb(const int *conf, const double *logProbs, int dim) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:71: warning: Member calc_mass(const int *conf, const double *masses, int dim) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:85: warning: Member printArray(const T *array, int size, const char *prefix="") (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:94: warning: Member printVector(const std::vector< T > &vec) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:99: warning: Member printOffsets(const T **array, int size, const T *offset, const char *prefix="") (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:108: warning: Member printNestedArray(const T **array, const int *shape, int size) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:133: warning: Member dealloc_table(T *tbl, int dim) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:142: warning: Member realloc_append(T **array, T what, size_t old_array_size) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:151: warning: Member get_order(T *order_array, size_t N) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:162: warning: Member get_inverse_order(T *order_array, size_t N) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:173: warning: Member impose_order(size_t *O, size_t N, TA *A, TB *B) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:26: warning: Member isospec_number_of_isotopic_entries (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:28: warning: Member elem_table_ID[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:325: warning: Member elem_table_atomicNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:621: warning: Member elem_table_mass[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:917: warning: Member elem_table_massNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:1213: warning: Member elem_table_extraNeutrons[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:1509: warning: Member elem_table_element[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:1805: warning: Member elem_table_symbol[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:2101: warning: Member elem_table_Radioactive[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:2397: warning: Member elem_table_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:2693: warning: Member elem_table_log_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:25: warning: Member aa_isotope_numbers[6] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:27: warning: Member aa_elem_masses[19] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:37: warning: Member aa_elem_nominal_masses[19] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:47: warning: Member aa_elem_probabilities[19] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:57: warning: Member aa_symbol_to_elem_counts[256 *6] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:44: warning: Member g_lfact_table (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:102: warning: Member sqrt_pi (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:149: warning: Member random_dev (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:53: warning: Member pi (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:54: warning: Member logpi (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:73: warning: Member random_gen (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:74: warning: Member stdunif (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:53: warning: The following parameters of IsoSpec::writeInitialConfiguration(const int atomCnt, const int isotopeNo, const double *lprobs, int *res) are not documented: parameter 'isotopeNo' parameter 'lprobs' parameter 'res' /build/isospec-2.2.1/IsoSpec++/allocator.h:42: warning: Member Allocator(const int dim, const int tabSize=10000) (function) of class IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/allocator.h:48: warning: Member shiftTables() (function) of class IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/allocator.h:50: warning: Member newConf() (function) of class IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/allocator.h:60: warning: Member makeCopy(const T *conf) (function) of class IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:59: warning: Member ConfEqual(int dim) (function) of class IsoSpec::ConfEqual is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:61: warning: Member operator()(const int *conf1, const int *conf2) const (function) of class IsoSpec::ConfEqual is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:79: warning: Member operator()(void *conf1, void *conf2) const (function) of class IsoSpec::ConfOrder is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:93: warning: Member ConfOrderMarginal(const double *logProbs, int dim) (function) of class IsoSpec::ConfOrderMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:95: warning: Member operator()(const Conf conf1, const Conf conf2) (function) of class IsoSpec::ConfOrderMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:108: warning: Member ConfOrderMarginalDescending(const double *logProbs, int dim) (function) of class IsoSpec::ConfOrderMarginalDescending is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:110: warning: Member operator()(const Conf conf1, const Conf conf2) (function) of class IsoSpec::ConfOrderMarginalDescending is not documented. /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:36: warning: Member DirtyAllocator(const int dim, const int tabSize=10000) (function) of class IsoSpec::DirtyAllocator is not documented. /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:42: warning: Member shiftTables() (function) of class IsoSpec::DirtyAllocator is not documented. /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:44: warning: Member newConf() (function) of class IsoSpec::DirtyAllocator is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:70: warning: Member FixedEnvelope(const FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:71: warning: Member FixedEnvelope(FixedEnvelope &&other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:73: warning: Member FixedEnvelope(double *masses, double *probs, size_t confs_no, bool masses_sorted=false, bool probs_sorted=false, double _total_prob=NAN) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:82: warning: Member operator+(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:83: warning: Member operator*(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:85: warning: Member confs_no() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:86: warning: Member getAllDim() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:88: warning: Member masses() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:89: warning: Member probs() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:90: warning: Member confs() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:92: warning: Member release_masses() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:93: warning: Member release_probs() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:94: warning: Member release_confs() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:95: warning: Member release_everything() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:98: warning: Member mass(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:99: warning: Member prob(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:100: warning: Member conf(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:102: warning: Member sort_by_mass() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:103: warning: Member sort_by_prob() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:105: warning: Member get_total_prob() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:106: warning: Member scale(double factor) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:107: warning: Member normalize() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:108: warning: Member shift_mass(double shift) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:109: warning: Member resample(size_t ionic_current, double beta_bias=1.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:111: warning: Member empiric_average_mass() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:112: warning: Member empiric_variance() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:113: warning: Member empiric_stddev() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:115: warning: Member WassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:116: warning: Member OrientedWassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:117: warning: Member AbyssalWassersteinDistance(FixedEnvelope &other, double abyss_depth, double other_scale=1.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:118: warning: Member WassersteinMatch(FixedEnvelope &other, double flow_distance, double other_scale=1.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:125: warning: Member bin(double bin_width=1.0, double middle=0.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:170: warning: Member threshold_init(Iso &&iso, double threshold, bool absolute) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:172: warning: Member addConfILG(const GenType &generator) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:181: warning: Member total_prob_init(Iso &&iso, double target_prob, bool trim) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:216: warning: Member stochastic_init(Iso &&iso, size_t _no_molecules, double _precision, double _beta_bias) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:121: warning: Member LinearCombination(const std::vector< const FixedEnvelope * > &spectra, const std::vector< double > &intensities) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:122: warning: Member LinearCombination(const FixedEnvelope *const *spectra, const double *intensities, size_t size) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:183: warning: Member FromThreshold(Iso &&iso, double threshold, bool absolute, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:194: warning: Member FromThreshold(const Iso &iso, double _threshold, bool _absolute, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:199: warning: Member FromTotalProb(Iso &&iso, double target_total_prob, bool optimize, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:211: warning: Member FromTotalProb(const Iso &iso, double _target_total_prob, bool _optimize, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:218: warning: Member FromStochastic(Iso &&iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:230: warning: Member FromStochastic(const Iso &iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:235: warning: Member Binned(Iso &&iso, double target_total_prob, double bin_width, double bin_middle=0.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:236: warning: Member Binned(const Iso &iso, double target_total_prob, double bin_width, double bin_middle=0.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:132: warning: Member store_conf(const T &generator) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:139: warning: Member store_conf(double _mass, double _prob) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:152: warning: Member swap(size_t idx1, size_t idx2, ISOSPEC_MAYBE_UNUSED int *conf_swapspace) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:166: warning: Member reallocate_memory(size_t new_size) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:167: warning: Member slow_reallocate_memory(size_t new_size) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:42: warning: Member _masses (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:43: warning: Member _probs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:44: warning: Member _confs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:45: warning: Member _confs_no (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:46: warning: Member allDim (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:47: warning: Member sorted_by_mass (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:48: warning: Member sorted_by_prob (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:49: warning: Member total_prob (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:50: warning: Member current_size (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:51: warning: Member tmasses (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:52: warning: Member tprobs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:53: warning: Member tconfs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:54: warning: Member allDimSizeofInt (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:241: warning: Member AbyssalWassersteinDistanceGrad(FixedEnvelope *const *envelopes, const double *scales, double *ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the) (friend) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:110: warning: Found unknown command '\use_nominal_masses' /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:111: warning: Found unknown command '\add_water' /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:106: warning: The following parameters of IsoSpec::Iso::FromFASTA(const char *fasta, bool use_nominal_masses=false, bool add_water=true) are not documented: parameter 'use_nominal_masses' parameter 'add_water' /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:483: warning: Member get_currentLThreshold() const (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:485: warning: Member IsoLayeredGenerator(Iso &&iso, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true, double t_prob_hint=0.99) (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:499: warning: Member advanceToNextConfigurationWithinLayer() (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:534: warning: Member nextLayer(double offset) (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:553: warning: Member IsoStochasticGenerator(Iso &&iso, size_t no_molecules, double precision=0.9999, double beta_bias=5.0) (function) of class IsoSpec::IsoStochasticGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:555: warning: Member count() const (function) of class IsoSpec::IsoStochasticGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:339: warning: argument 'tabSize' of command @param is not found in the argument list of IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator(Iso &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true) /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:339: warning: argument 'hashSize' of command @param is not found in the argument list of IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator(Iso &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true) /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:339: warning: The following parameters of IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator(Iso &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true) are not documented: parameter '_tabSize' parameter '_hashSize' parameter 'reorder_marginals' /build/isospec-2.2.1/IsoSpec++/operators.h:34: warning: Member KeyHasher(int dim) (function) of class IsoSpec::KeyHasher is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:36: warning: Member operator()(const int *conf) const noexcept (function) of class IsoSpec::KeyHasher is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:368: warning: The following parameter of IsoSpec::LayeredMarginal::LayeredMarginal(Marginal &&m, int tabSize=1000, int hashSize=1000) is not documented: parameter 'm' /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:378: warning: The following parameter of IsoSpec::LayeredMarginal::extend(double new_threshold, bool do_sort=true) is not documented: parameter 'do_sort' /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:59: warning: found documented return type for IsoSpec::Marginal::Marginal that does not return anything /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:233: warning: Member conf_lprobs() const (function) of class IsoSpec::MarginalTrek is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:234: warning: Member conf_masses() const (function) of class IsoSpec::MarginalTrek is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:235: warning: Member confs() const (function) of class IsoSpec::MarginalTrek is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:199: warning: The following parameter of IsoSpec::MarginalTrek::MarginalTrek(Marginal &&m, int tabSize=1000, int hashSize=1000) is not documented: parameter 'm' /build/isospec-2.2.1/IsoSpec++/operators.h:145: warning: Member OrderMarginalsBySizeDecresing(T const *const *const MT_) (function) of class IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:146: warning: Member operator()(int m1, int m2) (function) of class IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:254: warning: Member configurations (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:255: warning: Member confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:256: warning: Member no_confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:257: warning: Member masses (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:258: warning: Member lProbs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:259: warning: Member probs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:260: warning: Member allocator (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:264: warning: argument 'Marginal' of command @param is not found in the argument list of IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal(Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000) /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:264: warning: The following parameters of IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal(Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000) are not documented: parameter 'm' parameter 'tabSize' parameter 'hashSize' /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:264: warning: found documented return type for IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal that does not return anything /build/isospec-2.2.1/IsoSpec++/conf.h:30: warning: Member ProbAndConfPtr(double p, Conf c) (function) of struct IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:32: warning: Member operator<(const ProbAndConfPtr &other) const (function) of struct IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:27: warning: Member first (variable) of struct IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:28: warning: Member second (variable) of struct IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:121: warning: Member operator()(const T a, const T b) const (function) of class IsoSpec::ReverseOrder is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:35: warning: Member SSummator(const SSummator &other) (function) of class IsoSpec::SSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:39: warning: Member add(double x) (function) of class IsoSpec::SSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:61: warning: Member get() (function) of class IsoSpec::SSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:85: warning: Member add(double what) (function) of class IsoSpec::Summator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:93: warning: Member get() (function) of class IsoSpec::Summator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:128: warning: Member TableOrder(const T *_tbl) (function) of class IsoSpec::TableOrder is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:129: warning: Member operator()(unsigned int i, unsigned int j) (function) of class IsoSpec::TableOrder is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:107: warning: Member add(double what) (function) of class IsoSpec::TSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:111: warning: Member get() (function) of class IsoSpec::TSummator is not documented. soSpec++/pod_vector.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/python-build.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/summator.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/unity-build.cpp... Generating file documentation... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound pod_vector... Generating docs for compound unsafe_pod_vector... Generating docs for compound ws_match_res... Generating concept documentation... Generating namespace index... Generating docs for namespace IsoSpec Generating docs for compound IsoSpec::Allocator... Generating docs for compound IsoSpec::ConfEqual... Generating docs for compound IsoSpec::ConfOrder... Generating docs for compound IsoSpec::ConfOrderMarginal... Generating docs for compound IsoSpec::ConfOrderMarginalDescending... Generating docs for compound IsoSpec::DirtyAllocator... Generating docs for compound IsoSpec::FixedEnvelope... Generating docs for compound IsoSpec::Iso... Generating docs for compound IsoSpec::IsoGenerator... Generating docs for compound IsoSpec::IsoLayeredGenerator... Generating docs for compound IsoSpec::IsoOrderedGenerator... Generating docs for compound IsoSpec::IsoStochasticGenerator... Generating docs for compound IsoSpec::IsoThresholdGenerator... Generating docs for compound IsoSpec::KeyHasher... Generating docs for compound IsoSpec::LayeredMarginal... Generating docs for compound IsoSpec::Marginal... Generating docs for compound IsoSpec::MarginalTrek... Generating docs for compound IsoSpec::OrderMarginalsBySizeDecresing... Generating docs for compound IsoSpec::PrecalculatedMarginal... Generating docs for compound IsoSpec::ProbAndConfPtr... Generating docs for compound IsoSpec::ReverseOrder... Generating docs for compound IsoSpec::SSummator... Generating docs for compound IsoSpec::Summator... Generating docs for compound IsoSpec::TableOrder... Generating docs for compound IsoSpec::TSummator... Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... lookup cache used 1530/65536 hits=8386 misses=1622 finished... make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen [100%] Built target html_doc make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 0 make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen dh_auto_build -O--buildsyste=cmake -- pdf_doc cd obj-i686-linux-gnu && make -j15 "INSTALL=install --strip-program=true" pdf_doc VERBOSE=1 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 pdf_doc make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 1 make -f CMakeFiles/Makefile2 man/CMakeFiles/pdf_doc.dir/all make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make -f man/CMakeFiles/pdf_doc.dir/build.make man/CMakeFiles/pdf_doc.dir/depend make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/man /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/man /build/isospec-2.2.1/obj-i686-linux-gnu/man/CMakeFiles/pdf_doc.dir/DependInfo.cmake --color= make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f man/CMakeFiles/pdf_doc.dir/build.make man/CMakeFiles/pdf_doc.dir/build make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten [100%] Doxygen-based developer pdf documentation generation cd /build/isospec-2.2.1/man/latex && make make[6]: Verzeichnis „/build/isospec-2.2.1/man/latex“ wird betreten make[6]: Warnung: Kein Jobserver verfügbar: -j1 wird gesetzt. 