I: pbuilder: network access will be disabled during build I: Current time: Sat Dec 14 00:22:05 +14 2024 I: pbuilder-time-stamp: 1734085325 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [isospec_2.2.1-4.1.dsc] I: copying [./isospec_2.2.1.orig.tar.gz] I: copying [./isospec_2.2.1-4.1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Feb 28 11:51:10 2024 gpgv: using RSA key E3DE869822F99B6CBC35F279BF7DB622B303AC8B gpgv: issuer "slyon@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./isospec_2.2.1-4.1.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_2.2.1-4.1.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/3091672/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. 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 Dec 13 10:22 /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/3091672/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3091672/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=f05baacc807745e28309826c942a69b9 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-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=3091672 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.awAk1Smz/pbuilderrc_gTPp --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.awAk1Smz/b2 --logfile b2/build.log isospec_2.2.1-4.1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3091672/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: amd64 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: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), dh-exec, graphicsmagick-imagemagick-compat, cmake, d-shlibs, 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 ... 19965 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; 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; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; 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-dejavu-mono{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} libapache-pom-java{a} libarchive-zip-perl{a} libarchive13t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libbrotli1{a} libcairo2{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl4t64{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libgif7{a} libglib2.0-0t64{a} libgraphicsmagick-q16-3t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libhwy1t64{a} libice6{a} libicu72{a} libidn12{a} libijs-0.35{a} libimath-3-1-29t64{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp26{a} libjxl0.9{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm19{a} libmagic-mgc{a} libmagic1t64{a} libmpfi0{a} libnghttp2-14{a} libnsl2{a} libopenexr-3-1-30{a} libopenjp2-7{a} libpaper-utils{a} libpaper1{a} libpdfbox-java{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libpsl5t64{a} libptexenc1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libwebp7{a} libwebpmux3{a} libwmflite-0.2-7{a} libx11-6{a} libx11-data{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} libxt6t64{a} libz3-4{a} libzzip-0-13t64{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python3{a} python3-autocommand{a} python3-cffi{a} python3-cffi-backend{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-ply{a} python3-pycparser{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{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} tzdata{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 krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libspreadsheet-parseexcel-perl libx11-protocol-perl linux-sysctl-defaults 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, 204 newly installed, 0 to remove and 0 not upgraded. Need to get 292 MB of archives. After unpacking 1081 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.8-1 [815 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.8-1 [2163 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-4 [256 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.8-1 [1970 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.8-1 [677 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0045 [45.2 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.30.5-1 [2223 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.30.5-1 [11.4 MB] Get: 59 http://deb.debian.org/debian trixie/main amd64 d-shlibs all 0.108 [11.0 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 66 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 dh-exec amd64 0.30 [25.6 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 79 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.5-1 [26.0 MB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libclang-cpp19 amd64 1:19.1.5-1 [13.2 MB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libclang1-19 amd64 1:19.1.5-1 [7615 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 doxygen amd64 1.9.8+ds-2+b3 [5011 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libfontenc1 amd64 1:1.1.8-1+b1 [23.3 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 101 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libgs-common all 10.04.0~dfsg-2 [148 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libgs10-common all 10.04.0~dfsg-2 [475 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-15 [112 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-15 [44.1 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.15.90-1 [176 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-15 [48.1 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2 [251 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libidn12 amd64 1.42-2+b1 [81.4 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libijs-0.35 amd64 0.35-15.1+b2 [15.2 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libjbig2dec0 amd64 0.20-1+b3 [65.1 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 libgs10 amd64 10.04.0~dfsg-2 [2562 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 ghostscript amd64 10.04.0~dfsg-2 [50.6 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.19.3-1 [11.2 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.19.3-1 [15.0 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.19.3-1 [489 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libhwy1t64 amd64 1.2.0-2+b1 [676 kB] Get: 142 http://deb.debian.org/debian trixie/main amd64 libimath-3-1-29t64 amd64 3.1.12-1+b1 [42.0 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 libopenexr-3-1-30 amd64 3.1.5-5.1+b3 [934 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libjxl0.9 amd64 0.9.2-10+b1 [1052 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 146 http://deb.debian.org/debian trixie/main amd64 libwmflite-0.2-7 amd64 0.2.13-1.1+b3 [75.6 kB] Get: 147 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libgraphicsmagick-q16-3t64 amd64 1.4+really1.3.45-1+b1 [1229 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 graphicsmagick amd64 1.4+really1.3.45-1+b1 [1080 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 graphicsmagick-imagemagick-compat all 1.4+really1.3.45-1 [22.1 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 152 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.3-2 [1501 kB] Get: 162 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.1.0-1 [478 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 165 http://deb.debian.org/debian trixie/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5 [157 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get: 170 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 171 http://deb.debian.org/debian trixie/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5 [49.1 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.8-1 [2151 kB] Get: 175 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.8-1 [5136 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 178 http://deb.debian.org/debian trixie/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5 [62.7 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5 [114 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 libxmu6 amd64 2:1.1.3-3+b3 [58.8 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get: 186 http://deb.debian.org/debian trixie/main amd64 tex-common all 6.18 [32.5 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 preview-latex-style all 13.2-1 [350 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 python3-cffi-backend amd64 1.17.1-2+b1 [96.2 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 python3-ply all 3.11-7 [62.6 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 python3-pycparser all 2.22-2 [78.0 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 python3-cffi all 1.17.1-2 [89.4 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.8-1 [505 kB] Get: 193 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 194 http://deb.debian.org/debian trixie/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-5 [8492 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 texlive-base all 2024.20241115-1 [22.7 MB] Get: 198 http://deb.debian.org/debian trixie/main amd64 texlive-font-utils all 2024.20241115-1 [6980 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 texlive-fonts-recommended all 2024.20241115-1 [4991 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get: 201 http://deb.debian.org/debian trixie/main amd64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 203 http://deb.debian.org/debian trixie/main amd64 texlive-latex-extra all 2024.20241115-1 [24.6 MB] Get: 204 http://deb.debian.org/debian trixie/main amd64 texlive-plain-generic all 2024.20241115-1 [28.6 MB] Fetched 292 MB in 15s (20.0 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 ... 19965 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 libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.8-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-1_amd64.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:amd64 (3.12.8-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-1) ... 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 ... 20819 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... 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Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... 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Setting up python3.12 (3.12.8-1) ... Setting up debhelper (13.20) ... Setting up dh-exec (0.30) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3.12t64:amd64 (3.12.8-1) ... Setting up texlive-binaries (2024.20240313.70630+ds-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 texlive-base (2024.20241115-1) ... 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 libpython3-stdlib:amd64 (3.12.6-1) ... Setting up libgs10-common (10.04.0~dfsg-2) ... 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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... fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/3091672/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/3091672/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/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_2.2.1-4.1_source.changes dpkg-buildpackage: info: source package isospec dpkg-buildpackage: info: source version 2.2.1-4.1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Lukas Märdian dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 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 -j20 clean make[1]: Entering directory '/build/reproducible-path/isospec-2.2.1' rm -rf IsoSpecPy.egg-info build dist make[1]: Leaving directory '/build/reproducible-path/isospec-2.2.1' debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/isospec-2.2.1' dpkg-query: no packages found matching r-base-dev dpkg-query: no packages found matching r-base-core rm -rf obj-x86_64-linux-gnu rm -rf build rm -f compile_commands.json rm -rf .pc rm -rf IsoSpecPy.egg-info # 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\+\+2t64.substvars debian/python3-isospec.substvars debian/libisospec\+\+-doc.substvars debian/files rm -fr -- debian/libisospec\+\+-dev/ debian/tmp/ debian/libisospec\+\+2t64/ 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 \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) make[1]: Leaving directory '/build/reproducible-path/isospec-2.2.1' 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]: Entering directory '/build/reproducible-path/isospec-2.2.1' dpkg-query: no packages found matching r-base-dev dpkg-query: no packages found matching r-base-core dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 .. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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/reproducible-path/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/reproducible-path/isospec-2.2.1/obj-x86_64-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). gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb). -- 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 (6.7s) -- Generating done (0.0s) 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/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-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/reproducible-path/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/reproducible-path/isospec-2.2.1/obj-x86_64-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). gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb). -- 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 (3.3s) -- Generating done (0.0s) -- Build files have been written to: /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=. pybuild --configure -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py config running config dh override_dh_auto_configure --with python3 make[1]: Leaving directory '/build/reproducible-path/isospec-2.2.1' rm -f debian/libisospec\+\+-dev.debhelper.log debian/libisospec\+\+-doc.debhelper.log debian/libisospec\+\+2t64.debhelper.log debian/python3-isospec.debhelper.log debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/isospec-2.2.1' dpkg-query: no packages found matching r-base-dev dpkg-query: no packages found matching r-base-core dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=. pybuild --configure -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py config running config dh_auto_build -O--buildsystem=cmake -O--system=distutils --sourcedirectory=. cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/depend cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [ 25%] Building CXX object IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ && /usr/bin/c++ -DIsoSpec___shared_EXPORTS -I/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ -I/build/reproducible-path/isospec-2.2.1/IsoSpec++ -g -O2 -ffile-prefix-map=/build/reproducible-path/isospec-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++17 -fPIC -Wno-unknown-pragmas -Wall -Wextra -pedantic -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/reproducible-path/isospec-2.2.1/IsoSpec++/unity-build.cpp make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [ 50%] Building CXX object IsoSpec++/CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ && /usr/bin/c++ -I/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ -I/build/reproducible-path/isospec-2.2.1/IsoSpec++ -g -O2 -ffile-prefix-map=/build/reproducible-path/isospec-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++17 -Wno-unknown-pragmas -Wall -Wextra -pedantic -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/reproducible-path/isospec-2.2.1/IsoSpec++/unity-build.cpp In file included from /build/reproducible-path/isospec-2.2.1/IsoSpec++/unity-build.cpp:30: /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp: In constructor ‘IsoSpec::Iso::Iso()’: /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp:53:25: warning: allocation of insufficient size ‘0’ for type ‘int’ with size ‘4’ [-Walloc-size] 53 | isotopeNumbers(new int[0]), | ^ /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp:54:21: warning: allocation of insufficient size ‘0’ for type ‘int’ with size ‘4’ [-Walloc-size] 54 | atomCounts(new int[0]), | ^ /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp:57:26: warning: allocation of insufficient size ‘0’ for type ‘IsoSpec::Marginal*’ with size ‘8’ [-Walloc-size] 57 | marginals(new Marginal*[0]) | ^ In file included from /build/reproducible-path/isospec-2.2.1/IsoSpec++/unity-build.cpp:30: /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp: In constructor ‘IsoSpec::Iso::Iso()’: /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp:53:25: warning: allocation of insufficient size ‘0’ for type ‘int’ with size ‘4’ [-Walloc-size] 53 | isotopeNumbers(new int[0]), | ^ /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp:54:21: warning: allocation of insufficient size ‘0’ for type ‘int’ with size ‘4’ [-Walloc-size] 54 | atomCounts(new int[0]), | ^ /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp:57:26: warning: allocation of insufficient size ‘0’ for type ‘IsoSpec::Marginal*’ with size ‘8’ [-Walloc-size] 57 | marginals(new Marginal*[0]) | ^ [ 75%] Linking CXX static library libIsoSpec++.a cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ && /usr/bin/cmake -P CMakeFiles/IsoSpec++-static.dir/cmake_clean_target.cmake cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-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 make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [ 75%] Built target IsoSpec++-static [100%] Linking CXX shared library libIsoSpec++.so cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ && /usr/bin/cmake -E cmake_link_script CMakeFiles/IsoSpec++-shared.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/isospec-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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" cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ && /usr/bin/cmake -E cmake_symlink_library libIsoSpec++.so.2.2.1 libIsoSpec++.so.2 libIsoSpec++.so make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [100%] Built target IsoSpec++-shared make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-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/reproducible-path/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/reproducible-path/isospec-2.2.1/obj-x86_64-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). gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb). -- 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 (2.7s) -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/depend make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/depend cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/DependInfo.cmake "--color=" Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o.d" is newer than depends file "/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target IsoSpec++-static make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o.d" is newer than depends file "/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/compiler_depend.internal". make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build'. make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' Consolidate compiler generated dependencies of target IsoSpec++-shared make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build'. make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [ 50%] Built target IsoSpec++-static [100%] Built target IsoSpec++-shared make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-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/reproducible-path/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/reproducible-path/isospec-2.2.1/obj-x86_64-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). gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb). -- 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 (2.5s) -- Generating done (0.1s) -- Build files have been written to: /build/reproducible-path/isospec-2.2.1/obj-x86_64-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-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" html_doc VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 html_doc make[3]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 1 make -f CMakeFiles/Makefile2 man/CMakeFiles/html_doc.dir/all make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/depend make[5]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/man /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/man /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/man/CMakeFiles/html_doc.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/build make[5]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [100%] Doxygen-based developer html documentation generation cd /build/reproducible-path/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 'HTML_TIMESTAMP' at line 1256 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 'FORMULA_TRANSPARENT' at line 1545 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 'LATEX_TIMESTAMP' at line 1849 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" warning: Tag 'DOT_FONTNAME' at line 2257 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 'DOT_FONTSIZE' at line 2264 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 'DOT_TRANSPARENT' at line 2488 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: 1.9.8 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/reproducible-path/isospec-2.2.1/IsoSpec++ Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.h... Parsing file /build//build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h:33: warning: Compound IsoSpec::Allocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:53: warning: Compound IsoSpec::ConfEqual is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:75: warning: Compound IsoSpec::ConfOrder is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:87: warning: Compound IsoSpec::ConfOrderMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:102: warning: Compound IsoSpec::ConfOrderMarginalDescending is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:25: warning: Compound IsoSpec::DirtyAllocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:40: warning: Compound IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:439: warning: Compound IsoSpec::IsoLayeredGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:542: warning: Compound IsoSpec::IsoStochasticGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:28: warning: Compound IsoSpec::KeyHasher is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:141: warning: Compound IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:24: warning: Compound IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:117: warning: Compound IsoSpec::ReverseOrder is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:26: warning: Compound IsoSpec::SSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:76: warning: Compound IsoSpec::Summator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:99: warning: Compound IsoSpec::TSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:124: warning: Compound IsoSpec::TableOrder is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:32: warning: Compound pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h:146: warning: Compound ws_match_res is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command reproducible-path/isospec-2.2.1/IsoSpec++/mman.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/python-build.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/python-build.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/unity-build.cpp... Parsing file /build/reproducible-path/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... Associating documentation with modules... 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... Computing module relations... 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/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.cpp... Gene/build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:194: warning: Member iterator (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:195: warning: Member const_iterator (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:196: warning: Member value_type (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:197: warning: Member size_type (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:198: warning: Member reference (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:199: warning: Member const_reference (typedef) of class pod_vector is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:94: warning: Member reserve(size_t n) (function) of class pod_vector is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:149: warning: Member size() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:154: warning: Member capacity() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:159: warning: Member data() noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:164: warning: Member data() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:169: warning: Member empty() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:174: warning: Member back() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:180: warning: Member pop_back() noexcept (function) of class pod_vector is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:201: warning: Member begin() noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:202: warning: Member begin() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:203: warning: Member cbegin() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:204: warning: Member end() noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:205: warning: Member end() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:206: warning: Member cend() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:208: warning: Member front() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:214: warning: Member clear() (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:372: warning: Member iterator (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:373: warning: Member const_iterator (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:374: warning: Member value_type (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:375: warning: Member size_type (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:376: warning: Member reference (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:377: warning: Member const_reference (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:234: warning: Member init() (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:327: warning: Member size() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:332: warning: Member capacity() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:337: warning: Member data() noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:342: warning: Member data() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:347: warning: Member empty() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:352: warning: Member back() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:358: warning: Member pop_back() noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:379: warning: Member begin() noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:380: warning: Member begin() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:381: warning: Member cbegin() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:382: warning: Member end() noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:383: warning: Member end() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:384: warning: Member cend() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:386: warning: Member front() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:392: warning: Member clear() (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h:147: warning: Member res1 (variable) of struct ws_match_res is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h:148: warning: Member res2 (variable) of struct ws_match_res is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h:149: warning: Member flow (variable) of struct ws_match_res is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h:27: warning: Member RealType (typedef) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h:28: warning: Member IntType (typedef) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:22: warning: Member Conf (typedef) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:23: warning: Member release_g_lfact_table() (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:32: warning: Member alloc_lfact_table() (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:47: warning: Member RationalApproximation(double t) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:57: warning: Member NormalCDFInverse(double p) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:104: warning: Member LowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:131: warning: Member InverseLowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:150: warning: Member random_gen(random_dev()) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:151: warning: Member stdunif(0.0, 1.0) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:68: warning: Member InverseChiSquareCDF2(int k, double x) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:149: warning: Member get_loggamma_nominator(int x) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:156: warning: Member verify_atom_cnt(int atomCnt) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h:47: warning: Member getConf(void *conf) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h:54: warning: Member getLProb(void *conf) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h:94: warning: Member printVector(const std::vector< T > &vec) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h:133: warning: Member dealloc_table(T *tbl, int dim) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.cpp:26: warning: Member isospec_number_of_isotopic_entries (variable) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp:25: warning: Member aa_isotope_numbers[6] (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp:27: warning: Member aa_elem_masses[19] (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp:37: warning: Member aa_elem_nominal_masses[19] (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp:47: warning: Member aa_elem_probabilities[19] (variable) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:44: warning: Member g_lfact_table (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:102: warning: Member sqrt_pi (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:149: warning: Member random_dev (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:53: warning: Member pi (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:54: warning: Member logpi (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:73: warning: Member random_gen (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:74: warning: Member stdunif (variable) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h:48: warning: Member shiftTables() (function) of class IsoSpec::Allocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h:50: warning: Member newConf() (function) of class IsoSpec::Allocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h:60: warning: Member makeCopy(const T *conf) (function) of class IsoSpec::Allocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:59: warning: Member ConfEqual(int dim) (function) of class IsoSpec::ConfEqual is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:42: warning: Member shiftTables() (function) of class IsoSpec::DirtyAllocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:44: warning: Member newConf() (function) of class IsoSpec::DirtyAllocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:70: warning: Member FixedEnvelope(const FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:71: warning: Member FixedEnvelope(FixedEnvelope &&other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:82: warning: Member operator+(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:83: warning: Member operator*(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:85: warning: Member confs_no() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:86: warning: Member getAllDim() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:88: warning: Member masses() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:89: warning: Member probs() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:90: warning: Member confs() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:92: warning: Member release_masses() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:93: warning: Member release_probs() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:94: warning: Member release_confs() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:95: warning: Member release_everything() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:98: warning: Member mass(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:99: warning: Member prob(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:100: warning: Member conf(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:102: warning: Member sort_by_mass() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:103: warning: Member sort_by_prob() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:105: warning: Member get_total_prob() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:106: warning: Member scale(double factor) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:107: warning: Member normalize() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:108: warning: Member shift_mass(double shift) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:111: warning: Member empiric_average_mass() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:112: warning: Member empiric_variance() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:113: warning: Member empiric_stddev() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:115: warning: Member WassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:116: warning: Member OrientedWassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:172: warning: Member addConfILG(const GenType &generator) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:132: warning: Member store_conf(const T &generator) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:42: warning: Member _masses (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:43: warning: Member _probs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:44: warning: Member _confs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:45: warning: Member _confs_no (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:46: warning: Member allDim (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:47: warning: Member sorted_by_mass (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:48: warning: Member sorted_by_prob (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:49: warning: Member total_prob (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:50: warning: Member current_size (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:51: warning: Member tmasses (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:52: warning: Member tprobs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:53: warning: Member tconfs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:54: warning: Member allDimSizeofInt (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:110: warning: Found unknown command '\use_nominal_masses' /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:111: warning: Found unknown command '\add_water' /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:483: warning: Member get_currentLThreshold() const (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:499: warning: Member advanceToNextConfigurationWithinLayer() (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:534: warning: Member nextLayer(double offset) (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:555: warning: Member count() const (function) of class IsoSpec::IsoStochasticGenerator is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:34: warning: Member KeyHasher(int dim) (function) of class IsoSpec::KeyHasher is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:59: warning: found documented return type for IsoSpec::Marginal::Marginal that does not return anything /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:233: warning: Member conf_lprobs() const (function) of class IsoSpec::MarginalTrek is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:234: warning: Member conf_masses() const (function) of class IsoSpec::MarginalTrek is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:235: warning: Member confs() const (function) of class IsoSpec::MarginalTrek is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:146: warning: Member operator()(int m1, int m2) (function) of class IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:254: warning: Member configurations (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:255: warning: Member confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:256: warning: Member no_confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:257: warning: Member masses (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:258: warning: Member lProbs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:259: warning: Member probs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:260: warning: Member allocator (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:264: warning: found documented return type for IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal that does not return anything /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:30: warning: Member ProbAndConfPtr(double p, Conf c) (function) of struct IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:32: warning: Member operator<(const ProbAndConfPtr &other) const (function) of struct IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:27: warning: Member first (variable) of struct IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:28: warning: Member second (variable) of struct IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:35: warning: Member SSummator(const SSummator &other) (function) of class IsoSpec::SSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:39: warning: Member add(double x) (function) of class IsoSpec::SSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:61: warning: Member get() (function) of class IsoSpec::SSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:85: warning: Member add(double what) (function) of class IsoSpec::Summator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:93: warning: Member get() (function) of class IsoSpec::Summator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:128: warning: Member TableOrder(const T *_tbl) (function) of class IsoSpec::TableOrder is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:107: warning: Member add(double what) (function) of class IsoSpec::TSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:111: warning: Member get() (function) of class IsoSpec::TSummator is not documented. rating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/python-build.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h... Generating code for file /build/reproducible-path/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 module documentation... Generating namespace documentation... 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 topic index... Generating module index... Generating module member 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... type lookup cache used 3025/65536 hits=16502 misses=3117 symbol lookup cache used 2874/65536 hits=21953 misses=2874 finished... make[5]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [100%] Built target html_doc make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' dh_auto_build -O--buildsyste=cmake -- pdf_doc cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" pdf_doc VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 pdf_doc make[3]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 1 make -f CMakeFiles/Makefile2 man/CMakeFiles/pdf_doc.dir/all make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f man/CMakeFiles/pdf_doc.dir/build.make man/CMakeFiles/pdf_doc.dir/depend make[5]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/man /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/man /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/man/CMakeFiles/pdf_doc.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f man/CMakeFiles/pdf_doc.dir/build.make man/CMakeFiles/pdf_doc.dir/build make[5]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [100%] Doxygen-based developer pdf documentation generation cd /build/reproducible-path/isospec-2.2.1/man/latex && make make[6]: Entering directory '/build/reproducible-path/isospec-2.2.1/man/latex' make[6]: warning: jobserver unavailable: using -j1. 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LaTeX Warning: Reference `python-build_8cpp_source' on page 7 undefined on inpu t line 32. LaTeX Warning: Reference `summator_8h_source' on page 7 undefined on input line 33. LaTeX Warning: Reference `unity-build_8cpp_source' on page 7 undefined on input line 34. ) [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 (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [11] [12] [13] [14] [15] [16] [17] [18] Package longtable Warning: Column widths have changed (longtable) in table 5.1 on input line 663. [19] [20] 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[]_[][ ] [21] 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 ) [22] Chapter 6. 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[52]) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso _layered_generator.pdf> [53] [54] [55] Underfull \hbox (badness 10000) detected at line 177 [][][] [56] Underfull \hbox (badness 10000) in paragraph at lines 192--193 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer Underfull \hbox (badness 10000) in paragraph at lines 230--231 \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 236 [][][] Underfull \hbox (badness 10000) in paragraph at lines 251--252 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], [57] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) in paragraph at lines 282--283 \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 288 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex <./class_iso_spec_1_1_iso_ord ered_generator.pdf> [58] [59] [60] [61] Underfull \hbox (badness 10000) detected at line 188 [][][] Package longtable Warning: Column widths have changed (longtable) in table 6.4 on input line 213. ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 147--148 \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 153 [][][] [65] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) in paragraph at lines 217--218 \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 223 [][][] Underfull \hbox (badness 10000) in paragraph at lines 238--239 \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 244 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex <./class_iso_spec_1_1_iso_t hreshold_generator.pdf> [66] [67] [68] [69] Package longtable Warning: Column widths have changed (longtable) in table 6.5 on input line 173. 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(./allocator_8cpp_source.tex) (./allocator_8h_source.tex [117]) (./btrd_8h_source.tex [118] [119] [120]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [121] [122] [123] [124] 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), [125] 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)))); [126]) (./cwrapper_8h_source.tex [127] [128]) (./dirty_allocator_8cpp_source.tex [129]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [130] [131] [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]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [165] [166] [167] [168]) (./fasta_8h_source.tex [169]) (./fixed_envelopes_8cpp_source.tex [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183]) (./fixed_envelopes_8h_source.tex [184] [185] [186]) (./iso_math_8cpp_source.tex [187] [188]) (./iso_math_8h_source.tex [189]) (./iso_spec_09_09_8cpp_source.tex [190] [191] [192] [193] [194] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [195] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [196] [197] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200]) (./iso_spec_09_09_8h_source.tex [201] [202] [203] [204] [205] [206]) (./marginal_trek_09_09_8cpp_source.tex [207] [208] [209] [210] [211] [212] [213] [214]) (./marginal_trek_09_09_8h_source.tex [215] [216] [217] [218]) (./misc_8cpp_source.tex [219]) (./misc_8h_source.tex [220] [221]) (./mman_8cpp_source.tex [222] [223]) (./mman_8h_source.tex [224]) (./operators_8cpp_source.tex [225]) (./operators_8h_source.tex [226] [227]) (./platform_8h_source.tex [228]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [229] [230] [231] [232] [233]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [234] [235]) (./unity-build_8cpp_source.tex) [236] No file 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] Package longtable Warning: Column widths have changed (longtable) in table 5.1 on input line 663. [19] [20] 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[]_[][ ] [21] 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 ) [22] Chapter 6. (./class_iso_spec_1_1_allocator.tex [23]) (./class_iso_spec_1_1_conf_equal.tex [24]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [25]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [26]) (./class_iso_spec_1_1_dirty_allocator.tex [27]) (./class_iso_spec_1_1_fixed_envelope.tex [28] 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[] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [40] [41] [42] [43] [44] [45] [46] [47]) (./class_iso_spec_1_1_iso_generator.tex <./class_iso_spec_1_1_iso_generat or.pdf> [48] [49] [50] Underfull \hbox (badness 10000) detected at line 175 [][][] [51] Underfull \hbox (badness 10000) detected at line 206 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 211--212 []\T1/phv/m/n/10 Reimplemented in [], [], and []. 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[52]) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso _layered_generator.pdf> [53] [54] [55] Underfull \hbox (badness 10000) detected at line 177 [][][] [56] Underfull \hbox (badness 10000) in paragraph at lines 192--193 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer Underfull \hbox (badness 10000) in paragraph at lines 230--231 \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 236 [][][] Underfull \hbox (badness 10000) in paragraph at lines 251--252 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], [57] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) in paragraph at lines 282--283 \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 288 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex <./class_iso_spec_1_1_iso_ord ered_generator.pdf> [58] [59] [60] [61] Underfull \hbox (badness 10000) detected at line 188 [][][] ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 147--148 \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 153 [][][] [65] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) in paragraph at lines 217--218 \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 223 [][][] Underfull \hbox (badness 10000) in paragraph at lines 238--239 \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 244 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex <./class_iso_spec_1_1_iso_t hreshold_generator.pdf> [66] [67] [68] [69] Overfull \hbox (18.89209pt too wide) in paragraph at lines 195--196 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) in paragraph at lines 244--245 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) in paragraph at lines 265--266 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) in paragraph at lines 286--287 \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 292 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex) (./class_iso_spec_1_1_layered_marginal.tex [72] <./class_iso_spec_1_1_layered_marginal.pdf> [73] [74] Overfull \vbox (7.19118pt too high) has occurred while \output is active [75] Underfull \hbox (badness 10000) detected at line 168 [][][] [76] Underfull \hbox (badness 10000) detected at line 297 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [77] [78] Underfull \hbox (badness 10000) detected at line 119 [][][] [79] Underfull \hbox 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(./class_iso_spec_1_1_precalculated_marginal.tex <./class_iso_spec_1_1_pr ecalculated_marginal.pdf> [96] [97] [98] Underfull \hbox (badness 10000) detected at line 167 [][][] [99] Underfull \hbox (badness 10000) detected at line 206 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 245 [][][] [100] Underfull \hbox (badness 10000) detected at line 267 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] [101] Underfull \hbox (badness 10000) detected at line 323 [][][] Underfull \hbox (badness 10000) detected at line 340 [][][] Underfull \hbox (badness 10000) detected at line 357 [][][] [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]) (./structws__match__res.tex [115]) [116] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [117]) (./btrd_8h_source.tex [118] [119] [120]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [121] [122] [123] [124] 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), [125] Overfull \hbox (40.35553pt too wide) in 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[187] [188]) (./iso_math_8h_source.tex [189]) (./iso_spec_09_09_8cpp_source.tex [190] [191] [192] [193] [194] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [195] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [196] [197] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200]) (./iso_spec_09_09_8h_source.tex [201] [202] [203] [204] [205] [206]) (./marginal_trek_09_09_8cpp_source.tex [207] [208] [209] [210] [211] [212] [213] [214]) (./marginal_trek_09_09_8h_source.tex [215] [216] [217] [218]) (./misc_8cpp_source.tex [219]) (./misc_8h_source.tex [220] [221]) (./mman_8cpp_source.tex [222] [223]) (./mman_8h_source.tex [224]) (./operators_8cpp_source.tex [225]) (./operators_8h_source.tex [226] [227]) (./platform_8h_source.tex [228]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [229] [230] [231] [232] [233]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [234] [235]) (./unity-build_8cpp_source.tex) [236] (./refman.ind Overfull \hbox (28.18492pt too wide) in paragraph at lines 3--5 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp , Overfull \hbox (18.68105pt too wide) in paragraph at lines 5--7 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h, Overfull \hbox (31.09198pt too wide) in paragraph at lines 11--13 []\T1/phv/m/n/10 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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) Output written on refman.pdf (262 pages, 1054820 bytes). Transcript written on refman.log. latex_count=8 ; \ while grep -E -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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[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] [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] 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[]_[][ ] [21] 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 ) [22] Chapter 6. (./class_iso_spec_1_1_allocator.tex [23]) (./class_iso_spec_1_1_conf_equal.tex [24]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [25]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [26]) (./class_iso_spec_1_1_dirty_allocator.tex [27]) (./class_iso_spec_1_1_fixed_envelope.tex [28] 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[] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [40] [41] [42] [43] [44] [45] [46] [47]) (./class_iso_spec_1_1_iso_generator.tex <./class_iso_spec_1_1_iso_generat or.pdf> [48] [49] [50] Underfull \hbox (badness 10000) detected at line 175 [][][] [51] Underfull \hbox (badness 10000) detected at line 206 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 211--212 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 227 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 232--233 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 248 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 253--254 []\T1/phv/m/n/10 Reimplemented in [], [], and []. [52]) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso _layered_generator.pdf> [53] [54] [55] Underfull \hbox (badness 10000) detected at line 177 [][][] [56] Underfull \hbox (badness 10000) in paragraph at lines 192--193 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer Underfull \hbox (badness 10000) in paragraph at lines 230--231 \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 236 [][][] Underfull \hbox (badness 10000) in paragraph at lines 251--252 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], [57] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) in paragraph at lines 282--283 \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 288 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex <./class_iso_spec_1_1_iso_ord ered_generator.pdf> [58] [59] [60] [61] Underfull \hbox (badness 10000) detected at line 188 [][][] ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 147--148 \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 153 [][][] [65] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) in paragraph at lines 217--218 \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 223 [][][] Underfull \hbox (badness 10000) in paragraph at lines 238--239 \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 244 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex <./class_iso_spec_1_1_iso_t hreshold_generator.pdf> [66] [67] [68] [69] Overfull \hbox (18.89209pt too wide) in paragraph at lines 195--196 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) in paragraph at lines 244--245 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) in paragraph at lines 265--266 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) in paragraph at lines 286--287 \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 292 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex) (./class_iso_spec_1_1_layered_marginal.tex [72] <./class_iso_spec_1_1_layered_marginal.pdf> [73] [74] Overfull \vbox (7.19118pt too high) has occurred while \output is active [75] Underfull \hbox (badness 10000) detected at