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(./namespace_iso_spec.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) [9] [10] Overfull \hbox (152.89105pt too wide) in paragraph at lines 201--203 []\T1/phv/m/n/10 const dou-ble [] = 1.[]144729885849400174143427351353058711647 294812915311571513623071472137769884826079783623270275489708 (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [11] [12] [13] [14] [15] [16] [17] [18] [19] Package longtable Warning: Column widths have changed (longtable) in table 5.1 on input line 663. [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 871--872 \T1/pcr/m/n/8 ISOSPEC[]_[][]C[]_[][]API const size[]_[]t Iso[]Spec[]::isospec[] _[]number[]_[]of[]_[]isotopic[]_[]entries = ISOSPEC[]_[][]NUMBER[]_[][]OF[]_[][ ] Overfull \hbox (173.55629pt too wide) in paragraph at lines 881--882 \T1/pcr/m/n/8 const double Iso[]Spec[]::logpi = 1.[]144729885849400174143427351 353058711647294812915311571513623071472137769884826079783623270275489708 [23]) [24] Chapter 6. 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[57] Underfull \hbox (badness 10000) detected at line 176 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 181--182 []\T1/phv/m/n/10 Reimplemented in [], [], and []. ) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso_lay ered_generator.pdf> [58] [59] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) in paragraph at lines 99--100 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer [60] Underfull \hbox (badness 10000) in paragraph at lines 137--138 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) in paragraph at lines 158--159 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 164 [][][] [61] Underfull \hbox (badness 10000) in paragraph at lines 189--190 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex [62] <./class_iso_spec_1_1_is o_ordered_generator.pdf> [63] Underfull \hbox (badness 10000) detected at line 89 [][][] [64] Package longtable Warning: Column widths have changed (longtable) in table 6.4 on input line 114. ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [65] Underfull \hbox (badness 10000) in paragraph at lines 54--55 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Stochas tic[]Generator[]::advance[]To[]Next[]Configuration ( ) Underfull \hbox (badness 10000) detected at line 60 [][][] [66] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) in paragraph at lines 124--125 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) in paragraph at lines 145--146 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 151 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex [67] <./class_iso_spec_1_1_ iso_threshold_generator.pdf> [68] Package longtable Warning: Column widths have changed (longtable) in table 6.5 on input line 80. 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(./allocator_8cpp_source.tex) (./allocator_8h_source.tex [119]) (./btrd_8h_source.tex [120] [121] [122]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [123] [124] [125] [126] Overfull \hbox (44.55553pt too wide) in paragraph at lines 329--329 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinDistance(*[ ]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (78.1555pt too wide) in paragraph at lines 341--341 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->OrientedWassersteinDis tance(*[]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (69.75551pt too wide) in paragraph at lines 351--351 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->AbyssalWassersteinDist ance(*[]reinterpret_cast<[][]*[]>[](tabulator2), Overfull \hbox (27.75554pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinMatch(*[]re interpret_cast<[][]*[]>[](tabulator2), [127] Overfull \hbox (40.35553pt too wide) in paragraph at lines 374--374 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))+(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); Overfull \hbox (40.35553pt too wide) in paragraph at lines 380--380 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))*(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); [128]) (./cwrapper_8h_source.tex [129] [130]) (./dirty_allocator_8cpp_source.tex [131]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [167] [168] [169] [170]) (./fasta_8h_source.tex [171]) (./fixed_envelopes_8cpp_source.tex [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185]) (./fixed_envelopes_8h_source.tex [186] [187] [188]) (./iso_math_8cpp_source.tex [189] [190]) (./iso_math_8h_source.tex [191]) (./iso_spec_09_09_8cpp_source.tex [192] [193] [194] [195] [196] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [197] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200] [201] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [202]) (./iso_spec_09_09_8h_source.tex [203] [204] [205] [206] [207] [208]) (./marginal_trek_09_09_8cpp_source.tex [209] [210] [211] [212] [213] [214] [215] [216]) (./marginal_trek_09_09_8h_source.tex [217] [218] [219] [220]) (./misc_8cpp_source.tex [221]) (./misc_8h_source.tex [222] [223]) (./mman_8cpp_source.tex [224] [225]) (./mman_8h_source.tex [226]) (./operators_8cpp_source.tex [227]) (./operators_8h_source.tex [228] [229]) (./platform_8h_source.tex [230]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [231] [232] [233] [234] [235]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [236] [237]) (./unity-build_8cpp_source.tex) [238] No file refman.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. (./refman.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (240 pages, 914831 bytes). Transcript written on refman.log. makeindex refman.idx This is makeindex, version 2.16 [TeX Live 2022] (kpathsea + Thai support). Scanning input file refman.idx....done (815 entries accepted, 0 rejected). Sorting entries.........done (8587 comparisons). Generating output file refman.ind....done (1098 lines written, 0 warnings). Output written in refman.ind. 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(./namespaces.tex) [1] [2] Chapter 2. (./hierarchy.tex) [3] [4] Chapter 3. (./annotated.tex) [5] [6] Chapter 4. (./files.tex) [7] [8] Chapter 5. (./namespace_iso_spec.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) [9] [10] Overfull \hbox (152.89105pt too wide) in paragraph at lines 201--203 []\T1/phv/m/n/10 const dou-ble [] = 1.[]144729885849400174143427351353058711647 294812915311571513623071472137769884826079783623270275489708 [11] [12] [13] [14] [15] [16] [17] [18] [19] Package longtable Warning: Column widths have changed (longtable) in table 5.1 on input line 663. [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 871--872 \T1/pcr/m/n/8 ISOSPEC[]_[][]C[]_[][]API const size[]_[]t Iso[]Spec[]::isospec[] _[]number[]_[]of[]_[]isotopic[]_[]entries = ISOSPEC[]_[][]NUMBER[]_[][]OF[]_[][ ] Overfull \hbox (173.55629pt too wide) in paragraph at lines 881--882 \T1/pcr/m/n/8 const double Iso[]Spec[]::logpi = 1.[]144729885849400174143427351 353058711647294812915311571513623071472137769884826079783623270275489708 [23]) [24] Chapter 6. (./class_iso_spec_1_1_allocator.tex [25]) (./class_iso_spec_1_1_conf_equal.tex [26]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [27]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [28]) (./class_iso_spec_1_1_dirty_allocator.tex [29] [30]) (./class_iso_spec_1_1_fixed_envelope.tex [31] Underfull \hbox (badness 1072) in paragraph at lines 89--91 []\T1/phv/m/n/10 static [] [] ([] &&iso, dou-ble target[]_[]total[]_[]prob, boo l op-ti-mize, bool tget[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [45] [46] [47] [48] [49] [50] [51] [52] [53]) (./class_iso_spec_1_1_iso_generator.tex [54] <./ class_iso_spec_1_1_iso_generator.pdf> [55] Underfull \hbox (badness 10000) detected at line 103 [][][] [56] Underfull \hbox (badness 10000) detected at line 134 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 139--140 []\T1/phv/m/n/10 Reimplemented in [], [], and []. 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[57] Underfull \hbox (badness 10000) detected at line 176 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 181--182 []\T1/phv/m/n/10 Reimplemented in [], [], and []. ) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso_lay ered_generator.pdf> [58] [59] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) in paragraph at lines 99--100 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer [60] Underfull \hbox (badness 10000) in paragraph at lines 137--138 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) in paragraph at lines 158--159 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const 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124--125 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) in paragraph at lines 145--146 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 151 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex [67] <./class_iso_spec_1_1_ iso_threshold_generator.pdf> [68] Overfull \hbox (18.89209pt too wide) in paragraph at lines 102--103 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], [69] Underfull \hbox (badness 10000) detected at line 108 [][][] Underfull \hbox (badness 10000) in paragraph at lines 151--152 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres 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(./class_iso_spec_1_1_order_marginals_by_size_decresing.tex [87]) (./classpod__vector.tex [88] [89] [90] [91] [92] [93] [94] [95]) (./class_iso_spec_1_1_precalculated_marginal.tex [96] <./class_iso_spec_1_1_pre calculated_marginal.pdf> [97] Underfull \hbox (badness 10000) detected at line 100 [][][] [98] Underfull \hbox (badness 10000) detected at line 139 [][][] [99] Underfull \hbox (badness 10000) detected at line 161 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 200 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] [100] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] [101] [102]) (./struct_iso_spec_1_1_prob_and_conf_ptr.tex [103]) (./class_iso_spec_1_1_reverse_order.tex [104]) (./class_iso_spec_1_1_s_summator.tex [105]) (./class_iso_spec_1_1_summator.tex [106]) (./class_iso_spec_1_1_table_order.tex [107]) (./class_iso_spec_1_1_t_summator.tex [108]) (./classunsafe__pod__vector.tex [109] [110] [111] [112] [113] [114] [115] [116]) (./structws__match__res.tex [117]) [118] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [119]) (./btrd_8h_source.tex [120] [121] [122]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [123] [124] [125] [126] Overfull \hbox (44.55553pt too wide) in paragraph at lines 329--329 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinDistance(*[ ]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (78.1555pt too wide) in paragraph at lines 341--341 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->OrientedWassersteinDis tance(*[]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (69.75551pt too wide) in paragraph at lines 351--351 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->AbyssalWassersteinDist ance(*[]reinterpret_cast<[][]*[]>[](tabulator2), Overfull \hbox (27.75554pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinMatch(*[]re interpret_cast<[][]*[]>[](tabulator2), [127] Overfull \hbox (40.35553pt too wide) in paragraph at lines 374--374 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))+(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); Overfull \hbox (40.35553pt too wide) in paragraph at lines 380--380 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))*(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); [128]) (./cwrapper_8h_source.tex [129] [130]) (./dirty_allocator_8cpp_source.tex [131]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [167] [168] [169] [170]) (./fasta_8h_source.tex [171]) (./fixed_envelopes_8cpp_source.tex [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185]) (./fixed_envelopes_8h_source.tex [186] [187] [188]) (./iso_math_8cpp_source.tex [189] [190]) (./iso_math_8h_source.tex [191]) (./iso_spec_09_09_8cpp_source.tex [192] [193] [194] [195] [196] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [197] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200] [201] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [202]) (./iso_spec_09_09_8h_source.tex [203] [204] [205] [206] [207] [208]) (./marginal_trek_09_09_8cpp_source.tex [209] [210] [211] [212] [213] [214] [215] [216]) (./marginal_trek_09_09_8h_source.tex [217] [218] [219] [220]) (./misc_8cpp_source.tex [221]) (./misc_8h_source.tex [222] [223]) (./mman_8cpp_source.tex [224] [225]) (./mman_8h_source.tex [226]) (./operators_8cpp_source.tex [227]) (./operators_8h_source.tex [228] [229]) (./platform_8h_source.tex [230]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [231] [232] [233] [234] [235]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [236] [237]) (./unity-build_8cpp_source.tex) [238] (./refman.ind Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/element_tables.cpp, Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp, [239] [240] [241] [242] [243] [244] Underfull \hbox (badness 870) in paragraph at lines 818--820 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , Underfull \hbox (badness 870) in paragraph at lines 830--832 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , [245] [246] [247]) Package longtable Warning: Table widths have changed. Rerun LaTeX. (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (263 pages, 1023531 bytes). Transcript written on refman.log. latex_count=8 ; \ while egrep -s 'Rerun (LaTeX|to get cross-references right|to get bibliographical references right)' refman.log && [ $latex_count -gt 0 ] ;\ do \ echo "Rerunning latex...." ;\ pdflatex refman ;\ latex_count=`expr $latex_count - 1` ;\ done Package longtable Warning: Table widths have changed. Rerun LaTeX. Rerunning latex.... 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Check if current package is valid. ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty (/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty) (/usr/share/texlive/texmf-dist/tex/latex/caption/ltcaption.sty)) (/usr/share/texlive/texmf-dist/tex/latex/etoc/etoc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./refman.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (./refman.out) (./refman.out) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Chapter 1. (./namespaces.tex) [1] [2] Chapter 2. (./hierarchy.tex) [3] [4] Chapter 3. (./annotated.tex) [5] [6] Chapter 4. (./files.tex) [7] [8] Chapter 5. (./namespace_iso_spec.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) [9] [10] Overfull \hbox (152.89105pt too wide) in paragraph at lines 201--203 []\T1/phv/m/n/10 const dou-ble [] = 1.[]144729885849400174143427351353058711647 294812915311571513623071472137769884826079783623270275489708 [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 871--872 \T1/pcr/m/n/8 ISOSPEC[]_[][]C[]_[][]API const size[]_[]t Iso[]Spec[]::isospec[] _[]number[]_[]of[]_[]isotopic[]_[]entries = ISOSPEC[]_[][]NUMBER[]_[][]OF[]_[][ ] Overfull \hbox (173.55629pt too wide) in paragraph at lines 881--882 \T1/pcr/m/n/8 const double Iso[]Spec[]::logpi = 1.[]144729885849400174143427351 353058711647294812915311571513623071472137769884826079783623270275489708 [23]) [24] Chapter 6. (./class_iso_spec_1_1_allocator.tex [25]) (./class_iso_spec_1_1_conf_equal.tex [26]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [27]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [28]) (./class_iso_spec_1_1_dirty_allocator.tex [29] [30]) (./class_iso_spec_1_1_fixed_envelope.tex [31] Underfull \hbox (badness 1072) in paragraph at lines 89--91 []\T1/phv/m/n/10 static [] [] ([] &&iso, dou-ble target[]_[]total[]_[]prob, boo l op-ti-mize, bool tget[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [45] [46] [47] [48] [49] [50] [51] [52] [53]) (./class_iso_spec_1_1_iso_generator.tex [54] <./ class_iso_spec_1_1_iso_generator.pdf> [55] Underfull \hbox (badness 10000) detected at line 103 [][][] [56] Underfull \hbox (badness 10000) detected at line 134 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 139--140 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 155 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 160--161 []\T1/phv/m/n/10 Reimplemented in [], [], and []. [57] Underfull \hbox (badness 10000) detected at line 176 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 181--182 []\T1/phv/m/n/10 Reimplemented in [], [], and []. ) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso_lay ered_generator.pdf> [58] [59] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) in paragraph at lines 99--100 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer [60] Underfull \hbox (badness 10000) in paragraph at lines 137--138 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) in paragraph at lines 158--159 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 164 [][][] [61] Underfull \hbox (badness 10000) in paragraph at lines 189--190 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex [62] <./class_iso_spec_1_1_is o_ordered_generator.pdf> [63] Underfull \hbox (badness 10000) detected at line 89 [][][] [64]) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_ iso_stochastic_generator.pdf> [65] Underfull \hbox (badness 10000) in paragraph at lines 54--55 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Stochas tic[]Generator[]::advance[]To[]Next[]Configuration ( ) Underfull \hbox (badness 10000) detected at line 60 [][][] [66] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) in paragraph at lines 124--125 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) in paragraph at lines 145--146 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 151 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex [67] <./class_iso_spec_1_1_ iso_threshold_generator.pdf> [68] Overfull \hbox (18.89209pt too wide) in paragraph at lines 102--103 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], [69] Underfull \hbox (badness 10000) detected at line 108 [][][] Underfull \hbox (badness 10000) in paragraph at lines 151--152 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) in paragraph at lines 172--173 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) in paragraph at lines 193--194 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 199 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex [72]) (./class_iso_spec_1_1_layered_marginal.tex <./class_iso_spec_1_1_layered_margin al.pdf> [73] [74] Underfull \hbox (badness 10000) detected at line 101 [][][] [75] Underfull \hbox (badness 10000) detected at line 230 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [76] [77] Overfull \vbox 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(./class_iso_spec_1_1_order_marginals_by_size_decresing.tex [87]) (./classpod__vector.tex [88] [89] [90] [91] [92] [93] [94] [95]) (./class_iso_spec_1_1_precalculated_marginal.tex [96] <./class_iso_spec_1_1_pre calculated_marginal.pdf> [97] Underfull \hbox (badness 10000) detected at line 100 [][][] [98] Underfull \hbox (badness 10000) detected at line 139 [][][] [99] Underfull \hbox (badness 10000) detected at line 161 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 200 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] [100] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] [101] [102]) (./struct_iso_spec_1_1_prob_and_conf_ptr.tex [103]) (./class_iso_spec_1_1_reverse_order.tex [104]) (./class_iso_spec_1_1_s_summator.tex [105]) (./class_iso_spec_1_1_summator.tex [106]) (./class_iso_spec_1_1_table_order.tex [107]) (./class_iso_spec_1_1_t_summator.tex [108]) (./classunsafe__pod__vector.tex [109] [110] [111] [112] [113] [114] [115] [116]) (./structws__match__res.tex [117]) [118] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [119]) (./btrd_8h_source.tex [120] [121] [122]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [123] [124] [125] [126] Overfull \hbox (44.55553pt too wide) in paragraph at lines 329--329 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinDistance(*[ ]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (78.1555pt too wide) in paragraph at lines 341--341 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->OrientedWassersteinDis tance(*[]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (69.75551pt too wide) in paragraph at lines 351--351 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->AbyssalWassersteinDist ance(*[]reinterpret_cast<[][]*[]>[](tabulator2), Overfull \hbox (27.75554pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinMatch(*[]re interpret_cast<[][]*[]>[](tabulator2), [127] Overfull \hbox (40.35553pt too wide) in paragraph at lines 374--374 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))+(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); Overfull \hbox (40.35553pt too wide) in paragraph at lines 380--380 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))*(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); [128]) (./cwrapper_8h_source.tex [129] [130]) (./dirty_allocator_8cpp_source.tex [131]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [167] [168] [169] [170]) (./fasta_8h_source.tex [171]) (./fixed_envelopes_8cpp_source.tex [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185]) (./fixed_envelopes_8h_source.tex [186] [187] [188]) (./iso_math_8cpp_source.tex [189] [190]) (./iso_math_8h_source.tex [191]) (./iso_spec_09_09_8cpp_source.tex [192] [193] [194] [195] [196] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [197] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200] [201] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [202]) (./iso_spec_09_09_8h_source.tex [203] [204] [205] [206] [207] [208]) (./marginal_trek_09_09_8cpp_source.tex [209] [210] [211] [212] [213] [214] [215] [216]) (./marginal_trek_09_09_8h_source.tex [217] [218] [219] [220]) (./misc_8cpp_source.tex [221]) (./misc_8h_source.tex [222] [223]) (./mman_8cpp_source.tex [224] [225]) (./mman_8h_source.tex [226]) (./operators_8cpp_source.tex [227]) (./operators_8h_source.tex [228] [229]) (./platform_8h_source.tex [230]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [231] [232] [233] [234] [235]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [236] [237]) (./unity-build_8cpp_source.tex) [238] (./refman.ind Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/element_tables.cpp, Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp, [239] [240] [241] [242] [243] [244] Underfull \hbox (badness 870) in paragraph at lines 818--820 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , Underfull \hbox (badness 870) in paragraph at lines 830--832 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , [245] [246] [247]) (./refman.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (263 pages, 1023315 bytes). 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(./namespaces.tex) [1] [2] Chapter 2. (./hierarchy.tex) [3] [4] Chapter 3. (./annotated.tex) [5] [6] Chapter 4. (./files.tex) [7] [8] Chapter 5. (./namespace_iso_spec.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) [9] [10] Overfull \hbox (152.89105pt too wide) in paragraph at lines 201--203 []\T1/phv/m/n/10 const dou-ble [] = 1.[]144729885849400174143427351353058711647 294812915311571513623071472137769884826079783623270275489708 [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 871--872 \T1/pcr/m/n/8 ISOSPEC[]_[][]C[]_[][]API const size[]_[]t Iso[]Spec[]::isospec[] _[]number[]_[]of[]_[]isotopic[]_[]entries = ISOSPEC[]_[][]NUMBER[]_[][]OF[]_[][ ] Overfull \hbox (173.55629pt too wide) in paragraph at lines 881--882 \T1/pcr/m/n/8 const double Iso[]Spec[]::logpi = 1.[]144729885849400174143427351 353058711647294812915311571513623071472137769884826079783623270275489708 [23]) [24] Chapter 6. (./class_iso_spec_1_1_allocator.tex [25]) (./class_iso_spec_1_1_conf_equal.tex [26]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [27]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [28]) (./class_iso_spec_1_1_dirty_allocator.tex [29] [30]) (./class_iso_spec_1_1_fixed_envelope.tex [31] Underfull \hbox (badness 1072) in paragraph at lines 89--91 []\T1/phv/m/n/10 static [] [] ([] &&iso, dou-ble target[]_[]total[]_[]prob, boo l op-ti-mize, bool tget[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [45] [46] [47] [48] [49] [50] [51] [52] [53]) (./class_iso_spec_1_1_iso_generator.tex [54] <./ class_iso_spec_1_1_iso_generator.pdf> [55] Underfull \hbox (badness 10000) detected at line 103 [][][] [56] Underfull \hbox (badness 10000) detected at line 134 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 139--140 []\T1/phv/m/n/10 Reimplemented in [], [], and []. 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[57] Underfull \hbox (badness 10000) detected at line 176 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 181--182 []\T1/phv/m/n/10 Reimplemented in [], [], and []. ) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso_lay ered_generator.pdf> [58] [59] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) in paragraph at lines 99--100 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer [60] Underfull \hbox (badness 10000) in paragraph at lines 137--138 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) in paragraph at lines 158--159 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 164 [][][] [61] Underfull \hbox (badness 10000) in paragraph at lines 189--190 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex [62] <./class_iso_spec_1_1_is o_ordered_generator.pdf> [63] Underfull \hbox (badness 10000) detected at line 89 [][][] [64]) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_ iso_stochastic_generator.pdf> [65] Underfull \hbox (badness 10000) in paragraph at lines 54--55 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Stochas tic[]Generator[]::advance[]To[]Next[]Configuration ( ) Underfull \hbox (badness 10000) detected at line 60 [][][] [66] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) in paragraph at lines 124--125 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) in paragraph at lines 145--146 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 151 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex [67] <./class_iso_spec_1_1_ iso_threshold_generator.pdf> [68] Overfull \hbox (18.89209pt too wide) in paragraph at lines 102--103 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], [69] Underfull \hbox (badness 10000) detected at line 108 [][][] Underfull \hbox (badness 10000) in paragraph at lines 151--152 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) in paragraph at lines 172--173 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) in paragraph at lines 193--194 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 199 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex [72]) (./class_iso_spec_1_1_layered_marginal.tex <./class_iso_spec_1_1_layered_margin al.pdf> [73] [74] Underfull \hbox (badness 10000) detected at line 101 [][][] [75] Underfull \hbox (badness 10000) detected at line 230 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [76] [77] Overfull \vbox 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(./class_iso_spec_1_1_order_marginals_by_size_decresing.tex [87]) (./classpod__vector.tex [88] [89] [90] [91] [92] [93] [94] [95]) (./class_iso_spec_1_1_precalculated_marginal.tex [96] <./class_iso_spec_1_1_pre calculated_marginal.pdf> [97] Underfull \hbox (badness 10000) detected at line 100 [][][] [98] Underfull \hbox (badness 10000) detected at line 139 [][][] [99] Underfull \hbox (badness 10000) detected at line 161 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 200 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] [100] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] [101] [102]) (./struct_iso_spec_1_1_prob_and_conf_ptr.tex [103]) (./class_iso_spec_1_1_reverse_order.tex [104]) (./class_iso_spec_1_1_s_summator.tex [105]) (./class_iso_spec_1_1_summator.tex [106]) (./class_iso_spec_1_1_table_order.tex [107]) (./class_iso_spec_1_1_t_summator.tex [108]) (./classunsafe__pod__vector.tex [109] [110] [111] [112] [113] [114] [115] [116]) (./structws__match__res.tex [117]) [118] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [119]) (./btrd_8h_source.tex [120] [121] [122]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [123] [124] [125] [126] Overfull \hbox (44.55553pt too wide) in paragraph at lines 329--329 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinDistance(*[ ]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (78.1555pt too wide) in paragraph at lines 341--341 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->OrientedWassersteinDis tance(*[]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (69.75551pt too wide) in paragraph at lines 351--351 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->AbyssalWassersteinDist ance(*[]reinterpret_cast<[][]*[]>[](tabulator2), Overfull \hbox (27.75554pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinMatch(*[]re interpret_cast<[][]*[]>[](tabulator2), [127] Overfull \hbox (40.35553pt too wide) in paragraph at lines 374--374 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))+(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); Overfull \hbox (40.35553pt too wide) in paragraph at lines 380--380 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))*(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); [128]) (./cwrapper_8h_source.tex [129] [130]) (./dirty_allocator_8cpp_source.tex [131]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [167] [168] [169] [170]) (./fasta_8h_source.tex [171]) (./fixed_envelopes_8cpp_source.tex [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185]) (./fixed_envelopes_8h_source.tex [186] [187] [188]) (./iso_math_8cpp_source.tex [189] [190]) (./iso_math_8h_source.tex [191]) (./iso_spec_09_09_8cpp_source.tex [192] [193] [194] [195] [196] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [197] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200] [201] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [202]) (./iso_spec_09_09_8h_source.tex [203] [204] [205] [206] [207] [208]) (./marginal_trek_09_09_8cpp_source.tex [209] [210] [211] [212] [213] [214] [215] [216]) (./marginal_trek_09_09_8h_source.tex [217] [218] [219] [220]) (./misc_8cpp_source.tex [221]) (./misc_8h_source.tex [222] [223]) (./mman_8cpp_source.tex [224] [225]) (./mman_8h_source.tex [226]) (./operators_8cpp_source.tex [227]) (./operators_8h_source.tex [228] [229]) (./platform_8h_source.tex [230]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [231] [232] [233] [234] [235]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [236] [237]) (./unity-build_8cpp_source.tex) [238] (./refman.ind Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/element_tables.cpp, Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp, [239] [240] [241] [242] [243] [244] Underfull \hbox (badness 870) in paragraph at lines 818--820 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , Underfull \hbox (badness 870) in paragraph at lines 830--832 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , [245] [246] [247]) (./refman.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (263 pages, 1023315 bytes). Transcript written on refman.log. make[6]: Verzeichnis „/build/isospec-2.2.1/man/latex“ wird verlassen make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen [100%] Built target pdf_doc make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 0 make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen # sed-based replacement of the cloudflare URL with the MathJax.js file from the # libjs-mathjax package sh debian/replace-mathjax-cloudflare-url-local-file.sh # Recreate the symlink that was created by setup.py # and that we had to remove at the override_dh_clean target. ln -sf IsoSpec++ IsoSpecPy/IsoSpec++ make[1]: Verzeichnis „/build/isospec-2.2.1“ wird verlassen dh_auto_test rm -fr -- /tmp/dh-xdg-rundir-ksbE_PzR create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dpkg-query: no packages found matching r-base-dev dpkg-query: no packages found matching r-base-core dh binary --with python3 dh_testroot dh_prep rm -f -- debian/libisospec\+\+-dev.substvars debian/libisospec\+\+2.substvars debian/python3-isospec.substvars debian/libisospec\+\+-doc.substvars rm -fr -- debian/.debhelper/generated/libisospec\+\+-dev/ debian/libisospec\+\+-dev/ debian/tmp/ debian/.debhelper/generated/libisospec\+\+2/ debian/libisospec\+\+2/ debian/.debhelper/generated/python3-isospec/ debian/python3-isospec/ debian/.debhelper/generated/libisospec\+\+-doc/ debian/libisospec\+\+-doc/ rm -f debian/libisospec\+\+-dev.debhelper.log debian/libisospec\+\+-doc.debhelper.log debian/libisospec\+\+2.debhelper.log debian/python3-isospec.debhelper.log debian/rules override_dh_auto_install make[1]: Verzeichnis „/build/isospec-2.2.1“ wird betreten dpkg-query: Kein Paket gefunden, das auf r-base-dev passt dpkg-query: Kein Paket gefunden, das auf r-base-core passt dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=. pybuild --configure -i python{version} -p 3.11 I: pybuild base:240: python3.11 setup.py config running config dh_auto_build -O--buildsystem=cmake -O--system=distutils --sourcedirectory=. cd obj-i686-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles /build/isospec-2.2.1/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/depend make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/depend make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake --color= make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/DependInfo.cmake --color= Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o.d" is newer than depends file "/build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/compiler_depend.internal". Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o.d" is newer than depends file "/build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target IsoSpec++-static Consolidate compiler generated dependencies of target IsoSpec++-shared make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make[4]: Für das Ziel „IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build“ ist nichts zu tun. make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make[4]: Für das Ziel „IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build“ ist nichts zu tun. make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen [ 50%] Built target IsoSpec++-shared [100%] Built target IsoSpec++-static make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 .. Configuring build for project IsoSpec -- CMAKE_CXX_COMPILER: /usr/bin/c++ -- Setting definition -Wno-unknown-pragmas. -- Setting definition -Wall. -- Setting definition -Wextra. -- Setting definition -pedantic. -- CMAKE_SOURCE_DIR: /build/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/isospec-2.2.1/obj-i686-linux-gnu UNIX non APPLE environment ~~~~~~ Instructions ~~~~~~ On UNIX/GNU-Linux, please run the configuration like this: cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE= -DCMAKE_INSTALL_PREFIX= ../development -- Starting configuration for the doc material for IsoSpec  gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. -- Finished configuration of the doc material. -- Starting configuration for the example material for IsoSpec  -- Finished configuration for the example material. The build toolchain is: Linux  -- CMAKE_BUILD_TYPE: None. -- CMAKE_INSTALL_PREFIX: /usr. "Now configuring IsoSpec++/ for IsoSpec" -- Configuring done -- Generating done -- Build files have been written to: /build/isospec-2.2.1/obj-i686-linux-gnu dh_auto_build -O--buildsystem=cmake cd obj-i686-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles /build/isospec-2.2.1/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/depend make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/depend make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake --color= make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++ /build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/DependInfo.cmake --color= Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o.d" is newer than depends file "/build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/compiler_depend.internal". Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o.d" is newer than depends file "/build/isospec-2.2.1/obj-i686-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target IsoSpec++-shared make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen Consolidate compiler generated dependencies of target IsoSpec++-static make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make[4]: Für das Ziel „IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build“ ist nichts zu tun. make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make[4]: Für das Ziel „IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build“ ist nichts zu tun. make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen [ 50%] Built target IsoSpec++-shared [100%] Built target IsoSpec++-static make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 .. Configuring build for project IsoSpec -- CMAKE_CXX_COMPILER: /usr/bin/c++ -- Setting definition -Wno-unknown-pragmas. -- Setting definition -Wall. -- Setting definition -Wextra. -- Setting definition -pedantic. -- CMAKE_SOURCE_DIR: /build/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/isospec-2.2.1/obj-i686-linux-gnu UNIX non APPLE environment ~~~~~~ Instructions ~~~~~~ On UNIX/GNU-Linux, please run the configuration like this: cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE= -DCMAKE_INSTALL_PREFIX= ../development -- Starting configuration for the doc material for IsoSpec  gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb) [Datei oder Verzeichnis nicht gefunden]. -- Finished configuration of the doc material. -- Starting configuration for the example material for IsoSpec  -- Finished configuration for the example material. The build toolchain is: Linux  -- CMAKE_BUILD_TYPE: None. -- CMAKE_INSTALL_PREFIX: /usr. "Now configuring IsoSpec++/ for IsoSpec" -- Configuring done -- Generating done -- Build files have been written to: /build/isospec-2.2.1/obj-i686-linux-gnu # Generate the dev-doc in the man/hml and man/latex directories #doxygen man/doxyfile dh_auto_build -O--buildsyste=cmake -- html_doc cd obj-i686-linux-gnu && make -j15 "INSTALL=install --strip-program=true" html_doc VERBOSE=1 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 html_doc make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 1 make -f CMakeFiles/Makefile2 man/CMakeFiles/html_doc.dir/all make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/depend make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/man /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/man /build/isospec-2.2.1/obj-i686-linux-gnu/man/CMakeFiles/html_doc.dir/DependInfo.cmake --color= make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/build make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten [100%] Doxygen-based developer html documentation generation cd /build/isospec-2.2.1/man && doxygen doxyfile warning: Tag 'TCL_SUBST' at line 248 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: ignoring unsupported tag 'CLANG_COMPILATION_DATABASE_PATH' at line 1102, file doxyfile warning: Tag 'COLS_IN_ALPHA_INDEX' at line 1120 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1833 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'RTF_SOURCE_CODE' at line 1915 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOCBOOK_PROGRAMLISTING' at line 2013 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 2193 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 2206 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 2215 of file 'doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" Doxygen version used: 1.9.4 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/isospec-2.2.1/IsoSpec++ Reading and parsing tag files Parsing files Preprocessing /build/isospec-2.2.1/IsoSpec++/allocator.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/allocator.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/allocator.h... Parsing file /build/isospec-2.2.1/IsoSpec++/allocator.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/btrd.h... Parsing file /build/isospec-2.2.1/IsoSpec++/btrd.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/conf.h... Parsing file /build/isospec-2.2.1/IsoSpec++/conf.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/cwrapper.h... Parsing file /build/isospec-2.2.1/IsoSpec++/cwrapper.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Parsing file /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/element_tables.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/element_tables.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/element_tables.h... Parsing file /build/isospec-2.2.1/IsoSpec++/element_tables.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/fasta.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/fasta.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/fasta.h... Parsing file /build/isospec-2.2.1/IsoSpec++/fasta.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Parsing file /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/isoMath.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/isoMath.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/isoMath.h... Parsing file /build/isospec-2.2.1/IsoSpec++/isoMath.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/isoSpec++.h... Parsing file /build/isospec-2.2.1/IsoSpec++/isoSpec++.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Parsing file /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/misc.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/misc.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/misc.h... Parsing file /build/isospec-2.2.1/IsoSpec++/misc.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/mman.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/mman.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/mman.h... Parsing file /build/isospec-2.2.1/IsoSpec++/mman.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/operators.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/operators.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/operators.h... Parsing file /build/isospec-2.2.1/IsoSpec++/operators.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/platform.h... Parsing file /build/isospec-2.2.1/IsoSpec++/platform.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/platform_incl.h... Parsing file /build/isospec-2.2.1/IsoSpec++/platform_incl.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/pod_vector.h... Parsing file /build/isospec-2.2.1/IsoSpec++/pod_vector.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/python-build.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/python-build.cpp... Preprocessing /build/isospec-2.2.1/IsoSpec++/summator.h... Parsing file /build/isospec-2.2.1/I/build/isospec-2.2.1/IsoSpec++/allocator.h:33: warning: Compound IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:53: warning: Compound IsoSpec::ConfEqual is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:75: warning: Compound IsoSpec::ConfOrder is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:87: warning: Compound IsoSpec::ConfOrderMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:102: warning: Compound IsoSpec::ConfOrderMarginalDescending is not documented. /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:25: warning: Compound IsoSpec::DirtyAllocator is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:40: warning: Compound IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:439: warning: Compound IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:542: warning: Compound IsoSpec::IsoStochasticGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:28: warning: Compound IsoSpec::KeyHasher is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:141: warning: Compound IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:24: warning: Compound IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:117: warning: Compound IsoSpec::ReverseOrder is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:26: warning: Compound IsoSpec::SSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:76: warning: Compound IsoSpec::Summator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:99: warning: Compound IsoSpec::TSummator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:124: warning: Compound IsoSpec::TableOrder is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:32: warning: Compound pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/cwrapper.h:146: warning: Compound ws_match_res is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command soSpec++/summator.h... Preprocessing /build/isospec-2.2.1/IsoSpec++/unity-build.cpp... Parsing file /build/isospec-2.2.1/IsoSpec++/unity-build.cpp... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file /build/isospec-2.2.1/IsoSpec++/allocator.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/allocator.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/btrd.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/conf.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/cwrapper.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/element_tables.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/element_tables.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/fasta.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/fasta.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/isoMath.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/isoMath.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/isoSpec++.