line 168 [][][] [76] Underfull \hbox (badness 10000) detected at line 297 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [77] [78] Underfull \hbox (badness 10000) detected at line 119 [][][] [79] Underfull \hbox 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(./class_iso_spec_1_1_precalculated_marginal.tex <./class_iso_spec_1_1_pr ecalculated_marginal.pdf> [96] [97] [98] Underfull \hbox (badness 10000) detected at line 167 [][][] [99] Underfull \hbox (badness 10000) detected at line 206 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 245 [][][] [100] Underfull \hbox (badness 10000) detected at line 267 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] [101] Underfull \hbox (badness 10000) detected at line 323 [][][] Underfull \hbox (badness 10000) detected at line 340 [][][] Underfull \hbox (badness 10000) detected at line 357 [][][] [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]) (./structws__match__res.tex [115]) [116] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [117]) (./btrd_8h_source.tex [118] [119] [120]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [121] [122] [123] [124] 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), [125] 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)))); [126]) (./cwrapper_8h_source.tex [127] [128]) (./dirty_allocator_8cpp_source.tex [129]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [130] [131] [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]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [165] [166] [167] [168]) (./fasta_8h_source.tex [169]) (./fixed_envelopes_8cpp_source.tex [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183]) (./fixed_envelopes_8h_source.tex [184] [185] [186]) (./iso_math_8cpp_source.tex [187] [188]) (./iso_math_8h_source.tex [189]) (./iso_spec_09_09_8cpp_source.tex [190] [191] [192] [193] [194] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [195] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [196] [197] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200]) (./iso_spec_09_09_8h_source.tex [201] [202] [203] [204] [205] [206]) (./marginal_trek_09_09_8cpp_source.tex [207] [208] [209] [210] [211] [212] [213] [214]) (./marginal_trek_09_09_8h_source.tex [215] [216] [217] [218]) (./misc_8cpp_source.tex [219]) (./misc_8h_source.tex [220] [221]) (./mman_8cpp_source.tex [222] [223]) (./mman_8h_source.tex [224]) (./operators_8cpp_source.tex [225]) (./operators_8h_source.tex [226] [227]) (./platform_8h_source.tex [228]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [229] [230] [231] [232] [233]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [234] [235]) (./unity-build_8cpp_source.tex) [236] (./refman.ind Overfull \hbox (28.18492pt too wide) in paragraph at lines 3--5 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp , Overfull \hbox (18.68105pt too wide) in paragraph at lines 5--7 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h, Overfull \hbox (31.09198pt too wide) in paragraph at lines 11--13 []\T1/phv/m/n/10 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wide) in paragraph at lines 29--31 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelope s.h, Overfull \hbox (26.13304pt too wide) in paragraph at lines 31--33 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp, Overfull \hbox (16.62917pt too wide) in paragraph at lines 33--35 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h, Overfull \hbox (37.14894pt too wide) in paragraph at lines 35--37 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp , Overfull \hbox (27.64507pt too wide) in paragraph at lines 37--39 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h, Overfull \hbox (56.56161pt too wide) in paragraph at lines 39--41 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek+ +.cpp, Overfull \hbox (47.05774pt too wide) in paragraph at lines 41--43 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek+ +.h, Overfull \hbox (19.62622pt too wide) in paragraph at lines 47--49 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp, Overfull \hbox (32.41495pt too wide) in paragraph at lines 51--53 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp , Overfull \hbox (22.91107pt too wide) in paragraph at lines 53--55 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h, Overfull \hbox (17.58307pt too wide) in paragraph at lines 55--57 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h, Overfull \hbox (36.08676pt too wide) in paragraph at lines 57--59 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl .h, Overfull \hbox (28.96791pt too wide) in paragraph at lines 59--61 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h, Overfull \hbox (24.67503pt too wide) in paragraph at lines 63--65 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h, Underfull \hbox (badness 10000) in paragraph at lines 65--67 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/unity- [237] [238] [239] [240] [241] [242] Underfull \hbox (badness 870) in paragraph at lines 842--844 []| \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 , [243] Underfull \hbox (badness 870) in paragraph at lines 856--858 []| \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 , [244] [245] [246]) (./refman.aux) ) (see the transcript file for additional information) Output written on refman.pdf (262 pages, 1054870 bytes). Transcript written on refman.log. makeindex refman.idx This is makeindex, version 2.17 [TeX Live 2025/dev] (kpathsea + Thai support). Scanning input file refman.idx....done (815 entries accepted, 0 rejected). Sorting entries.........done (8611 comparisons). Generating output file refman.ind....done (1125 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] [20] 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[]_[][ ] [21] 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 ) [22] Chapter 6. (./class_iso_spec_1_1_allocator.tex [23]) (./class_iso_spec_1_1_conf_equal.tex [24]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [25]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [26]) (./class_iso_spec_1_1_dirty_allocator.tex [27]) (./class_iso_spec_1_1_fixed_envelope.tex [28] 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[] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [40] [41] [42] [43] [44] [45] [46] [47]) (./class_iso_spec_1_1_iso_generator.tex <./class_iso_spec_1_1_iso_generat or.pdf> [48] [49] [50] Underfull \hbox (badness 10000) detected at line 175 [][][] [51] Underfull \hbox (badness 10000) detected at line 206 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 211--212 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 227 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 232--233 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 248 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 253--254 []\T1/phv/m/n/10 Reimplemented in [], [], and []. [52]) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso _layered_generator.pdf> [53] [54] [55] Underfull \hbox (badness 10000) detected at line 177 [][][] [56] Underfull \hbox (badness 10000) in paragraph at lines 192--193 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer Underfull \hbox (badness 10000) in paragraph at lines 230--231 \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 236 [][][] Underfull \hbox (badness 10000) in paragraph at lines 251--252 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], [57] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) in paragraph at lines 282--283 \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 288 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex <./class_iso_spec_1_1_iso_ord ered_generator.pdf> [58] [59] [60] [61] Underfull \hbox (badness 10000) detected at line 188 [][][] ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 147--148 \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 153 [][][] [65] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) in paragraph at lines 217--218 \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 223 [][][] Underfull \hbox (badness 10000) in paragraph at lines 238--239 \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 244 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex <./class_iso_spec_1_1_iso_t hreshold_generator.pdf> [66] [67] [68] [69] Overfull \hbox (18.89209pt too wide) in paragraph at lines 195--196 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) in paragraph at lines 244--245 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) in paragraph at lines 265--266 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) in paragraph at lines 286--287 \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 292 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex) (./class_iso_spec_1_1_layered_marginal.tex [72] <./class_iso_spec_1_1_layered_marginal.pdf> [73] [74] Overfull \vbox (7.19118pt too high) has occurred while \output is active [75] Underfull \hbox (badness 10000) detected at line 168 [][][] [76] Underfull \hbox (badness 10000) detected at line 297 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [77] [78] Underfull \hbox (badness 10000) detected at line 119 [][][] [79] Underfull \hbox 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(./class_iso_spec_1_1_precalculated_marginal.tex <./class_iso_spec_1_1_pr ecalculated_marginal.pdf> [96] [97] [98] Underfull \hbox (badness 10000) detected at line 167 [][][] [99] Underfull \hbox (badness 10000) detected at line 206 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 245 [][][] [100] Underfull \hbox (badness 10000) detected at line 267 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] [101] Underfull \hbox (badness 10000) detected at line 323 [][][] Underfull \hbox (badness 10000) detected at line 340 [][][] Underfull \hbox (badness 10000) detected at line 357 [][][] [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]) (./structws__match__res.tex [115]) [116] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [117]) (./btrd_8h_source.tex [118] [119] [120]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [121] [122] [123] [124] 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), [125] 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)))); [126]) (./cwrapper_8h_source.tex [127] [128]) (./dirty_allocator_8cpp_source.tex [129]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [130] [131] [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]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [165] [166] [167] [168]) (./fasta_8h_source.tex [169]) (./fixed_envelopes_8cpp_source.tex [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183]) (./fixed_envelopes_8h_source.tex [184] [185] [186]) (./iso_math_8cpp_source.tex [187] [188]) (./iso_math_8h_source.tex [189]) (./iso_spec_09_09_8cpp_source.tex [190] [191] [192] [193] [194] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [195] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [196] [197] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200]) (./iso_spec_09_09_8h_source.tex [201] [202] [203] [204] [205] [206]) (./marginal_trek_09_09_8cpp_source.tex [207] [208] [209] [210] [211] [212] [213] [214]) (./marginal_trek_09_09_8h_source.tex [215] [216] [217] [218]) (./misc_8cpp_source.tex [219]) (./misc_8h_source.tex [220] [221]) (./mman_8cpp_source.tex [222] [223]) (./mman_8h_source.tex [224]) (./operators_8cpp_source.tex [225]) (./operators_8h_source.tex [226] [227]) (./platform_8h_source.tex [228]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [229] [230] [231] [232] [233]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [234] [235]) (./unity-build_8cpp_source.tex) [236] (./refman.ind Overfull \hbox (28.18492pt too wide) in paragraph at lines 3--5 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp , Overfull \hbox (18.68105pt too wide) in paragraph at lines 5--7 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h, Overfull \hbox (31.09198pt too wide) in paragraph at lines 11--13 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.cpp, Overfull \hbox (21.5881pt too wide) in paragraph at lines 13--15 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h, Overfull \hbox (46.54446pt too wide) in paragraph at lines 15--17 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocato r.cpp, Overfull \hbox (37.04059pt too wide) in paragraph at lines 17--19 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocato r.h, Overfull \hbox (55.33754pt too wide) in paragraph at lines 19--21 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_table s.cpp, Overfull \hbox (45.83366pt too wide) in paragraph at lines 21--23 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_table s.h, Overfull \hbox (54.84283pt too wide) in paragraph at lines 27--29 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelope s.cpp, Overfull \hbox (45.33896pt too wide) in paragraph at lines 29--31 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelope s.h, Overfull \hbox (26.13304pt too wide) in paragraph at lines 31--33 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp, Overfull \hbox (16.62917pt too wide) in paragraph at lines 33--35 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h, Overfull \hbox (37.14894pt too wide) in paragraph at lines 35--37 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp , Overfull \hbox (27.64507pt too wide) in paragraph at lines 37--39 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h, Overfull \hbox (56.56161pt too wide) in paragraph at lines 39--41 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek+ +.cpp, Overfull \hbox (47.05774pt too wide) in paragraph at lines 41--43 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek+ +.h, Overfull \hbox (19.62622pt too wide) in paragraph at lines 47--49 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp, Overfull \hbox (32.41495pt too wide) in paragraph at lines 51--53 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp , Overfull \hbox (22.91107pt too wide) in paragraph at lines 53--55 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h, Overfull \hbox (17.58307pt too wide) in paragraph at lines 55--57 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h, Overfull \hbox (36.08676pt too wide) in paragraph at lines 57--59 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl .h, Overfull \hbox (28.96791pt too wide) in paragraph at lines 59--61 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h, Overfull \hbox (24.67503pt too wide) in paragraph at lines 63--65 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h, Underfull \hbox (badness 10000) in paragraph at lines 65--67 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/unity- [237] [238] [239] [240] [241] [242] Underfull \hbox (badness 870) in paragraph at lines 842--844 []| \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 , [243] Underfull \hbox (badness 870) in paragraph at lines 856--858 []| \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 , [244] [245] [246]) (./refman.aux) ) (see the transcript file for additional information) Output written on refman.pdf (262 pages, 1054870 bytes). Transcript written on refman.log. make[6]: Leaving directory '/build/reproducible-path/isospec-2.2.1/man/latex' make[5]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [100%] Built target pdf_doc make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' # 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]: Leaving directory '/build/reproducible-path/isospec-2.2.1' dh_auto_test rm -fr -- /tmp/dh-xdg-rundir-RAwwNu3k 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\+\+2t64.