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/misc.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/misc.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/mman.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/mman.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/operators.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/operators.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/platform.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/platform_incl.h... Generating code for file /build/isospec-2.2.1/I/build/isospec-2.2.1/IsoSpec++/pod_vector.h:194: warning: Member iterator (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:195: warning: Member const_iterator (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:196: warning: Member value_type (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:197: warning: Member size_type (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:198: warning: Member reference (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:199: warning: Member const_reference (typedef) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:39: warning: Member pod_vector(size_t initial_size=16) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:54: warning: Member operator=(pod_vector< T > &&other) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:64: warning: Member pod_vector(pod_vector< T > &&other) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:74: warning: Member pod_vector(unsafe_pod_vector< T > &&other) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:82: warning: Member fast_reserve(size_t n) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:94: warning: Member reserve(size_t n) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:100: warning: Member resize(size_t new_size) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:114: warning: Member resize_and_wipe(size_t new_size) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:122: warning: Member nocheck_push_back(const T &val) noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:129: warning: Member push_back(const T &val) (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:137: warning: Member operator[](size_t n) noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:143: warning: Member operator[](size_t n) const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:149: warning: Member size() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:154: warning: Member capacity() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:159: warning: Member data() noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:164: warning: Member data() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:169: warning: Member empty() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:174: warning: Member back() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:180: warning: Member pop_back() noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:187: warning: Member swap(pod_vector< T > &other) noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:201: warning: Member begin() noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:202: warning: Member begin() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:203: warning: Member cbegin() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:204: warning: Member end() noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:205: warning: Member end() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:206: warning: Member cend() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:208: warning: Member front() const noexcept (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:214: warning: Member clear() (function) of class pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:372: warning: Member iterator (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:373: warning: Member const_iterator (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:374: warning: Member value_type (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:375: warning: Member size_type (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:376: warning: Member reference (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:377: warning: Member const_reference (typedef) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:234: warning: Member init() (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:242: warning: Member init(size_t initial_size) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:261: warning: Member fast_reserve(size_t n) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:272: warning: Member reserve(size_t n) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:278: warning: Member resize(size_t new_size) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:292: warning: Member resize_and_wipe(size_t new_size) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:300: warning: Member nocheck_push_back(const T &val) noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:307: warning: Member push_back(const T &val) (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:315: warning: Member operator[](size_t n) noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:321: warning: Member operator[](size_t n) const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:327: warning: Member size() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:332: warning: Member capacity() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:337: warning: Member data() noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:342: warning: Member data() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:347: warning: Member empty() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:352: warning: Member back() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:358: warning: Member pop_back() noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:365: warning: Member swap(pod_vector< T > &other) noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:379: warning: Member begin() noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:380: warning: Member begin() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:381: warning: Member cbegin() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:382: warning: Member end() noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:383: warning: Member end() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:384: warning: Member cend() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:386: warning: Member front() const noexcept (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/pod_vector.h:392: warning: Member clear() (function) of class unsafe_pod_vector is not documented. /build/isospec-2.2.1/IsoSpec++/cwrapper.h:147: warning: Member res1 (variable) of struct ws_match_res is not documented. /build/isospec-2.2.1/IsoSpec++/cwrapper.h:148: warning: Member res2 (variable) of struct ws_match_res is not documented. /build/isospec-2.2.1/IsoSpec++/cwrapper.h:149: warning: Member flow (variable) of struct ws_match_res is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:27: warning: Member RealType (typedef) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:28: warning: Member IntType (typedef) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:22: warning: Member Conf (typedef) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/allocator.h:26: warning: Member copyConf(const T *source, T *destination, int dim) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:77: warning: Member btrd(IntType _t, RealType p, IntType m, std::mt19937 &urng=random_gen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:160: warning: Member invert(IntType t, RealType p, std::mt19937 &urng=random_gen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/btrd.h:189: warning: Member boost_binomial_distribution_variate(IntType t_arg, RealType p_arg, std::mt19937 &urng=random_gen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.h:33: warning: Member parse_fasta(const char *fasta, int atomCounts[6]) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp:134: warning: Member reorder_array(T *arr, size_t *order, size_t size, bool can_destroy=false) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:37: warning: Member AbyssalWassersteinDistanceGrad(FixedEnvelope *const *envelopes, const double *scales, double *ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:23: warning: Member release_g_lfact_table() (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:32: warning: Member alloc_lfact_table() (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:47: warning: Member RationalApproximation(double t) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:57: warning: Member NormalCDFInverse(double p) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:65: warning: Member NormalCDFInverse(double p, double mean, double stdev) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:70: warning: Member NormalCDF(double x, double mean, double stdev) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:95: warning: Member NormalPDF(double x, double mean, double stdev) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:104: warning: Member LowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:131: warning: Member InverseLowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:150: warning: Member random_gen(random_dev()) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:151: warning: Member stdunif(0.0, 1.0) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:153: warning: Member rdvariate_binom(size_t tries, double succ_prob, std::mt19937 &rgen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:68: warning: Member InverseChiSquareCDF2(int k, double x) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:76: warning: Member rdvariate_beta_1_b(double b, std::mt19937 &rgen=random_gen) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.cpp:355: warning: Member parse_formula(const char *formula, std::vector< double > &isotope_masses, std::vector< double > &isotope_probabilities, int **isotopeNumbers, int **atomCounts, unsigned int *confSize, bool use_nominal_masses) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:149: warning: Member get_loggamma_nominator(int x) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:156: warning: Member verify_atom_cnt(int atomCnt) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.cpp:28: warning: Member quickselect(void **array, int n, int start, int end) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:29: warning: Member combinedSum(const int *conf, const std::vector< double > **valuesContainer, int dimNumber) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:38: warning: Member combinedSum(const int *conf, const pod_vector< double > **valuesContainer, int dimNumber) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:47: warning: Member getConf(void *conf) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:54: warning: Member getLProb(void *conf) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:61: warning: Member unnormalized_logProb(const int *conf, const double *logProbs, int dim) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:71: warning: Member calc_mass(const int *conf, const double *masses, int dim) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:85: warning: Member printArray(const T *array, int size, const char *prefix="") (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:94: warning: Member printVector(const std::vector< T > &vec) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:99: warning: Member printOffsets(const T **array, int size, const T *offset, const char *prefix="") (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:108: warning: Member printNestedArray(const T **array, const int *shape, int size) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:133: warning: Member dealloc_table(T *tbl, int dim) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:142: warning: Member realloc_append(T **array, T what, size_t old_array_size) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:151: warning: Member get_order(T *order_array, size_t N) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:162: warning: Member get_inverse_order(T *order_array, size_t N) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/misc.h:173: warning: Member impose_order(size_t *O, size_t N, TA *A, TB *B) (function) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:26: warning: Member isospec_number_of_isotopic_entries (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:28: warning: Member elem_table_ID[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:325: warning: Member elem_table_atomicNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:621: warning: Member elem_table_mass[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:917: warning: Member elem_table_massNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:1213: warning: Member elem_table_extraNeutrons[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:1509: warning: Member elem_table_element[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:1805: warning: Member elem_table_symbol[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:2101: warning: Member elem_table_Radioactive[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:2397: warning: Member elem_table_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/element_tables.cpp:2693: warning: Member elem_table_log_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:25: warning: Member aa_isotope_numbers[6] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:27: warning: Member aa_elem_masses[19] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:37: warning: Member aa_elem_nominal_masses[19] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:47: warning: Member aa_elem_probabilities[19] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/fasta.cpp:57: warning: Member aa_symbol_to_elem_counts[256 *6] (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:44: warning: Member g_lfact_table (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:102: warning: Member sqrt_pi (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.cpp:149: warning: Member random_dev (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:53: warning: Member pi (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:54: warning: Member logpi (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:73: warning: Member random_gen (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/isoMath.h:74: warning: Member stdunif (variable) of namespace IsoSpec is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:53: warning: The following parameters of IsoSpec::writeInitialConfiguration(const int atomCnt, const int isotopeNo, const double *lprobs, int *res) are not documented: parameter 'isotopeNo' parameter 'lprobs' parameter 'res' /build/isospec-2.2.1/IsoSpec++/allocator.h:42: warning: Member Allocator(const int dim, const int tabSize=10000) (function) of class IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/allocator.h:48: warning: Member shiftTables() (function) of class IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/allocator.h:50: warning: Member newConf() (function) of class IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/allocator.h:60: warning: Member makeCopy(const T *conf) (function) of class IsoSpec::Allocator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:59: warning: Member ConfEqual(int dim) (function) of class IsoSpec::ConfEqual is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:61: warning: Member operator()(const int *conf1, const int *conf2) const (function) of class IsoSpec::ConfEqual is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:79: warning: Member operator()(void *conf1, void *conf2) const (function) of class IsoSpec::ConfOrder is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:93: warning: Member ConfOrderMarginal(const double *logProbs, int dim) (function) of class IsoSpec::ConfOrderMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:95: warning: Member operator()(const Conf conf1, const Conf conf2) (function) of class IsoSpec::ConfOrderMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:108: warning: Member ConfOrderMarginalDescending(const double *logProbs, int dim) (function) of class IsoSpec::ConfOrderMarginalDescending is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:110: warning: Member operator()(const Conf conf1, const Conf conf2) (function) of class IsoSpec::ConfOrderMarginalDescending is not documented. /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:36: warning: Member DirtyAllocator(const int dim, const int tabSize=10000) (function) of class IsoSpec::DirtyAllocator is not documented. /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:42: warning: Member shiftTables() (function) of class IsoSpec::DirtyAllocator is not documented. /build/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:44: warning: Member newConf() (function) of class IsoSpec::DirtyAllocator is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:70: warning: Member FixedEnvelope(const FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:71: warning: Member FixedEnvelope(FixedEnvelope &&other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:73: warning: Member FixedEnvelope(double *masses, double *probs, size_t confs_no, bool masses_sorted=false, bool probs_sorted=false, double _total_prob=NAN) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:82: warning: Member operator+(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:83: warning: Member operator*(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:85: warning: Member confs_no() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:86: warning: Member getAllDim() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:88: warning: Member masses() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:89: warning: Member probs() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:90: warning: Member confs() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:92: warning: Member release_masses() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:93: warning: Member release_probs() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:94: warning: Member release_confs() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:95: warning: Member release_everything() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:98: warning: Member mass(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:99: warning: Member prob(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:100: warning: Member conf(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:102: warning: Member sort_by_mass() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:103: warning: Member sort_by_prob() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:105: warning: Member get_total_prob() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:106: warning: Member scale(double factor) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:107: warning: Member normalize() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:108: warning: Member shift_mass(double shift) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:109: warning: Member resample(size_t ionic_current, double beta_bias=1.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:111: warning: Member empiric_average_mass() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:112: warning: Member empiric_variance() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:113: warning: Member empiric_stddev() (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:115: warning: Member WassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:116: warning: Member OrientedWassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:117: warning: Member AbyssalWassersteinDistance(FixedEnvelope &other, double abyss_depth, double other_scale=1.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:118: warning: Member WassersteinMatch(FixedEnvelope &other, double flow_distance, double other_scale=1.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:125: warning: Member bin(double bin_width=1.0, double middle=0.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:170: warning: Member threshold_init(Iso &&iso, double threshold, bool absolute) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:172: warning: Member addConfILG(const GenType &generator) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:181: warning: Member total_prob_init(Iso &&iso, double target_prob, bool trim) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:216: warning: Member stochastic_init(Iso &&iso, size_t _no_molecules, double _precision, double _beta_bias) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:121: warning: Member LinearCombination(const std::vector< const FixedEnvelope * > &spectra, const std::vector< double > &intensities) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:122: warning: Member LinearCombination(const FixedEnvelope *const *spectra, const double *intensities, size_t size) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:183: warning: Member FromThreshold(Iso &&iso, double threshold, bool absolute, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:194: warning: Member FromThreshold(const Iso &iso, double _threshold, bool _absolute, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:199: warning: Member FromTotalProb(Iso &&iso, double target_total_prob, bool optimize, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:211: warning: Member FromTotalProb(const Iso &iso, double _target_total_prob, bool _optimize, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:218: warning: Member FromStochastic(Iso &&iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:230: warning: Member FromStochastic(const Iso &iso, size_t _no_molecules, double _precision=0.9999, double _beta_bias=5.0, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:235: warning: Member Binned(Iso &&iso, double target_total_prob, double bin_width, double bin_middle=0.