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\+\+2t64/ debian/libisospec\+\+2t64/ 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\+\+2t64.debhelper.log debian/python3-isospec.debhelper.log debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/isospec-2.2.1' dpkg-query: no packages found matching r-base-dev dpkg-query: no packages found matching r-base-core dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=. pybuild --configure -i python{version} -p 3.12 I: pybuild base:311: python3.12 setup.py config running config dh_auto_build -O--buildsystem=cmake -O--system=distutils --sourcedirectory=. cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' 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]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-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/reproducible-path/isospec-2.2.1/obj-x86_64-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/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target IsoSpec++-shared make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build Consolidate compiler generated dependencies of target IsoSpec++-static make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build'. make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build'. make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [ 50%] Built target IsoSpec++-shared [100%] Built target IsoSpec++-static make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-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/reproducible-path/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/reproducible-path/isospec-2.2.1/obj-x86_64-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). gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb). -- 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 (4.1s) -- Generating done (1.0s) -- Build files have been written to: /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu dh_auto_build -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' 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]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++ /build/reproducible-path/isospec-2.2.1/obj-x86_64-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/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target IsoSpec++-shared make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o.d" is newer than depends file "/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target IsoSpec++-static make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build'. make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[4]: Nothing to be done for 'IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build'. make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [ 50%] Built target IsoSpec++-shared [100%] Built target IsoSpec++-static make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' dh_auto_configure -O--buildsystem=cmake -- \ -DCMAKE_INSTALL_PREFIX=/usr \ -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/x86_64-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/reproducible-path/isospec-2.2.1 -- CMAKE_BINARY_DIR: /build/reproducible-path/isospec-2.2.1/obj-x86_64-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). gm convert: Unable to read font (/usr/share/fonts/type1/gsfonts/n019003l.pfb). -- 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 (3.2s) -- Generating done (0.2s) -- Build files have been written to: /build/reproducible-path/isospec-2.2.1/obj-x86_64-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-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" html_doc VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 html_doc make[3]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 1 make -f CMakeFiles/Makefile2 man/CMakeFiles/html_doc.dir/all make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/depend make[5]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/man /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/man /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/man/CMakeFiles/html_doc.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/build make[5]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [100%] Doxygen-based developer html documentation generation cd /build/reproducible-path/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 'HTML_TIMESTAMP' at line 1256 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 'FORMULA_TRANSPARENT' at line 1545 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 'LATEX_TIMESTAMP' at line 1849 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" warning: Tag 'DOT_FONTNAME' at line 2257 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 'DOT_FONTSIZE' at line 2264 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 'DOT_TRANSPARENT' at line 2488 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: 1.9.8 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/reproducible-path/isospec-2.2.1/IsoSpec++ Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.h... Parsing file /build//build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h:33: warning: Compound IsoSpec::Allocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:53: warning: Compound IsoSpec::ConfEqual is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:75: warning: Compound IsoSpec::ConfOrder is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:87: warning: Compound IsoSpec::ConfOrderMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:102: warning: Compound IsoSpec::ConfOrderMarginalDescending is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:25: warning: Compound IsoSpec::DirtyAllocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:40: warning: Compound IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:439: warning: Compound IsoSpec::IsoLayeredGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:542: warning: Compound IsoSpec::IsoStochasticGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:28: warning: Compound IsoSpec::KeyHasher is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:141: warning: Compound IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:24: warning: Compound IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:117: warning: Compound IsoSpec::ReverseOrder is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:26: warning: Compound IsoSpec::SSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:76: warning: Compound IsoSpec::Summator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:99: warning: Compound IsoSpec::TSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:124: warning: Compound IsoSpec::TableOrder is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:32: warning: Compound pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h:146: warning: Compound ws_match_res is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command reproducible-path/isospec-2.2.1/IsoSpec++/mman.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/python-build.cpp... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/python-build.cpp... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h... Parsing file /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h... Preprocessing /build/reproducible-path/isospec-2.2.1/IsoSpec++/unity-build.cpp... Parsing file /build/reproducible-path/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... Associating documentation with modules... 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... Computing module relations... 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/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.cpp... Gene/build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:194: warning: Member iterator (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:195: warning: Member const_iterator (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:196: warning: Member value_type (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:197: warning: Member size_type (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:198: warning: Member reference (typedef) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:199: warning: Member const_reference (typedef) of class pod_vector is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:94: warning: Member reserve(size_t n) (function) of class pod_vector is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:149: warning: Member size() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:154: warning: Member capacity() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:159: warning: Member data() noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:164: warning: Member data() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:169: warning: Member empty() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:174: warning: Member back() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:180: warning: Member pop_back() noexcept (function) of class pod_vector is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:201: warning: Member begin() noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:202: warning: Member begin() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:203: warning: Member cbegin() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:204: warning: Member end() noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:205: warning: Member end() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:206: warning: Member cend() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:208: warning: Member front() const noexcept (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:214: warning: Member clear() (function) of class pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:372: warning: Member iterator (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:373: warning: Member const_iterator (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:374: warning: Member value_type (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:375: warning: Member size_type (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:376: warning: Member reference (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:377: warning: Member const_reference (typedef) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:234: warning: Member init() (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:327: warning: Member size() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:332: warning: Member capacity() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:337: warning: Member data() noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:342: warning: Member data() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:347: warning: Member empty() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:352: warning: Member back() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:358: warning: Member pop_back() noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:379: warning: Member begin() noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:380: warning: Member begin() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:381: warning: Member cbegin() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:382: warning: Member end() noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:383: warning: Member end() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:384: warning: Member cend() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:386: warning: Member front() const noexcept (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h:392: warning: Member clear() (function) of class unsafe_pod_vector is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h:147: warning: Member res1 (variable) of struct ws_match_res is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h:148: warning: Member res2 (variable) of struct ws_match_res is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h:149: warning: Member flow (variable) of struct ws_match_res is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h:27: warning: Member RealType (typedef) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/btrd.h:28: warning: Member IntType (typedef) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:22: warning: Member Conf (typedef) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:23: warning: Member release_g_lfact_table() (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:32: warning: Member alloc_lfact_table() (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:47: warning: Member RationalApproximation(double t) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:57: warning: Member NormalCDFInverse(double p) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:104: warning: Member LowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:131: warning: Member InverseLowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:150: warning: Member random_gen(random_dev()) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:151: warning: Member stdunif(0.0, 1.0) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:68: warning: Member InverseChiSquareCDF2(int k, double x) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:149: warning: Member get_loggamma_nominator(int x) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp:156: warning: Member verify_atom_cnt(int atomCnt) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h:47: warning: Member getConf(void *conf) (function) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h:54: warning: Member getLProb(void *conf) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h:94: warning: Member printVector(const std::vector< T > &vec) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h:133: warning: Member dealloc_table(T *tbl, int dim) (function) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.cpp:26: warning: Member isospec_number_of_isotopic_entries (variable) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp:25: warning: Member aa_isotope_numbers[6] (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp:27: warning: Member aa_elem_masses[19] (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp:37: warning: Member aa_elem_nominal_masses[19] (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp:47: warning: Member aa_elem_probabilities[19] (variable) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:44: warning: Member g_lfact_table (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:102: warning: Member sqrt_pi (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp:149: warning: Member random_dev (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:53: warning: Member pi (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:54: warning: Member logpi (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:73: warning: Member random_gen (variable) of namespace IsoSpec is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h:74: warning: Member stdunif (variable) of namespace IsoSpec is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h:48: warning: Member shiftTables() (function) of class IsoSpec::Allocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h:50: warning: Member newConf() (function) of class IsoSpec::Allocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h:60: warning: Member makeCopy(const T *conf) (function) of class IsoSpec::Allocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:59: warning: Member ConfEqual(int dim) (function) of class IsoSpec::ConfEqual is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:42: warning: Member shiftTables() (function) of class IsoSpec::DirtyAllocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocator.h:44: warning: Member newConf() (function) of class IsoSpec::DirtyAllocator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:70: warning: Member FixedEnvelope(const FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:71: warning: Member FixedEnvelope(FixedEnvelope &&other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:82: warning: Member operator+(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:83: warning: Member operator*(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:85: warning: Member confs_no() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:86: warning: Member getAllDim() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:88: warning: Member masses() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:89: warning: Member probs() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:90: warning: Member confs() const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:92: warning: Member release_masses() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:93: warning: Member release_probs() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:94: warning: Member release_confs() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:95: warning: Member release_everything() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:98: warning: Member mass(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:99: warning: Member prob(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:100: warning: Member conf(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:102: warning: Member sort_by_mass() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:103: warning: Member sort_by_prob() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:105: warning: Member get_total_prob() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:106: warning: Member scale(double factor) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:107: warning: Member normalize() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:108: warning: Member shift_mass(double shift) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:111: warning: Member empiric_average_mass() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:112: warning: Member empiric_variance() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:113: warning: Member empiric_stddev() (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:115: warning: Member WassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:116: warning: Member OrientedWassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:172: warning: Member addConfILG(const GenType &generator) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:132: warning: Member store_conf(const T &generator) (function) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:42: warning: Member _masses (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:43: warning: Member _probs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:44: warning: Member _confs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:45: warning: Member _confs_no (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:46: warning: Member allDim (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:47: warning: Member sorted_by_mass (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:48: warning: Member sorted_by_prob (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:49: warning: Member total_prob (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:50: warning: Member current_size (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:51: warning: Member tmasses (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:52: warning: Member tprobs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:53: warning: Member tconfs (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h:54: warning: Member allDimSizeofInt (variable) of class IsoSpec::FixedEnvelope is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:110: warning: Found unknown command '\use_nominal_masses' /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:111: warning: Found unknown command '\add_water' /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:483: warning: Member get_currentLThreshold() const (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:499: warning: Member advanceToNextConfigurationWithinLayer() (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:534: warning: Member nextLayer(double offset) (function) of class IsoSpec::IsoLayeredGenerator is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:555: warning: Member count() const (function) of class IsoSpec::IsoStochasticGenerator is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:34: warning: Member KeyHasher(int dim) (function) of class IsoSpec::KeyHasher is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:59: warning: found documented return type for IsoSpec::Marginal::Marginal that does not return anything /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:233: warning: Member conf_lprobs() const (function) of class IsoSpec::MarginalTrek is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:234: warning: Member conf_masses() const (function) of class IsoSpec::MarginalTrek is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:235: warning: Member confs() const (function) of class IsoSpec::MarginalTrek is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:146: warning: Member operator()(int m1, int m2) (function) of class IsoSpec::OrderMarginalsBySizeDecresing is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:254: warning: Member configurations (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:255: warning: Member confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:256: warning: Member no_confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:257: warning: Member masses (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:258: warning: Member lProbs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:259: warning: Member probs (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:260: warning: Member allocator (variable) of class IsoSpec::PrecalculatedMarginal is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented. /build/reproducible-path/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/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h:264: warning: found documented return type for IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal that does not return anything /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:30: warning: Member ProbAndConfPtr(double p, Conf c) (function) of struct IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:32: warning: Member operator<(const ProbAndConfPtr &other) const (function) of struct IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:27: warning: Member first (variable) of struct IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/conf.h:28: warning: Member second (variable) of struct IsoSpec::ProbAndConfPtr is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:35: warning: Member SSummator(const SSummator &other) (function) of class IsoSpec::SSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:39: warning: Member add(double x) (function) of class IsoSpec::SSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:61: warning: Member get() (function) of class IsoSpec::SSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:85: warning: Member add(double what) (function) of class IsoSpec::Summator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:93: warning: Member get() (function) of class IsoSpec::Summator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h:128: warning: Member TableOrder(const T *_tbl) (function) of class IsoSpec::TableOrder is not documented. /build/reproducible-path/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/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:107: warning: Member add(double what) (function) of class IsoSpec::TSummator is not documented. /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h:111: warning: Member get() (function) of class IsoSpec::TSummator is not documented. rating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_tables.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fasta.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelopes.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek++.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/misc.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/python-build.cpp... Generating code for file /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h... Generating code for file /build/reproducible-path/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 module documentation... Generating namespace documentation... 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 topic index... Generating module index... Generating module member 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... type lookup cache used 3025/65536 hits=16502 misses=3117 symbol lookup cache used 2874/65536 hits=21953 misses=2874 finished... make[5]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [100%] Built target html_doc make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' dh_auto_build -O--buildsyste=cmake -- pdf_doc cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" pdf_doc VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 pdf_doc make[3]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 1 make -f CMakeFiles/Makefile2 man/CMakeFiles/pdf_doc.dir/all make[4]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f man/CMakeFiles/pdf_doc.dir/build.make man/CMakeFiles/pdf_doc.dir/depend make[5]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/isospec-2.2.1 /build/reproducible-path/isospec-2.2.1/man /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/man /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/man/CMakeFiles/pdf_doc.dir/DependInfo.cmake "--color=" make[5]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make -f man/CMakeFiles/pdf_doc.dir/build.make man/CMakeFiles/pdf_doc.dir/build make[5]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [100%] Doxygen-based developer pdf documentation generation cd /build/reproducible-path/isospec-2.2.1/man/latex && make make[6]: Entering directory '/build/reproducible-path/isospec-2.2.1/man/latex' make[6]: warning: jobserver unavailable: using -j1. 