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:236: warning: Member Binned(const Iso &iso, double target_total_prob, double bin_width, double bin_middle=0.0) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:132: warning: Member store_conf(const T &generator) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:139: warning: Member store_conf(double _mass, double _prob) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:152: warning: Member swap(size_t idx1, size_t idx2, ISOSPEC_MAYBE_UNUSED int *conf_swapspace) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:166: warning: Member reallocate_memory(size_t new_size) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:167: warning: Member slow_reallocate_memory(size_t new_size) (function) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:42: warning: Member _masses (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:43: warning: Member _probs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:44: warning: Member _confs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:45: warning: Member _confs_no (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:46: warning: Member allDim (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:47: warning: Member sorted_by_mass (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:48: warning: Member sorted_by_prob (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:49: warning: Member total_prob (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:50: warning: Member current_size (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:51: warning: Member tmasses (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:52: warning: Member tprobs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:53: warning: Member tconfs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:54: warning: Member allDimSizeofInt (variable) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:241: warning: Member AbyssalWassersteinDistanceGrad(FixedEnvelope *const *envelopes, const double *scales, double *ret_gradient, size_t N, double abyss_depth_exp, double abyss_depth_the) (friend) of class IsoSpec::FixedEnvelope is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:110: warning: Found unknown command '\use_nominal_masses' /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:111: warning: Found unknown command '\add_water' /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:106: warning: The following parameters of IsoSpec::Iso::FromFASTA(const char *fasta, bool use_nominal_masses=false, bool add_water=true) are not documented: parameter 'use_nominal_masses' parameter 'add_water' /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:483: warning: Member get_currentLThreshold() const (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:485: warning: Member IsoLayeredGenerator(Iso &&iso, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true, double t_prob_hint=0.99) (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:499: warning: Member advanceToNextConfigurationWithinLayer() (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:534: warning: Member nextLayer(double offset) (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:553: warning: Member IsoStochasticGenerator(Iso &&iso, size_t no_molecules, double precision=0.9999, double beta_bias=5.0) (function) of class IsoSpec::IsoStochasticGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:555: warning: Member count() const (function) of class IsoSpec::IsoStochasticGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:90: warning: Member Iso(int _dimNumber, const int *_isotopeNumbers, const int *_atomCounts, const double *const *_isotopeMasses, const double *const *_isotopeProbabilities) (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:339: warning: argument 'tabSize' of command @param is not found in the argument list of IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator(Iso &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true) /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:339: warning: argument 'hashSize' of command @param is not found in the argument list of IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator(Iso &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true) /build/isospec-2.2.1/IsoSpec++/isoSpec++.h:339: warning: The following parameters of IsoSpec::IsoThresholdGenerator::IsoThresholdGenerator(Iso &&iso, double _threshold, bool _absolute=true, int _tabSize=1000, int _hashSize=1000, bool reorder_marginals=true) are not documented: parameter '_tabSize' parameter '_hashSize' parameter 'reorder_marginals' /build/isospec-2.2.1/IsoSpec++/operators.h:34: warning: Member KeyHasher(int dim) (function) of class IsoSpec::KeyHasher is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:36: warning: Member operator()(const int *conf) const noexcept (function) of class IsoSpec::KeyHasher is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:368: warning: The following parameter of IsoSpec::LayeredMarginal::LayeredMarginal(Marginal &&m, int tabSize=1000, int hashSize=1000) is not documented: parameter 'm' /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:378: warning: The following parameter of IsoSpec::LayeredMarginal::extend(double new_threshold, bool do_sort=true) is not documented: parameter 'do_sort' /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:59: warning: found documented return type for IsoSpec::Marginal::Marginal that does not return anything /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:233: warning: Member conf_lprobs() const (function) of class IsoSpec::MarginalTrek is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:234: warning: Member conf_masses() const (function) of class IsoSpec::MarginalTrek is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:235: warning: Member confs() const (function) of class IsoSpec::MarginalTrek is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:199: warning: The following parameter of IsoSpec::MarginalTrek::MarginalTrek(Marginal &&m, int tabSize=1000, int hashSize=1000) is not documented: parameter 'm' /build/isospec-2.2.1/IsoSpec++/operators.h:145: warning: Member OrderMarginalsBySizeDecresing(T const *const *const MT_) (function) of class IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:146: warning: Member operator()(int m1, int m2) (function) of class IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:254: warning: Member configurations (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:255: warning: Member confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:256: warning: Member no_confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:257: warning: Member masses (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:258: warning: Member lProbs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:259: warning: Member probs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:260: warning: Member allocator (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:264: warning: argument 'Marginal' of command @param is not found in the argument list of IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal(Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000) /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:264: warning: The following parameters of IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal(Marginal &&m, double lCutOff, bool sort=true, int tabSize=1000, int hashSize=1000) are not documented: parameter 'm' parameter 'tabSize' parameter 'hashSize' /build/isospec-2.2.1/IsoSpec++/marginalTrek++.h:264: warning: found documented return type for IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal that does not return anything /build/isospec-2.2.1/IsoSpec++/conf.h:30: warning: Member ProbAndConfPtr(double p, Conf c) (function) of struct IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:32: warning: Member operator<(const ProbAndConfPtr &other) const (function) of struct IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:27: warning: Member first (variable) of struct IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/conf.h:28: warning: Member second (variable) of struct IsoSpec::ProbAndConfPtr is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:121: warning: Member operator()(const T a, const T b) const (function) of class IsoSpec::ReverseOrder is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:35: warning: Member SSummator(const SSummator &other) (function) of class IsoSpec::SSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:39: warning: Member add(double x) (function) of class IsoSpec::SSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:61: warning: Member get() (function) of class IsoSpec::SSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:85: warning: Member add(double what) (function) of class IsoSpec::Summator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:93: warning: Member get() (function) of class IsoSpec::Summator is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:128: warning: Member TableOrder(const T *_tbl) (function) of class IsoSpec::TableOrder is not documented. /build/isospec-2.2.1/IsoSpec++/operators.h:129: warning: Member operator()(unsigned int i, unsigned int j) (function) of class IsoSpec::TableOrder is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:107: warning: Member add(double what) (function) of class IsoSpec::TSummator is not documented. /build/isospec-2.2.1/IsoSpec++/summator.h:111: warning: Member get() (function) of class IsoSpec::TSummator is not documented. soSpec++/pod_vector.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/python-build.cpp... Generating code for file /build/isospec-2.2.1/IsoSpec++/summator.h... Generating code for file /build/isospec-2.2.1/IsoSpec++/unity-build.cpp... Generating file documentation... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound pod_vector... Generating docs for compound unsafe_pod_vector... Generating docs for compound ws_match_res... Generating concept documentation... Generating namespace index... Generating docs for namespace IsoSpec Generating docs for compound IsoSpec::Allocator... Generating docs for compound IsoSpec::ConfEqual... Generating docs for compound IsoSpec::ConfOrder... Generating docs for compound IsoSpec::ConfOrderMarginal... Generating docs for compound IsoSpec::ConfOrderMarginalDescending... Generating docs for compound IsoSpec::DirtyAllocator... Generating docs for compound IsoSpec::FixedEnvelope... Generating docs for compound IsoSpec::Iso... Generating docs for compound IsoSpec::IsoGenerator... Generating docs for compound IsoSpec::IsoLayeredGenerator... Generating docs for compound IsoSpec::IsoOrderedGenerator... Generating docs for compound IsoSpec::IsoStochasticGenerator... Generating docs for compound IsoSpec::IsoThresholdGenerator... Generating docs for compound IsoSpec::KeyHasher... Generating docs for compound IsoSpec::LayeredMarginal... Generating docs for compound IsoSpec::Marginal... Generating docs for compound IsoSpec::MarginalTrek... Generating docs for compound IsoSpec::OrderMarginalsBySizeDecresing... Generating docs for compound IsoSpec::PrecalculatedMarginal... Generating docs for compound IsoSpec::ProbAndConfPtr... Generating docs for compound IsoSpec::ReverseOrder... Generating docs for compound IsoSpec::SSummator... Generating docs for compound IsoSpec::Summator... Generating docs for compound IsoSpec::TableOrder... Generating docs for compound IsoSpec::TSummator... Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... lookup cache used 1530/65536 hits=8386 misses=1622 finished... make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen [100%] Built target html_doc make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 0 make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen dh_auto_build -O--buildsyste=cmake -- pdf_doc cd obj-i686-linux-gnu && make -j15 "INSTALL=install --strip-program=true" pdf_doc VERBOSE=1 make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 pdf_doc make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 1 make -f CMakeFiles/Makefile2 man/CMakeFiles/pdf_doc.dir/all make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make -f man/CMakeFiles/pdf_doc.dir/build.make man/CMakeFiles/pdf_doc.dir/depend make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten cd /build/isospec-2.2.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/isospec-2.2.1 /build/isospec-2.2.1/man /build/isospec-2.2.1/obj-i686-linux-gnu /build/isospec-2.2.1/obj-i686-linux-gnu/man /build/isospec-2.2.1/obj-i686-linux-gnu/man/CMakeFiles/pdf_doc.dir/DependInfo.cmake --color= make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make -f man/CMakeFiles/pdf_doc.dir/build.make man/CMakeFiles/pdf_doc.dir/build make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten [100%] Doxygen-based developer pdf documentation generation cd /build/isospec-2.2.1/man/latex && make make[6]: Verzeichnis „/build/isospec-2.2.1/man/latex“ wird betreten make[6]: Warnung: Kein Jobserver verfügbar: -j1 wird gesetzt. 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(/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] Chapter 1. (./namespaces.tex LaTeX Warning: Reference `namespace_iso_spec' on page 1 undefined on input line 3. ) [1] [2] Chapter 2. (./hierarchy.tex LaTeX Warning: Reference `class_iso_spec_1_1_allocator' on page 3 undefined on input line 3. LaTeX Warning: Reference `class_iso_spec_1_1_allocator' on page 3 undefined on input line 4. LaTeX Warning: Reference `class_iso_spec_1_1_conf_equal' on page 3 undefined on input line 5. LaTeX Warning: Reference `class_iso_spec_1_1_conf_order' on page 3 undefined on input line 6. LaTeX Warning: Reference `class_iso_spec_1_1_conf_order_marginal' on page 3 und efined on input line 7. LaTeX Warning: Reference `class_iso_spec_1_1_conf_order_marginal_descending' on page 3 undefined on input line 8. 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LaTeX Warning: Reference `structws__match__res' on page 3 undefined on input li ne 44. ) [3] [4] Chapter 3. (./annotated.tex LaTeX Warning: Reference `class_iso_spec_1_1_allocator' on page 5 undefined on input line 3. LaTeX Warning: Reference `class_iso_spec_1_1_conf_equal' on page 5 undefined on input line 4. LaTeX Warning: Reference `class_iso_spec_1_1_conf_order' on page 5 undefined on input line 5. LaTeX Warning: Reference `class_iso_spec_1_1_conf_order_marginal' on page 5 und efined on input line 6. LaTeX Warning: Reference `class_iso_spec_1_1_conf_order_marginal_descending' on page 5 undefined on input line 7. LaTeX Warning: Reference `class_iso_spec_1_1_dirty_allocator' on page 5 undefin ed on input line 8. LaTeX Warning: Reference `class_iso_spec_1_1_fixed_envelope' on page 5 undefine d on input line 9. LaTeX Warning: Reference `class_iso_spec_1_1_iso' on page 5 undefined on input line 10. 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LaTeX Warning: Reference `structws__match__res' on page 5 undefined on input li ne 30. ) [5] [6] Chapter 4. (./files.tex LaTeX Warning: Reference `allocator_8cpp_source' on page 7 undefined on input l ine 3. LaTeX Warning: Reference `allocator_8h_source' on page 7 undefined on input lin e 4. LaTeX Warning: Reference `btrd_8h_source' on page 7 undefined on input line 5. LaTeX Warning: Reference `conf_8h_source' on page 7 undefined on input line 6. LaTeX Warning: Reference `cwrapper_8cpp_source' on page 7 undefined on input li ne 7. LaTeX Warning: Reference `cwrapper_8h_source' on page 7 undefined on input line 8. LaTeX Warning: Reference `dirty_allocator_8cpp_source' on page 7 undefined on i nput line 9. LaTeX Warning: Reference `dirty_allocator_8h_source' on page 7 undefined on inp ut line 10. LaTeX Warning: Reference `element__tables_8cpp_source' on page 7 undefined on i nput line 11. LaTeX Warning: Reference `element__tables_8h_source' on page 7 undefined on inp ut line 12. LaTeX Warning: Reference `fasta_8cpp_source' on page 7 undefined on input line 13. LaTeX Warning: Reference `fasta_8h_source' on page 7 undefined on input line 14 . LaTeX Warning: Reference `fixed_envelopes_8cpp_source' on page 7 undefined on i nput line 15. LaTeX Warning: Reference `fixed_envelopes_8h_source' on page 7 undefined on inp ut line 16. LaTeX Warning: Reference `iso_math_8cpp_source' on page 7 undefined on input li ne 17. LaTeX Warning: Reference `iso_math_8h_source' on page 7 undefined on input line 18. LaTeX Warning: Reference `iso_spec_09_09_8cpp_source' on page 7 undefined on in put line 19. LaTeX Warning: Reference `iso_spec_09_09_8h_source' on page 7 undefined on inpu t line 20. LaTeX Warning: Reference `marginal_trek_09_09_8cpp_source' on page 7 undefined on input line 21. LaTeX Warning: Reference `marginal_trek_09_09_8h_source' on page 7 undefined on input line 22. LaTeX Warning: Reference `misc_8cpp_source' on page 7 undefined on input line 2 3. 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(./namespace_iso_spec.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) [9] [10] Overfull \hbox (152.89105pt too wide) in paragraph at lines 201--203 []\T1/phv/m/n/10 const dou-ble [] = 1.[]144729885849400174143427351353058711647 294812915311571513623071472137769884826079783623270275489708 (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [11] [12] [13] [14] [15] [16] [17] [18] [19] Package longtable Warning: Column widths have changed (longtable) in table 5.1 on input line 663. [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 871--872 \T1/pcr/m/n/8 ISOSPEC[]_[][]C[]_[][]API const size[]_[]t Iso[]Spec[]::isospec[] _[]number[]_[]of[]_[]isotopic[]_[]entries = ISOSPEC[]_[][]NUMBER[]_[][]OF[]_[][ ] Overfull \hbox (173.55629pt too wide) in paragraph at lines 881--882 \T1/pcr/m/n/8 const double Iso[]Spec[]::logpi = 1.[]144729885849400174143427351 353058711647294812915311571513623071472137769884826079783623270275489708 [23]) [24] Chapter 6. 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[57] Underfull \hbox (badness 10000) detected at line 176 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 181--182 []\T1/phv/m/n/10 Reimplemented in [], [], and []. ) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso_lay ered_generator.pdf> [58] [59] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) in paragraph at lines 99--100 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer [60] Underfull \hbox (badness 10000) in paragraph at lines 137--138 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) in paragraph at lines 158--159 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 164 [][][] [61] Underfull \hbox (badness 10000) in paragraph at lines 189--190 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex [62] <./class_iso_spec_1_1_is o_ordered_generator.pdf> [63] Underfull \hbox (badness 10000) detected at line 89 [][][] [64] Package longtable Warning: Column widths have changed (longtable) in table 6.4 on input line 114. ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [65] Underfull \hbox (badness 10000) in paragraph at lines 54--55 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Stochas tic[]Generator[]::advance[]To[]Next[]Configuration ( ) Underfull \hbox (badness 10000) detected at line 60 [][][] [66] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) in paragraph at lines 124--125 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) in paragraph at lines 145--146 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 151 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex [67] <./class_iso_spec_1_1_ iso_threshold_generator.pdf> [68] Package longtable Warning: Column widths have changed (longtable) in table 6.5 on input line 80. 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(./allocator_8cpp_source.tex) (./allocator_8h_source.tex [119]) (./btrd_8h_source.tex [120] [121] [122]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [123] [124] [125] [126] Overfull \hbox (44.55553pt too wide) in paragraph at lines 329--329 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinDistance(*[ ]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (78.1555pt too wide) in paragraph at lines 341--341 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->OrientedWassersteinDis tance(*[]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (69.75551pt too wide) in paragraph at lines 351--351 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->AbyssalWassersteinDist ance(*[]reinterpret_cast<[][]*[]>[](tabulator2), Overfull \hbox (27.75554pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinMatch(*[]re interpret_cast<[][]*[]>[](tabulator2), [127] Overfull \hbox (40.35553pt too wide) in paragraph at lines 374--374 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))+(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); Overfull \hbox (40.35553pt too wide) in paragraph at lines 380--380 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))*(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); [128]) (./cwrapper_8h_source.tex [129] [130]) (./dirty_allocator_8cpp_source.tex [131]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [167] [168] [169] [170]) (./fasta_8h_source.tex [171]) (./fixed_envelopes_8cpp_source.tex [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185]) (./fixed_envelopes_8h_source.tex [186] [187] [188]) (./iso_math_8cpp_source.tex [189] [190]) (./iso_math_8h_source.tex [191]) (./iso_spec_09_09_8cpp_source.tex [192] [193] [194] [195] [196] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [197] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200] [201] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [202]) (./iso_spec_09_09_8h_source.tex [203] [204] [205] [206] [207] [208]) (./marginal_trek_09_09_8cpp_source.tex [209] [210] [211] [212] [213] [214] [215] [216]) (./marginal_trek_09_09_8h_source.tex [217] [218] [219] [220]) (./misc_8cpp_source.tex [221]) (./misc_8h_source.tex [222] [223]) (./mman_8cpp_source.tex [224] [225]) (./mman_8h_source.tex [226]) (./operators_8cpp_source.tex [227]) (./operators_8h_source.tex [228] [229]) (./platform_8h_source.tex [230]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [231] [232] [233] [234] [235]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [236] [237]) (./unity-build_8cpp_source.tex) [238] No file refman.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. (./refman.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (240 pages, 914831 bytes). Transcript written on refman.log. makeindex refman.idx This is makeindex, version 2.16 [TeX Live 2022] (kpathsea + Thai support). Scanning input file refman.idx....done (815 entries accepted, 0 rejected). Sorting entries.........done (8587 comparisons). Generating output file refman.ind....done (1098 lines written, 0 warnings). Output written in refman.ind. 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(./namespaces.tex) [1] [2] Chapter 2. (./hierarchy.tex) [3] [4] Chapter 3. (./annotated.tex) [5] [6] Chapter 4. (./files.tex) [7] [8] Chapter 5. (./namespace_iso_spec.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) [9] [10] Overfull \hbox (152.89105pt too wide) in paragraph at lines 201--203 []\T1/phv/m/n/10 const dou-ble [] = 1.[]144729885849400174143427351353058711647 294812915311571513623071472137769884826079783623270275489708 [11] [12] [13] [14] [15] [16] [17] [18] [19] Package longtable Warning: Column widths have changed (longtable) in table 5.1 on input line 663. [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 871--872 \T1/pcr/m/n/8 ISOSPEC[]_[][]C[]_[][]API const size[]_[]t Iso[]Spec[]::isospec[] _[]number[]_[]of[]_[]isotopic[]_[]entries = ISOSPEC[]_[][]NUMBER[]_[][]OF[]_[][ ] Overfull \hbox (173.55629pt too wide) in paragraph at lines 881--882 \T1/pcr/m/n/8 const double Iso[]Spec[]::logpi = 1.[]144729885849400174143427351 353058711647294812915311571513623071472137769884826079783623270275489708 [23]) [24] Chapter 6. (./class_iso_spec_1_1_allocator.tex [25]) (./class_iso_spec_1_1_conf_equal.tex [26]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [27]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [28]) (./class_iso_spec_1_1_dirty_allocator.tex [29] [30]) (./class_iso_spec_1_1_fixed_envelope.tex [31] Underfull \hbox (badness 1072) in paragraph at lines 89--91 []\T1/phv/m/n/10 static [] [] ([] &&iso, dou-ble target[]_[]total[]_[]prob, boo l op-ti-mize, bool tget[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [45] [46] [47] [48] [49] [50] [51] [52] [53]) (./class_iso_spec_1_1_iso_generator.tex [54] <./ class_iso_spec_1_1_iso_generator.pdf> [55] Underfull \hbox (badness 10000) detected at line 103 [][][] [56] Underfull \hbox (badness 10000) detected at line 134 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 139--140 []\T1/phv/m/n/10 Reimplemented in [], [], and []. 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[57] Underfull \hbox (badness 10000) detected at line 176 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 181--182 []\T1/phv/m/n/10 Reimplemented in [], [], and []. ) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso_lay ered_generator.pdf> [58] [59] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) in paragraph at lines 99--100 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer [60] Underfull \hbox (badness 10000) in paragraph at lines 137--138 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) in paragraph at lines 158--159 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const 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124--125 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) in paragraph at lines 145--146 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 151 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex [67] <./class_iso_spec_1_1_ iso_threshold_generator.pdf> [68] Overfull \hbox (18.89209pt too wide) in paragraph at lines 102--103 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], [69] Underfull \hbox (badness 10000) detected at line 108 [][][] Underfull \hbox (badness 10000) in paragraph at lines 151--152 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres 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(./class_iso_spec_1_1_order_marginals_by_size_decresing.tex [87]) (./classpod__vector.tex [88] [89] [90] [91] [92] [93] [94] [95]) (./class_iso_spec_1_1_precalculated_marginal.tex [96] <./class_iso_spec_1_1_pre calculated_marginal.pdf> [97] Underfull \hbox (badness 10000) detected at line 100 [][][] [98] Underfull \hbox (badness 10000) detected at line 139 [][][] [99] Underfull \hbox (badness 10000) detected at line 161 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 200 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] [100] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] [101] [102]) (./struct_iso_spec_1_1_prob_and_conf_ptr.tex [103]) (./class_iso_spec_1_1_reverse_order.tex [104]) 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(./allocator_8cpp_source.tex) (./allocator_8h_source.tex [119]) (./btrd_8h_source.tex [120] [121] [122]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [123] [124] [125] [126] Overfull \hbox (44.55553pt too wide) in paragraph at lines 329--329 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinDistance(*[ ]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (78.1555pt too wide) in paragraph at lines 341--341 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->OrientedWassersteinDis tance(*[]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (69.75551pt too wide) in paragraph at lines 351--351 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->AbyssalWassersteinDist ance(*[]reinterpret_cast<[][]*[]>[](tabulator2), Overfull \hbox (27.75554pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinMatch(*[]re interpret_cast<[][]*[]>[](tabulator2), [127] Overfull \hbox (40.35553pt too wide) in paragraph at lines 374--374 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))+(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); Overfull \hbox (40.35553pt too wide) in paragraph at lines 380--380 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))*(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); [128]) (./cwrapper_8h_source.tex [129] [130]) (./dirty_allocator_8cpp_source.tex [131]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [167] [168] [169] [170]) (./fasta_8h_source.tex [171]) (./fixed_envelopes_8cpp_source.tex [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185]) (./fixed_envelopes_8h_source.tex [186] [187] [188]) (./iso_math_8cpp_source.tex [189] [190]) (./iso_math_8h_source.tex [191]) (./iso_spec_09_09_8cpp_source.tex [192] [193] [194] [195] [196] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [197] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200] [201] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [202]) (./iso_spec_09_09_8h_source.tex [203] [204] [205] [206] [207] [208]) (./marginal_trek_09_09_8cpp_source.tex [209] [210] [211] [212] [213] [214] [215] [216]) (./marginal_trek_09_09_8h_source.tex [217] [218] [219] [220]) (./misc_8cpp_source.tex [221]) (./misc_8h_source.tex [222] [223]) (./mman_8cpp_source.tex [224] [225]) (./mman_8h_source.tex [226]) (./operators_8cpp_source.tex [227]) (./operators_8h_source.tex [228] [229]) (./platform_8h_source.tex [230]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [231] [232] [233] [234] [235]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [236] [237]) (./unity-build_8cpp_source.tex) [238] (./refman.ind Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/element_tables.cpp, Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp, [239] [240] [241] [242] [243] [244] Underfull \hbox (badness 870) in paragraph at lines 818--820 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , Underfull \hbox (badness 870) in paragraph at lines 830--832 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , [245] [246] [247]) Package longtable Warning: Table widths have changed. Rerun LaTeX. (./refman.aux) Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (263 pages, 1023531 bytes). Transcript written on refman.log. latex_count=8 ; \ while egrep -s 'Rerun (LaTeX|to get cross-references right|to get bibliographical references right)' refman.log && [ $latex_count -gt 0 ] ;\ do \ echo "Rerunning latex...." ;\ pdflatex refman ;\ latex_count=`expr $latex_count - 1` ;\ done Package longtable Warning: Table widths have changed. Rerun LaTeX. Rerunning latex.... 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(./namespaces.tex) [1] [2] Chapter 2. (./hierarchy.tex) [3] [4] Chapter 3. (./annotated.tex) [5] [6] Chapter 4. (./files.tex) [7] [8] Chapter 5. (./namespace_iso_spec.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) [9] [10] Overfull \hbox (152.89105pt too wide) in paragraph at lines 201--203 []\T1/phv/m/n/10 const dou-ble [] = 1.[]144729885849400174143427351353058711647 294812915311571513623071472137769884826079783623270275489708 [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 871--872 \T1/pcr/m/n/8 ISOSPEC[]_[][]C[]_[][]API const size[]_[]t Iso[]Spec[]::isospec[] _[]number[]_[]of[]_[]isotopic[]_[]entries = ISOSPEC[]_[][]NUMBER[]_[][]OF[]_[][ ] Overfull \hbox (173.55629pt too wide) in paragraph at lines 881--882 \T1/pcr/m/n/8 const double Iso[]Spec[]::logpi = 1.[]144729885849400174143427351 353058711647294812915311571513623071472137769884826079783623270275489708 [23]) [24] Chapter 6. (./class_iso_spec_1_1_allocator.tex [25]) (./class_iso_spec_1_1_conf_equal.tex [26]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [27]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [28]) (./class_iso_spec_1_1_dirty_allocator.tex [29] [30]) (./class_iso_spec_1_1_fixed_envelope.tex [31] Underfull \hbox (badness 1072) in paragraph at lines 89--91 []\T1/phv/m/n/10 static [] [] ([] &&iso, dou-ble target[]_[]total[]_[]prob, boo l op-ti-mize, bool tget[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [45] [46] [47] [48] [49] [50] [51] [52] [53]) (./class_iso_spec_1_1_iso_generator.tex [54] <./ class_iso_spec_1_1_iso_generator.pdf> [55] Underfull \hbox (badness 10000) detected at line 103 [][][] [56] Underfull \hbox (badness 10000) detected at line 134 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 139--140 []\T1/phv/m/n/10 Reimplemented in [], [], and []. 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[57] Underfull \hbox (badness 10000) detected at line 176 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 181--182 []\T1/phv/m/n/10 Reimplemented in [], [], and []. ) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso_lay ered_generator.pdf> [58] [59] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) in paragraph at lines 99--100 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer [60] Underfull \hbox (badness 10000) in paragraph at lines 137--138 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) in paragraph at lines 158--159 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 164 [][][] [61] Underfull \hbox (badness 10000) in paragraph at lines 189--190 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex [62] <./class_iso_spec_1_1_is o_ordered_generator.pdf> [63] Underfull \hbox (badness 10000) detected at line 89 [][][] [64]) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_ iso_stochastic_generator.pdf> [65] Underfull \hbox (badness 10000) in paragraph at lines 54--55 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Stochas tic[]Generator[]::advance[]To[]Next[]Configuration ( ) Underfull \hbox (badness 10000) detected at line 60 [][][] [66] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) in paragraph at lines 124--125 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) in paragraph at lines 145--146 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 151 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex [67] <./class_iso_spec_1_1_ iso_threshold_generator.pdf> [68] Overfull \hbox (18.89209pt too wide) in paragraph at lines 102--103 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], [69] Underfull \hbox (badness 10000) detected at line 108 [][][] Underfull \hbox (badness 10000) in paragraph at lines 151--152 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) in paragraph at lines 172--173 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) in paragraph at lines 193--194 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 199 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex [72]) (./class_iso_spec_1_1_layered_marginal.tex <./class_iso_spec_1_1_layered_margin al.pdf> [73] [74] Underfull \hbox (badness 10000) detected at line 101 [][][] [75] Underfull \hbox (badness 10000) detected at line 230 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [76] [77] Overfull \vbox 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(./class_iso_spec_1_1_order_marginals_by_size_decresing.tex [87]) (./classpod__vector.tex [88] [89] [90] [91] [92] [93] [94] [95]) (./class_iso_spec_1_1_precalculated_marginal.tex [96] <./class_iso_spec_1_1_pre calculated_marginal.pdf> [97] Underfull \hbox (badness 10000) detected at line 100 [][][] [98] Underfull \hbox (badness 10000) detected at line 139 [][][] [99] Underfull \hbox (badness 10000) detected at line 161 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 200 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] [100] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] [101] [102]) (./struct_iso_spec_1_1_prob_and_conf_ptr.tex [103]) (./class_iso_spec_1_1_reverse_order.tex [104]) (./class_iso_spec_1_1_s_summator.tex [105]) (./class_iso_spec_1_1_summator.tex [106]) (./class_iso_spec_1_1_table_order.tex [107]) (./class_iso_spec_1_1_t_summator.tex [108]) (./classunsafe__pod__vector.tex [109] [110] [111] [112] [113] [114] [115] [116]) (./structws__match__res.tex [117]) [118] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [119]) (./btrd_8h_source.tex [120] [121] [122]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [123] [124] [125] [126] Overfull \hbox (44.55553pt too wide) in paragraph at lines 329--329 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinDistance(*[ ]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (78.1555pt too wide) in paragraph at lines 341--341 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->OrientedWassersteinDis tance(*[]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (69.75551pt too wide) in paragraph at lines 351--351 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->AbyssalWassersteinDist ance(*[]reinterpret_cast<[][]*[]>[](tabulator2), Overfull \hbox (27.75554pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinMatch(*[]re interpret_cast<[][]*[]>[](tabulator2), [127] Overfull \hbox (40.35553pt too wide) in paragraph at lines 374--374 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))+(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); Overfull \hbox (40.35553pt too wide) in paragraph at lines 380--380 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))*(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); [128]) (./cwrapper_8h_source.tex [129] [130]) (./dirty_allocator_8cpp_source.tex [131]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [167] [168] [169] [170]) (./fasta_8h_source.tex [171]) (./fixed_envelopes_8cpp_source.tex [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185]) (./fixed_envelopes_8h_source.tex [186] [187] [188]) (./iso_math_8cpp_source.tex [189] [190]) (./iso_math_8h_source.tex [191]) (./iso_spec_09_09_8cpp_source.tex [192] [193] [194] [195] [196] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [197] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200] [201] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [202]) (./iso_spec_09_09_8h_source.tex [203] [204] [205] [206] [207] [208]) (./marginal_trek_09_09_8cpp_source.tex [209] [210] [211] [212] [213] [214] [215] [216]) (./marginal_trek_09_09_8h_source.tex [217] [218] [219] [220]) (./misc_8cpp_source.tex [221]) (./misc_8h_source.tex [222] [223]) (./mman_8cpp_source.tex [224] [225]) (./mman_8h_source.tex [226]) (./operators_8cpp_source.tex [227]) (./operators_8h_source.tex [228] [229]) (./platform_8h_source.tex [230]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [231] [232] [233] [234] [235]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [236] [237]) (./unity-build_8cpp_source.tex) [238] (./refman.ind Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/element_tables.cpp, Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp, [239] [240] [241] [242] [243] [244] Underfull \hbox (badness 870) in paragraph at lines 818--820 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , Underfull \hbox (badness 870) in paragraph at lines 830--832 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , [245] [246] [247]) (./refman.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (263 pages, 1023315 bytes). 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Check if current package is valid. ) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def) (/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty (/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty) (/usr/share/texlive/texmf-dist/tex/latex/caption/ltcaption.sty)) (/usr/share/texlive/texmf-dist/tex/latex/etoc/etoc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./refman.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (./refman.out) (./refman.out) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] Chapter 1. (./namespaces.tex) [1] [2] Chapter 2. (./hierarchy.tex) [3] [4] Chapter 3. (./annotated.tex) [5] [6] Chapter 4. (./files.tex) [7] [8] Chapter 5. (./namespace_iso_spec.tex (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) [9] [10] Overfull \hbox (152.89105pt too wide) in paragraph at lines 201--203 []\T1/phv/m/n/10 const dou-ble [] = 1.[]144729885849400174143427351353058711647 294812915311571513623071472137769884826079783623270275489708 [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] Underfull \hbox (badness 10000) in paragraph at lines 871--872 \T1/pcr/m/n/8 ISOSPEC[]_[][]C[]_[][]API const size[]_[]t Iso[]Spec[]::isospec[] _[]number[]_[]of[]_[]isotopic[]_[]entries = ISOSPEC[]_[][]NUMBER[]_[][]OF[]_[][ ] Overfull \hbox (173.55629pt too wide) in paragraph at lines 881--882 \T1/pcr/m/n/8 const double Iso[]Spec[]::logpi = 1.[]144729885849400174143427351 353058711647294812915311571513623071472137769884826079783623270275489708 [23]) [24] Chapter 6. (./class_iso_spec_1_1_allocator.tex [25]) (./class_iso_spec_1_1_conf_equal.tex [26]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [27]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [28]) (./class_iso_spec_1_1_dirty_allocator.tex [29] [30]) (./class_iso_spec_1_1_fixed_envelope.tex [31] Underfull \hbox (badness 1072) in paragraph at lines 89--91 []\T1/phv/m/n/10 static [] [] ([] &&iso, dou-ble target[]_[]total[]_[]prob, boo l op-ti-mize, bool tget[] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [45] [46] [47] [48] [49] [50] [51] [52] [53]) (./class_iso_spec_1_1_iso_generator.tex [54] <./ class_iso_spec_1_1_iso_generator.pdf> [55] Underfull \hbox (badness 10000) detected at line 103 [][][] [56] Underfull \hbox (badness 10000) detected at line 134 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 139--140 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 155 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 160--161 []\T1/phv/m/n/10 Reimplemented in [], [], and []. [57] Underfull \hbox (badness 10000) detected at line 176 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 181--182 []\T1/phv/m/n/10 Reimplemented in [], [], and []. ) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso_lay ered_generator.pdf> [58] [59] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) in paragraph at lines 99--100 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer [60] Underfull \hbox (badness 10000) in paragraph at lines 137--138 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) in paragraph at lines 158--159 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 164 [][][] [61] Underfull \hbox (badness 10000) in paragraph at lines 189--190 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex [62] <./class_iso_spec_1_1_is o_ordered_generator.pdf> [63] Underfull \hbox (badness 10000) detected at line 89 [][][] [64]) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_ iso_stochastic_generator.pdf> [65] Underfull \hbox (badness 10000) in paragraph at lines 54--55 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Stochas tic[]Generator[]::advance[]To[]Next[]Configuration ( ) Underfull \hbox (badness 10000) detected at line 60 [][][] [66] Underfull \hbox (badness 10000) detected at line 109 [][][] Underfull \hbox (badness 10000) in paragraph at lines 124--125 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) in paragraph at lines 145--146 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Stoch astic[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 151 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex [67] <./class_iso_spec_1_1_ iso_threshold_generator.pdf> [68] Overfull \hbox (18.89209pt too wide) in paragraph at lines 102--103 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], [69] Underfull \hbox (badness 10000) detected at line 108 [][][] Underfull \hbox (badness 10000) in paragraph at lines 151--152 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) in paragraph at lines 172--173 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) in paragraph at lines 193--194 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::prob ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 199 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex [72]) (./class_iso_spec_1_1_layered_marginal.tex <./class_iso_spec_1_1_layered_margin al.pdf> [73] [74] Underfull \hbox (badness 10000) detected at line 101 [][][] [75] Underfull \hbox (badness 10000) detected at line 230 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [76] [77] Overfull \vbox (7.22813pt too high) has occurred while \output is active [78] Underfull \hbox (badness 10000) detected at line 119 [][][] Underfull \hbox (badness 10000) detected at line 181 [][][] [79] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 266 [][][] [80] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] [81] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 379 [][][] [82] Underfull \hbox (badness 10000) detected at line 411 [][][] [83]) (./class_iso_spec_1_1_marginal_trek.tex [84] <./class_iso_spec_1_1_margin al_trek.pdf> [85] [86] Underfull \hbox (badness 10000) detected at line 124 [][][] Underfull \hbox (badness 10000) detected at line 148 [][][] ) (./class_iso_spec_1_1_order_marginals_by_size_decresing.tex [87]) (./classpod__vector.tex [88] [89] [90] [91] [92] [93] [94] [95]) (./class_iso_spec_1_1_precalculated_marginal.tex [96] <./class_iso_spec_1_1_pre calculated_marginal.pdf> [97] Underfull \hbox (badness 10000) detected at line 100 [][][] [98] Underfull \hbox (badness 10000) detected at line 139 [][][] [99] Underfull \hbox (badness 10000) detected at line 161 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] Underfull \hbox (badness 10000) detected at line 200 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] [100] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 290 [][][] [101] [102]) (./struct_iso_spec_1_1_prob_and_conf_ptr.tex [103]) (./class_iso_spec_1_1_reverse_order.tex [104]) (./class_iso_spec_1_1_s_summator.tex [105]) (./class_iso_spec_1_1_summator.tex [106]) (./class_iso_spec_1_1_table_order.tex [107]) (./class_iso_spec_1_1_t_summator.tex [108]) (./classunsafe__pod__vector.tex [109] [110] [111] [112] [113] [114] [115] [116]) (./structws__match__res.tex [117]) [118] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [119]) (./btrd_8h_source.tex [120] [121] [122]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [123] [124] [125] [126] Overfull \hbox (44.55553pt too wide) in paragraph at lines 329--329 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinDistance(*[ ]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (78.1555pt too wide) in paragraph at lines 341--341 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->OrientedWassersteinDis tance(*[]reinterpret_cast<[][]*[]>[](tabulator2)); Overfull \hbox (69.75551pt too wide) in paragraph at lines 351--351 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->AbyssalWassersteinDist ance(*[]reinterpret_cast<[][]*[]>[](tabulator2), Overfull \hbox (27.75554pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/7 reinterpret_cast<[][]*[]>[](tabulator1)->WassersteinMatch(*[]re interpret_cast<[][]*[]>[](tabulator2), [127] Overfull \hbox (40.35553pt too wide) in paragraph at lines 374--374 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))+(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); Overfull \hbox (40.35553pt too wide) in paragraph at lines 380--380 []\T1/pcr/m/n/7 ((*[]reinterpret_cast<[][]*[]>[](tabulator1))*(*[]reinterpret_c ast<[][]*[]>[](tabulator2)))); [128]) (./cwrapper_8h_source.tex [129] [130]) (./dirty_allocator_8cpp_source.tex [131]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [167] [168] [169] [170]) (./fasta_8h_source.tex [171]) (./fixed_envelopes_8cpp_source.tex [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183] [184] [185]) (./fixed_envelopes_8h_source.tex [186] [187] [188]) (./iso_math_8cpp_source.tex [189] [190]) (./iso_math_8h_source.tex [191]) (./iso_spec_09_09_8cpp_source.tex [192] [193] [194] [195] [196] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [197] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200] [201] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [202]) (./iso_spec_09_09_8h_source.tex [203] [204] [205] [206] [207] [208]) (./marginal_trek_09_09_8cpp_source.tex [209] [210] [211] [212] [213] [214] [215] [216]) (./marginal_trek_09_09_8h_source.tex [217] [218] [219] [220]) (./misc_8cpp_source.tex [221]) (./misc_8h_source.tex [222] [223]) (./mman_8cpp_source.tex [224] [225]) (./mman_8h_source.tex [226]) (./operators_8cpp_source.tex [227]) (./operators_8h_source.tex [228] [229]) (./platform_8h_source.tex [230]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [231] [232] [233] [234] [235]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [236] [237]) (./unity-build_8cpp_source.tex) [238] (./refman.ind Underfull \hbox (badness 10000) in paragraph at lines 15--17 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/element_tables.cpp, Underfull \hbox (badness 10000) in paragraph at lines 30--32 []\T1/phv/m/n/10 /build/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp, [239] [240] [241] [242] [243] [244] Underfull \hbox (badness 870) in paragraph at lines 818--820 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , Underfull \hbox (badness 870) in paragraph at lines 830--832 []| \T1/phv/m/n/10 IsoSpec::OrderMarginalsBySizeDecresing$\OML/cmm/m/it/10 <$ \ T1/phv/m/n/10 T $\OML/cmm/m/it/10 >$\T1/phv/m/n/10 , [245] [246] [247]) (./refman.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on refman.pdf (263 pages, 1023315 bytes). Transcript written on refman.log. make[6]: Verzeichnis „/build/isospec-2.2.1/man/latex“ wird verlassen make[5]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen [100%] Built target pdf_doc make[4]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen /usr/bin/cmake -E cmake_progress_start /build/isospec-2.2.1/obj-i686-linux-gnu/CMakeFiles 0 make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen # sed-based replacement of the cloudflare URL with the MathJax.js file from the # libjs-mathjax package sh debian/replace-mathjax-cloudflare-url-local-file.sh # Recreate the symlink that was created by setup.py # and that we had to remove at the override_dh_clean target. ln -sf IsoSpec++ IsoSpecPy/IsoSpec++ # Install the Python module dh_auto_install -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=. install -m0755 -d /build/isospec-2.2.1/debian/tmp pybuild --install -i python{version} -p 3.11 --dest-dir /build/isospec-2.2.1/debian/tmp I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/isospec-2.2.1/debian/python3-isospec running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/IsoSpecPyOld.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/Advanced.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/Distributions.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/confs_passthrough.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/approximations.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/IsoSpecPy.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/__init__.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/Formulas.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/isoFFI.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/PeriodicTbl.py -> /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy running build_ext building 'IsoSpecCppPy' extension creating build creating build/temp.linux-i386-cpython-311 creating build/temp.linux-i386-cpython-311/IsoSpec++ i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/isospec-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.11 -c IsoSpec++/python-build.cpp -o build/temp.linux-i386-cpython-311/IsoSpec++/python-build.o -O3 -std=c++17 i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/isospec-2.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/IsoSpec++/python-build.o -L/usr/lib/i386-linux-gnu -o /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecCppPy.cpython-311-i386-linux-gnu.so running install_lib creating /build/isospec-2.2.1/debian/python3-isospec creating /build/isospec-2.2.1/debian/python3-isospec/usr creating /build/isospec-2.2.1/debian/python3-isospec/usr/lib creating /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11 creating /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecCppPy.cpython-311-i386-linux-gnu.so -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages creating /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/IsoSpecPyOld.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/Advanced.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/Distributions.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/confs_passthrough.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/approximations.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/IsoSpecPy.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/__init__.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/Formulas.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/isoFFI.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/PeriodicTbl.py -> /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/IsoSpecPyOld.py to IsoSpecPyOld.cpython-311.pyc byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/Advanced.py to Advanced.cpython-311.pyc byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/Distributions.py to Distributions.cpython-311.pyc byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/confs_passthrough.py to confs_passthrough.cpython-311.pyc byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/approximations.py to approximations.cpython-311.pyc byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/IsoSpecPy.py to IsoSpecPy.cpython-311.pyc byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/__init__.py to __init__.cpython-311.pyc byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/Formulas.py to Formulas.cpython-311.pyc byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/isoFFI.py to isoFFI.cpython-311.pyc byte-compiling /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/PeriodicTbl.py to PeriodicTbl.cpython-311.pyc running install_egg_info running egg_info creating IsoSpecPy.egg-info writing IsoSpecPy.egg-info/PKG-INFO writing dependency_links to IsoSpecPy.egg-info/dependency_links.txt writing requirements to IsoSpecPy.egg-info/requires.txt writing top-level names to IsoSpecPy.egg-info/top_level.txt writing manifest file 'IsoSpecPy.egg-info/SOURCES.txt' reading manifest file 'IsoSpecPy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'IsoSpecPy/*.dll' adding license file 'LICENCE' writing manifest file 'IsoSpecPy.egg-info/SOURCES.txt' Copying IsoSpecPy.egg-info to /build/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy-2.2.1.egg-info Skipping SOURCES.txt running install_scripts # Install the C++ library dh_auto_install -O--buildsystem=cmake install -m0755 -d /build/isospec-2.2.1/debian/tmp cd obj-i686-linux-gnu && make -j15 install DESTDIR=/build/isospec-2.2.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten /usr/bin/cmake -S/build/isospec-2.2.1 -B/build/isospec-2.2.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird betreten make[3]: Für das Ziel „preinstall“ ist nichts zu tun. make[3]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/isospec-2.2.1/debian/tmp/usr/lib/i386-linux-gnu/cmake/isospec++/FindIsoSpec++.cmake -- Installing: /build/isospec-2.2.1/debian/tmp/usr/lib/i386-linux-gnu/cmake/isospec++/IsoSpec++Config.cmake -- Installing: /build/isospec-2.2.1/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig/libisospec++.pc -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/logo2_high.pdf -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/logo2_long.pdf -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/isospec_logo2_long_versioned.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/isospec_logo2_high_versioned.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/isospec_logo2_long_versioned.svg -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/isospec_logo2_high_versioned.svg -- 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/build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_allocator.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_table_order-members.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/conf_8h_source.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/dirty_allocator_8h_source.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_marginal_trek.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/classunsafe__pod__vector.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/element__tables_8cpp_source.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/fasta_8cpp_source.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/operators_8cpp_source.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_marginal.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/struct_iso_spec_1_1_prob_and_conf_ptr.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/functions_func.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_stochastic_generator.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/classpod__vector-members.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_layered_generator.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_stochastic_generator.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/namespaces.html -- Installing: 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/build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_5.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_c.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_0.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_f.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_f.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/variables_3.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_7.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/variables_5.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_6.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_a.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_12.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_4.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_8.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/variables_6.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_3.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/search.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_11.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_e.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_8.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/mag_sel.svg -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_f.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_b.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_b.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_0.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/variables_6.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_c.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/namespaces_0.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_d.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_5.js -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_precalculated_marginal-members.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/open.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/sync_off.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_layered_marginal.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_threshold_generator-members.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_order_marginals_by_size_decresing.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/summator_8h_source.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/folderclosed.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/bdwn.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/folderopen.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_table_order.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_s_summator.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/doxygen.svg -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/tab_h.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_generator.png -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/marginal_trek_09_09_8cpp_source.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/namespace_iso_spec.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/misc_8h_source.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/marginal_trek_09_09_8h_source.html -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/pdf/refman.pdf -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_Allocator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ConfEqual.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ConfOrder.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_DirtyAllocator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_FixedEnvelope.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_Iso.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoGenerator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_KeyHasher.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_LayeredMarginal.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_Marginal.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_MarginalTrek.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ReverseOrder.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_SSummator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_Summator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_TSummator.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_TableOrder.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/pod_vector.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/unsafe_pod_vector.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/man/man3/ws_match_res.3 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/C++ -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/C++/radiolabelling.cpp -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/C++/water.cpp -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/C++/COMPILING -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python/radiolabelling.py -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python/water.py -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python/custom_elements.py -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python/fasta.py -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/R -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/R/water.R -- Installing: /build/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/R/radiolabelling.R -- Installing: /build/isospec-2.2.1/debian/tmp/usr/lib/i386-linux-gnu/libIsoSpec++.so.2.2.1 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/lib/i386-linux-gnu/libIsoSpec++.so.2 -- Installing: /build/isospec-2.2.1/debian/tmp/usr/lib/i386-linux-gnu/libIsoSpec++.a make[2]: Verzeichnis „/build/isospec-2.2.1/obj-i686-linux-gnu“ wird verlassen # Now remove the links, that we'll provide using d/*.links # So that we can use libIsoSpec++.so.* in d/*.install rm -f debian/tmp/usr/lib/*/libIsoSpec++.so rm -f debian/tmp/usr/lib/*/libIsoSpec++.so.2 make[1]: Verzeichnis „/build/isospec-2.2.1“ wird verlassen dh_install install -m0755 -d debian/libisospec\+\+-dev//usr/lib/i386-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/i386-linux-gnu/libIsoSpec\+\+.a debian/libisospec\+\+-dev//usr/lib/i386-linux-gnu/ install -m0755 -d debian/libisospec\+\+-dev//usr/lib/i386-linux-gnu/cmake cp --reflink=auto -a debian/tmp/usr/lib/i386-linux-gnu/cmake/isospec\+\+ debian/libisospec\+\+-dev//usr/lib/i386-linux-gnu/cmake/ install -m0755 -d debian/libisospec\+\+-dev//usr/lib/i386-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/i386-linux-gnu/pkgconfig/libisospec\+\+.pc debian/libisospec\+\+-dev//usr/lib/i386-linux-gnu/pkgconfig/ install -m0755 -d debian/libisospec\+\+-dev/usr/include/IsoSpec\+\+ cp --reflink=auto -a ./IsoSpec\+\+/allocator.h ./IsoSpec\+\+/btrd.h ./IsoSpec\+\+/conf.h ./IsoSpec\+\+/cwrapper.h ./IsoSpec\+\+/dirtyAllocator.h ./IsoSpec\+\+/element_tables.h ./IsoSpec\+\+/fasta.h ./IsoSpec\+\+/fixedEnvelopes.h ./IsoSpec\+\+/isoMath.h ./IsoSpec\+\+/isoSpec\+\+.h ./IsoSpec\+\+/marginalTrek\+\+.h ./IsoSpec\+\+/misc.h ./IsoSpec\+\+/mman.h ./IsoSpec\+\+/operators.h ./IsoSpec\+\+/platform.h ./IsoSpec\+\+/platform_incl.h ./IsoSpec\+\+/pod_vector.h ./IsoSpec\+\+/summator.h debian/libisospec\+\+-dev/usr/include/IsoSpec\+\+/ install -m0755 -d debian/libisospec\+\+2//usr/lib/i386-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so.2.2.1 debian/libisospec\+\+2//usr/lib/i386-linux-gnu/ install -m0755 -d debian/libisospec\+\+-doc//usr/share/doc cp --reflink=auto -a debian/tmp/usr/share/doc/isospec debian/libisospec\+\+-doc//usr/share/doc/ dh_installdocs install -m0755 -d debian/libisospec\+\+-dev/usr/share/doc/libisospec\+\+-dev install -p -m0644 debian/copyright debian/libisospec\+\+-dev/usr/share/doc/libisospec\+\+-dev/copyright install -m0755 -d debian/libisospec\+\+2/usr/share/doc/libisospec\+\+2 install -p -m0644 debian/copyright debian/libisospec\+\+2/usr/share/doc/libisospec\+\+2/copyright install -m0755 -d debian/python3-isospec/usr/share/doc/python3-isospec install -p -m0644 debian/copyright debian/python3-isospec/usr/share/doc/python3-isospec/copyright install -m0755 -d debian/libisospec\+\+-doc/usr/share/doc/libisospec\+\+-doc install -p -m0644 debian/copyright debian/libisospec\+\+-doc/usr/share/doc/libisospec\+\+-doc/copyright install -m0755 -d debian/libisospec\+\+-doc/usr/share/doc-base/ install -p -m0644 debian/libisospec\+\+-doc.doc-base debian/libisospec\+\+-doc/usr/share/doc-base/libisospec\+\+-doc.libisospec\+\+ dh_installchangelogs install -m0755 -d debian/libisospec\+\+2/usr/share/doc/libisospec\+\+2 install -p -m0644 debian/.debhelper/generated/libisospec\+\+2/dh_installchangelogs.dch.trimmed debian/libisospec\+\+2/usr/share/doc/libisospec\+\+2/changelog.Debian install -p -m0644 ./CHANGELOG debian/libisospec\+\+2/usr/share/doc/libisospec\+\+2/changelog install -m0755 -d debian/libisospec\+\+-dev/usr/share/doc/libisospec\+\+-dev install -p -m0644 debian/.debhelper/generated/libisospec\+\+-dev/dh_installchangelogs.dch.trimmed debian/libisospec\+\+-dev/usr/share/doc/libisospec\+\+-dev/changelog.Debian install -p -m0644 ./CHANGELOG debian/libisospec\+\+-dev/usr/share/doc/libisospec\+\+-dev/changelog install -m0755 -d debian/python3-isospec/usr/share/doc/python3-isospec install -p -m0644 debian/.debhelper/generated/python3-isospec/dh_installchangelogs.dch.trimmed debian/python3-isospec/usr/share/doc/python3-isospec/changelog.Debian install -p -m0644 ./CHANGELOG debian/python3-isospec/usr/share/doc/python3-isospec/changelog install -m0755 -d debian/libisospec\+\+-doc/usr/share/doc/libisospec\+\+-doc install -p -m0644 debian/.debhelper/generated/libisospec\+\+-doc/dh_installchangelogs.dch.trimmed debian/libisospec\+\+-doc/usr/share/doc/libisospec\+\+-doc/changelog.Debian install -p -m0644 ./CHANGELOG debian/libisospec\+\+-doc/usr/share/doc/libisospec\+\+-doc/changelog dh_installman install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_Allocator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Allocator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ConfEqual.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfEqual.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ConfOrder.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrder.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_DirtyAllocator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_DirtyAllocator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_FixedEnvelope.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_FixedEnvelope.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_Iso.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Iso.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_KeyHasher.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_KeyHasher.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_LayeredMarginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_LayeredMarginal.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_Marginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Marginal.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_MarginalTrek.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_MarginalTrek.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ReverseOrder.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ReverseOrder.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_SSummator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_SSummator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_Summator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Summator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_TableOrder.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TableOrder.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_TSummator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TSummator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/pod_vector.3 debian/libisospec\+\+-dev/usr/share/man/man3/pod_vector.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/unsafe_pod_vector.3 debian/libisospec\+\+-dev/usr/share/man/man3/unsafe_pod_vector.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/ws_match_res.3 debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Allocator.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfEqual.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrder.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_DirtyAllocator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_FixedEnvelope.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Iso.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoGenerator.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_KeyHasher.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_LayeredMarginal.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Marginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_MarginalTrek.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ReverseOrder.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_SSummator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Summator.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TSummator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TableOrder.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/pod_vector.3 debian/libisospec\+\+-dev/usr/share/man/man3/unsafe_pod_vector.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Allocator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Allocator.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Allocator.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_KeyHasher.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_KeyHasher.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_LayeredMarginal.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_LayeredMarginal.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_KeyHasher.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_LayeredMarginal.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_DirtyAllocator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_DirtyAllocator.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_FixedEnvelope.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_FixedEnvelope.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_DirtyAllocator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_FixedEnvelope.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ReverseOrder.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ReverseOrder.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ReverseOrder.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Iso.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Iso.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoGenerator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoGenerator.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Iso.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoGenerator.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfEqual.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfEqual.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrder.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrder.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfEqual.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrder.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Marginal.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Marginal.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_MarginalTrek.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_MarginalTrek.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Marginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_MarginalTrek.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_SSummator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_SSummator.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Summator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Summator.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_SSummator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Summator.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/pod_vector.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/pod_vector.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/unsafe_pod_vector.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/unsafe_pod_vector.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/pod_vector.3 debian/libisospec\+\+-dev/usr/share/man/man3/unsafe_pod_vector.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TSummator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TSummator.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TableOrder.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TableOrder.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TSummator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TableOrder.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 dh_python3 D: dh_python3 dh_python3:179: version: 5.20230130 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=None) D: dh_python3 dh_python3:182: supported Python versions: 3.11 (default=3.11) D: dh_python3 debhelper:175: skipping package libisospec++-dev (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:175: skipping package libisospec++2 (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:175: skipping package libisospec++-doc (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:183: source=isospec, binary packages=['python3-isospec'] D: dh_python3 dh_python3:204: processing package python3-isospec... D: dh_python3 fs:52: moving files from debian/python3-isospec/usr/lib/python3.11/dist-packages to debian/python3-isospec/usr/lib/python3/dist-packages/ D: dh_python3 fs:400: package python3-isospec details = {'requires.txt': {'debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecPy-2.2.1.egg-info/requires.txt'}, 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.11')}, 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package python3-isospec D: dh_python3 pydist:173: trying to find dependency for cffi (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:218: dependency: requirement already has hardcoded version D: dh_python3 depends:281: D={'python3 (<< 3.12)', 'python3:any', 'python3-cffi-backend-api-min (<= 9729), python3-cffi-backend-api-max (>= 9729)', 'python3 (>= 3.11~)'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_perl dh_link install -m0755 -d debian/libisospec\+\+-dev/usr/lib/i386-linux-gnu rm -f debian/libisospec\+\+-dev/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so ln -s libIsoSpec\+\+.so.2.2.1 debian/libisospec\+\+-dev/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so install -m0755 -d debian/libisospec\+\+2/usr/lib/i386-linux-gnu rm -f debian/libisospec\+\+2/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so.2 ln -s libIsoSpec\+\+.so.2.2.1 debian/libisospec\+\+2/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so.2 dh_strip_nondeterminism Using 1668287129 as canonical time Normalizing debian/libisospec++-doc/usr/share/doc/isospec/images/isospec_logo2_long_versioned.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/images/isospec_logo2_high_versioned.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/sync_on.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_marginal_trek.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_layered_generator.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_stochastic_generator.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_threshold_generator.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/nav_h.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/bc_s.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/closed.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_iso.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_ordered_generator.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/tab_s.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/isospec_logo2_high_versioned.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_marginal.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/nav_g.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/tab_a.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_precalculated_marginal.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/nav_f.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/splitbar.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/tab_b.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/doc.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/open.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/sync_off.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_layered_marginal.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/folderclosed.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/bdwn.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/folderopen.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/tab_h.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_generator.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/search/search_r.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/search/search_m.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/search/search_l.png using File::StripNondeterminism::handlers::png dh_compress cd debian/libisospec++-dev cd debian/libisospec++2 cd debian/python3-isospec cd debian/libisospec++-doc chmod a-x usr/share/doc/libisospec\+\+2/changelog usr/share/doc/libisospec\+\+2/changelog.Debian chmod a-x usr/share/doc/python3-isospec/changelog usr/share/doc/python3-isospec/changelog.Debian gzip -9nf usr/share/doc/libisospec\+\+2/changelog usr/share/doc/libisospec\+\+2/changelog.Debian gzip -9nf usr/share/doc/python3-isospec/changelog usr/share/doc/python3-isospec/changelog.Debian cd '/build/isospec-2.2.1' cd '/build/isospec-2.2.1' chmod a-x usr/share/doc/libisospec\+\+-dev/changelog usr/share/doc/libisospec\+\+-dev/changelog.Debian usr/share/man/man3/IsoSpec.3 usr/share/man/man3/IsoSpec_Allocator.3 usr/share/man/man3/IsoSpec_ConfEqual.3 usr/share/man/man3/IsoSpec_ConfOrder.3 usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 usr/share/man/man3/IsoSpec_DirtyAllocator.3 usr/share/man/man3/IsoSpec_FixedEnvelope.3 usr/share/man/man3/IsoSpec_Iso.3 usr/share/man/man3/IsoSpec_IsoGenerator.3 usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 usr/share/man/man3/IsoSpec_KeyHasher.3 usr/share/man/man3/IsoSpec_LayeredMarginal.3 usr/share/man/man3/IsoSpec_Marginal.3 usr/share/man/man3/IsoSpec_MarginalTrek.3 usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 usr/share/man/man3/IsoSpec_ReverseOrder.3 usr/share/man/man3/IsoSpec_SSummator.3 usr/share/man/man3/IsoSpec_Summator.3 usr/share/man/man3/IsoSpec_TSummator.3 usr/share/man/man3/IsoSpec_TableOrder.3 usr/share/man/man3/pod_vector.3 usr/share/man/man3/unsafe_pod_vector.3 usr/share/man/man3/ws_match_res.3 gzip -9nf usr/share/doc/libisospec\+\+-dev/changelog usr/share/doc/libisospec\+\+-dev/changelog.Debian usr/share/man/man3/IsoSpec.3 usr/share/man/man3/IsoSpec_Allocator.3 usr/share/man/man3/IsoSpec_ConfEqual.3 usr/share/man/man3/IsoSpec_ConfOrder.3 usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 usr/share/man/man3/IsoSpec_DirtyAllocator.3 usr/share/man/man3/IsoSpec_FixedEnvelope.3 usr/share/man/man3/IsoSpec_Iso.3 usr/share/man/man3/IsoSpec_IsoGenerator.3 usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 usr/share/man/man3/IsoSpec_KeyHasher.3 usr/share/man/man3/IsoSpec_LayeredMarginal.3 usr/share/man/man3/IsoSpec_Marginal.3 usr/share/man/man3/IsoSpec_MarginalTrek.3 usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 usr/share/man/man3/IsoSpec_ReverseOrder.3 usr/share/man/man3/IsoSpec_SSummator.3 usr/share/man/man3/IsoSpec_Summator.3 usr/share/man/man3/IsoSpec_TSummator.3 usr/share/man/man3/IsoSpec_TableOrder.3 usr/share/man/man3/pod_vector.3 usr/share/man/man3/unsafe_pod_vector.3 usr/share/man/man3/ws_match_res.3 chmod a-x usr/share/doc/isospec/examples/C\+\+/water.cpp usr/share/doc/isospec/images/logo2_high.pdf usr/share/doc/isospec/images/logo2_long.pdf usr/share/doc/isospec/pdf/refman.pdf usr/share/doc/libisospec\+\+-doc/changelog usr/share/doc/libisospec\+\+-doc/changelog.Debian gzip -9nf usr/share/doc/isospec/examples/C\+\+/water.cpp usr/share/doc/isospec/images/logo2_high.pdf usr/share/doc/isospec/images/logo2_long.pdf usr/share/doc/isospec/pdf/refman.pdf usr/share/doc/libisospec\+\+-doc/changelog usr/share/doc/libisospec\+\+-doc/changelog.Debian cd '/build/isospec-2.2.1' cd '/build/isospec-2.2.1' dh_fixperms find debian/libisospec++-dev -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libisospec++2 -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/python3-isospec -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libisospec++-doc -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libisospec\+\+2 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-isospec ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libisospec\+\+-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libisospec\+\+2/usr/share/doc -type f -a -true -a ! -regex 'debian/libisospec++2/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-isospec/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-isospec/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libisospec\+\+2/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libisospec\+\+-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/libisospec++-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libisospec\+\+-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-isospec/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libisospec\+\+2 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libisospec\+\+-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-isospec -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libisospec\+\+2/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libisospec\+\+-dev/usr/share/man debian/libisospec\+\+-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-isospec/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libisospec\+\+-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libisospec\+\+-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/libisospec++-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libisospec\+\+-dev/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/libisospec\+\+-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libisospec\+\+-doc -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing dh_dwz -a dwz -- debian/libisospec\+\+2/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so.2.2.1 dwz -- debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-311-i386-linux-gnu.so dh_strip -a strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/libisospec\+\+-dev/usr/lib/i386-linux-gnu/libIsoSpec\+\+.a install -m0755 -d debian/.debhelper/libisospec\+\+2/dbgsym-root/usr/lib/debug/.build-id/82 objcopy --only-keep-debug --compress-debug-sections debian/libisospec\+\+2/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so.2.2.1 debian/.debhelper/libisospec\+\+2/dbgsym-root/usr/lib/debug/.build-id/82/a5f1170e94777698fa2002a10eb9a6a5e5e60d.debug install -m0755 -d debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/1e objcopy --only-keep-debug --compress-debug-sections debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-311-i386-linux-gnu.so debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/1e/5015a615cba794340005ede855392e7d45c140.debug chmod 0644 -- debian/.debhelper/libisospec\+\+2/dbgsym-root/usr/lib/debug/.build-id/82/a5f1170e94777698fa2002a10eb9a6a5e5e60d.debug chown 0:0 -- debian/.debhelper/libisospec\+\+2/dbgsym-root/usr/lib/debug/.build-id/82/a5f1170e94777698fa2002a10eb9a6a5e5e60d.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libisospec\+\+2/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so.2.2.1 chmod 0644 -- debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/1e/5015a615cba794340005ede855392e7d45c140.debug chown 0:0 -- debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/1e/5015a615cba794340005ede855392e7d45c140.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-311-i386-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/libisospec\+\+2/dbgsym-root/usr/lib/debug/.build-id/82/a5f1170e94777698fa2002a10eb9a6a5e5e60d.debug debian/libisospec\+\+2/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so.2.2.1 objcopy --add-gnu-debuglink debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/1e/5015a615cba794340005ede855392e7d45c140.debug debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-311-i386-linux-gnu.so install -m0755 -d debian/.debhelper/libisospec\+\+2/dbgsym-root/usr/share/doc ln -s libisospec\+\+2 debian/.debhelper/libisospec\+\+2/dbgsym-root/usr/share/doc/libisospec\+\+2-dbgsym install -m0755 -d debian/.debhelper/libisospec\+\+2 install -m0755 -d debian/.debhelper/python3-isospec/dbgsym-root/usr/share/doc ln -s python3-isospec debian/.debhelper/python3-isospec/dbgsym-root/usr/share/doc/python3-isospec-dbgsym install -m0755 -d debian/.debhelper/python3-isospec dh_makeshlibs -a rm -f debian/libisospec\+\+-dev/DEBIAN/shlibs rm -f debian/libisospec\+\+2/DEBIAN/shlibs install -m0755 -d debian/libisospec\+\+2/DEBIAN echo "libIsoSpec++ 2 libisospec++2 (>= 2.2.1)" >> debian/libisospec\+\+2/DEBIAN/shlibs chmod 0644 -- debian/libisospec\+\+2/DEBIAN/shlibs chown 0:0 -- debian/libisospec\+\+2/DEBIAN/shlibs mv debian/.debhelper/generated/libisospec\+\+2/triggers.new debian/.debhelper/generated/libisospec\+\+2/triggers rm -f debian/python3-isospec/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/libisospec\+\+2/DEBIAN dpkg-shlibdeps -Tdebian/libisospec\+\+2.substvars debian/libisospec\+\+2/usr/lib/i386-linux-gnu/libIsoSpec\+\+.so.2.2.1 install -m0755 -d debian/python3-isospec/DEBIAN dpkg-shlibdeps -Tdebian/python3-isospec.substvars debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-311-i386-linux-gnu.so dh_installdeb install -m0755 -d debian/libisospec\+\+-dev/DEBIAN install -m0755 -d debian/libisospec\+\+2/DEBIAN install -p -m0644 debian/.debhelper/generated/libisospec\+\+2/triggers debian/libisospec\+\+2/DEBIAN/triggers install -m0755 -d debian/python3-isospec/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-isospec/DEBIAN/postinst cat debian/python3-isospec.postinst.debhelper >> debian/python3-isospec/DEBIAN/postinst chmod 0755 -- debian/python3-isospec/DEBIAN/postinst chown 0:0 -- debian/python3-isospec/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-isospec/DEBIAN/prerm cat debian/python3-isospec.prerm.debhelper >> debian/python3-isospec/DEBIAN/prerm chmod 0755 -- debian/python3-isospec/DEBIAN/prerm chown 0:0 -- debian/python3-isospec/DEBIAN/prerm install -m0755 -d debian/libisospec\+\+-doc/DEBIAN dh_gencontrol install -m0755 -d debian/libisospec\+\+-dev/DEBIAN echo misc:Depends= >> debian/libisospec++-dev.substvars echo misc:Pre-Depends= >> debian/libisospec++-dev.substvars dpkg-gencontrol -plibisospec\+\+-dev -ldebian/changelog -Tdebian/libisospec\+\+-dev.substvars -Pdebian/libisospec\+\+-dev install -m0755 -d debian/libisospec\+\+-doc/DEBIAN echo misc:Depends= >> debian/libisospec++-doc.substvars echo misc:Pre-Depends= >> debian/libisospec++-doc.substvars dpkg-gencontrol -plibisospec\+\+-doc -ldebian/changelog -Tdebian/libisospec\+\+-doc.substvars -Pdebian/libisospec\+\+-doc install -m0755 -d debian/python3-isospec/DEBIAN echo misc:Depends= >> debian/python3-isospec.substvars echo misc:Pre-Depends= >> debian/python3-isospec.substvars install -m0755 -d debian/.debhelper/python3-isospec/dbgsym-root/DEBIAN dpkg-gencontrol -ppython3-isospec -ldebian/changelog -Tdebian/python3-isospec.substvars -Pdebian/.debhelper/python3-isospec/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=python3-isospec-dbgsym "-DDepends=python3-isospec (= \${binary:Version})" "-DDescription=debug symbols for python3-isospec" -DBuild-Ids=1e5015a615cba794340005ede855392e7d45c140 -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/libisospec\+\+2/DEBIAN echo misc:Depends= >> debian/libisospec++2.substvars echo misc:Pre-Depends= >> debian/libisospec++2.substvars install -m0755 -d debian/.debhelper/libisospec\+\+2/dbgsym-root/DEBIAN dpkg-gencontrol -plibisospec\+\+2 -ldebian/changelog -Tdebian/libisospec\+\+2.substvars -Pdebian/.debhelper/libisospec\+\+2/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=libisospec\+\+2-dbgsym "-DDepends=libisospec++2 (= \${binary:Version})" "-DDescription=debug symbols for libisospec++2" -DBuild-Ids=82a5f1170e94777698fa2002a10eb9a6a5e5e60d -DSection=debug -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/libisospec\+\+2/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/libisospec\+\+2/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibisospec\+\+2 -ldebian/changelog -Tdebian/libisospec\+\+2.substvars -Pdebian/libisospec\+\+2 chmod 0644 -- debian/.debhelper/python3-isospec/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/python3-isospec/dbgsym-root/DEBIAN/control dpkg-gencontrol -ppython3-isospec -ldebian/changelog -Tdebian/python3-isospec.substvars -Pdebian/python3-isospec chmod 0644 -- debian/libisospec\+\+-dev/DEBIAN/control chown 0:0 -- debian/libisospec\+\+-dev/DEBIAN/control chmod 0644 -- debian/libisospec\+\+-doc/DEBIAN/control chown 0:0 -- debian/libisospec\+\+-doc/DEBIAN/control chmod 0644 -- debian/libisospec\+\+2/DEBIAN/control chown 0:0 -- debian/libisospec\+\+2/DEBIAN/control chmod 0644 -- debian/python3-isospec/DEBIAN/control chown 0:0 -- debian/python3-isospec/DEBIAN/control dh_md5sums install -m0755 -d debian/python3-isospec/DEBIAN install -m0755 -d debian/libisospec\+\+2/DEBIAN install -m0755 -d debian/libisospec\+\+-dev/DEBIAN install -m0755 -d debian/libisospec\+\+-doc/DEBIAN cd debian/libisospec++2 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/python3-isospec >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libisospec++-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libisospec++-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libisospec\+\+2/DEBIAN/md5sums chown 0:0 -- debian/libisospec\+\+2/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libisospec\+\+2/dbgsym-root/DEBIAN chmod 0644 -- debian/python3-isospec/DEBIAN/md5sums chown 0:0 -- debian/python3-isospec/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-isospec/dbgsym-root/DEBIAN chmod 0644 -- debian/libisospec\+\+-dev/DEBIAN/md5sums chown 0:0 -- debian/libisospec\+\+-dev/DEBIAN/md5sums cd debian/.debhelper/libisospec++2/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/python3-isospec/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/libisospec\+\+2/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/libisospec\+\+2/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-isospec/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/python3-isospec/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/libisospec\+\+-doc/DEBIAN/md5sums chown 0:0 -- debian/libisospec\+\+-doc/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/libisospec\+\+-dev .. dpkg-deb --build debian/libisospec\+\+2 .. dpkg-deb --root-owner-group --build debian/.debhelper/libisospec\+\+2/dbgsym-root .. dpkg-deb --build debian/python3-isospec .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-isospec/dbgsym-root .. dpkg-deb --build debian/libisospec\+\+-doc .. dpkg-deb: Paket »libisospec++-dev« wird in »../libisospec++-dev_2.2.1-1_i386.deb« gebaut. dpkg-deb: Paket »libisospec++2-dbgsym« wird in »../libisospec++2-dbgsym_2.2.1-1_i386.deb« gebaut. dpkg-deb: Paket »libisospec++2« wird in »../libisospec++2_2.2.1-1_i386.deb« gebaut. dpkg-deb: Paket »python3-isospec-dbgsym« wird in »../python3-isospec-dbgsym_2.2.1-1_i386.deb« gebaut. dpkg-deb: Paket »python3-isospec« wird in »../python3-isospec_2.2.1-1_i386.deb« gebaut. dpkg-deb: Paket »libisospec++-doc« wird in »../libisospec++-doc_2.2.1-1_all.deb« gebaut. dpkg-genbuildinfo --build=binary -O../isospec_2.2.1-1_i386.buildinfo dpkg-genchanges --build=binary -O../isospec_2.2.1-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/44200/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/44200/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/44200 and its subdirectories I: Current time: Tue May 21 09:21:55 +14 2024 I: pbuilder-time-stamp: 1716232915