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(/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 No file refman.toc. (/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/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] [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. 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LaTeX Warning: Reference `class_iso_spec_1_1_table_order' on page 5 undefined o n input line 27. LaTeX Warning: Reference `class_iso_spec_1_1_t_summator' on page 5 undefined on input line 28. LaTeX Warning: Reference `classunsafe__pod__vector' on page 5 undefined on inpu t line 29. 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. 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LaTeX Warning: Reference `python-build_8cpp_source' on page 7 undefined on inpu t line 32. LaTeX Warning: Reference `summator_8h_source' on page 7 undefined on input line 33. LaTeX Warning: Reference `unity-build_8cpp_source' on page 7 undefined on input line 34. ) [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 (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [11] [12] [13] [14] [15] [16] [17] [18] Package longtable Warning: Column widths have changed (longtable) in table 5.1 on input line 663. [19] [20] 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[]_[][ ] [21] 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 ) [22] Chapter 6. (./class_iso_spec_1_1_allocator.tex [23]) (./class_iso_spec_1_1_conf_equal.tex [24]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [25]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [26]) (./class_iso_spec_1_1_dirty_allocator.tex [27]) (./class_iso_spec_1_1_fixed_envelope.tex [28] 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[] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [40] [41] [42] Package longtable Warning: Column widths have changed (longtable) in table 6.1 on input line 135. [43] Package longtable Warning: Column widths have changed (longtable) in table 6.2 on input line 208. [44] Package longtable Warning: Column widths have changed (longtable) in table 6.3 on input line 268. [45] [46] [47]) (./class_iso_spec_1_1_iso_generator.tex <./class_iso_spec_1_1_iso_generat or.pdf> [48] [49] [50] Underfull \hbox (badness 10000) detected at line 175 [][][] [51] Underfull \hbox (badness 10000) detected at line 206 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 211--212 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 227 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 232--233 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 248 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 253--254 []\T1/phv/m/n/10 Reimplemented in [], [], and []. [52]) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso _layered_generator.pdf> [53] [54] [55] Underfull \hbox (badness 10000) detected at line 177 [][][] [56] Underfull \hbox (badness 10000) in paragraph at lines 192--193 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer Underfull \hbox (badness 10000) in paragraph at lines 230--231 \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 236 [][][] Underfull \hbox (badness 10000) in paragraph at lines 251--252 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], [57] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) in paragraph at lines 282--283 \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 288 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex <./class_iso_spec_1_1_iso_ord ered_generator.pdf> [58] [59] [60] [61] Underfull \hbox (badness 10000) detected at line 188 [][][] Package longtable Warning: Column widths have changed (longtable) in table 6.4 on input line 213. ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 147--148 \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 153 [][][] [65] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) in paragraph at lines 217--218 \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 223 [][][] Underfull \hbox (badness 10000) in paragraph at lines 238--239 \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 244 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex <./class_iso_spec_1_1_iso_t hreshold_generator.pdf> [66] [67] [68] [69] Package longtable Warning: Column widths have changed (longtable) in table 6.5 on input line 173. Overfull \hbox (18.89209pt too wide) in paragraph at lines 195--196 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) in paragraph at lines 244--245 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) in paragraph at lines 265--266 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) in paragraph at lines 286--287 \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 292 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex) (./class_iso_spec_1_1_layered_marginal.tex [72] <./class_iso_spec_1_1_layered_marginal.pdf> [73] [74] Package longtable Warning: Column widths have changed (longtable) in table 6.6 on input line 145. Package longtable Warning: Column widths have changed (longtable) in table 6.7 on input line 167. Overfull \vbox (7.19118pt too high) has occurred while \output is active [75] Underfull \hbox (badness 10000) detected at line 168 [][][] [76] Underfull \hbox (badness 10000) detected at line 297 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [77] [78] Package longtable Warning: Column widths have changed (longtable) in table 6.8 on input line 118. 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(./allocator_8cpp_source.tex) (./allocator_8h_source.tex [117]) (./btrd_8h_source.tex [118] [119] [120]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [121] [122] [123] [124] 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), [125] 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)))); [126]) (./cwrapper_8h_source.tex [127] [128]) (./dirty_allocator_8cpp_source.tex [129]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [130] [131] [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]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [165] [166] [167] [168]) (./fasta_8h_source.tex [169]) (./fixed_envelopes_8cpp_source.tex [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183]) (./fixed_envelopes_8h_source.tex [184] [185] [186]) (./iso_math_8cpp_source.tex [187] [188]) (./iso_math_8h_source.tex [189]) (./iso_spec_09_09_8cpp_source.tex [190] [191] [192] [193] [194] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [195] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [196] [197] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200]) (./iso_spec_09_09_8h_source.tex [201] [202] [203] [204] [205] [206]) (./marginal_trek_09_09_8cpp_source.tex [207] [208] [209] [210] [211] [212] [213] [214]) (./marginal_trek_09_09_8h_source.tex [215] [216] [217] [218]) (./misc_8cpp_source.tex [219]) (./misc_8h_source.tex [220] [221]) (./mman_8cpp_source.tex [222] [223]) (./mman_8h_source.tex [224]) (./operators_8cpp_source.tex [225]) (./operators_8h_source.tex [226] [227]) (./platform_8h_source.tex [228]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [229] [230] [231] [232] [233]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [234] [235]) (./unity-build_8cpp_source.tex) [236] 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) Output written on refman.pdf (238 pages, 944470 bytes). Transcript written on refman.log. makeindex refman.idx This is makeindex, version 2.17 [TeX Live 2025/dev] (kpathsea + Thai support). Scanning input file refman.idx....done (815 entries accepted, 0 rejected). Sorting entries.........done (8611 comparisons). Generating output file refman.ind....done (1125 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] Package longtable Warning: Column widths have changed (longtable) in table 5.1 on input line 663. [19] [20] 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[]_[][ ] [21] 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 ) [22] Chapter 6. (./class_iso_spec_1_1_allocator.tex [23]) (./class_iso_spec_1_1_conf_equal.tex [24]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [25]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [26]) (./class_iso_spec_1_1_dirty_allocator.tex [27]) (./class_iso_spec_1_1_fixed_envelope.tex [28] 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[] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [40] [41] [42] [43] [44] [45] [46] [47]) (./class_iso_spec_1_1_iso_generator.tex <./class_iso_spec_1_1_iso_generat or.pdf> [48] [49] [50] Underfull \hbox (badness 10000) detected at line 175 [][][] [51] Underfull \hbox (badness 10000) detected at line 206 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 211--212 []\T1/phv/m/n/10 Reimplemented in [], [], and []. 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[52]) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso _layered_generator.pdf> [53] [54] [55] Underfull \hbox (badness 10000) detected at line 177 [][][] [56] Underfull \hbox (badness 10000) in paragraph at lines 192--193 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer Underfull \hbox (badness 10000) in paragraph at lines 230--231 \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 236 [][][] Underfull \hbox (badness 10000) in paragraph at lines 251--252 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], [57] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) in paragraph at lines 282--283 \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 288 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex <./class_iso_spec_1_1_iso_ord ered_generator.pdf> [58] [59] [60] [61] Underfull \hbox (badness 10000) detected at line 188 [][][] ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 147--148 \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 153 [][][] [65] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) in paragraph at lines 217--218 \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 223 [][][] Underfull \hbox (badness 10000) in paragraph at lines 238--239 \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 244 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex <./class_iso_spec_1_1_iso_t hreshold_generator.pdf> [66] [67] [68] [69] Overfull \hbox (18.89209pt too wide) in paragraph at lines 195--196 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) in paragraph at lines 244--245 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 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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) Output written on refman.pdf (262 pages, 1054820 bytes). Transcript written on refman.log. latex_count=8 ; \ while grep -E -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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[52]) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso _layered_generator.pdf> [53] [54] [55] Underfull \hbox (badness 10000) detected at line 177 [][][] [56] Underfull \hbox (badness 10000) in paragraph at lines 192--193 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer Underfull \hbox (badness 10000) in paragraph at lines 230--231 \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 236 [][][] Underfull \hbox (badness 10000) in paragraph at lines 251--252 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], [57] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) in paragraph at lines 282--283 \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 288 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex <./class_iso_spec_1_1_iso_ord ered_generator.pdf> [58] [59] [60] [61] Underfull \hbox (badness 10000) detected at line 188 [][][] ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 147--148 \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 153 [][][] [65] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) in paragraph at lines 217--218 \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 223 [][][] Underfull \hbox (badness 10000) in paragraph at lines 238--239 \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 244 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex <./class_iso_spec_1_1_iso_t hreshold_generator.pdf> [66] [67] [68] [69] Overfull \hbox (18.89209pt too wide) in paragraph at lines 195--196 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) in paragraph at lines 244--245 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) in paragraph at lines 265--266 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) in paragraph at lines 286--287 \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 292 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex) (./class_iso_spec_1_1_layered_marginal.tex [72] <./class_iso_spec_1_1_layered_marginal.pdf> [73] [74] Overfull \vbox (7.19118pt too high) has occurred while \output is active [75] Underfull \hbox (badness 10000) detected at line 168 [][][] [76] Underfull \hbox (badness 10000) detected at line 297 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [77] [78] Underfull \hbox (badness 10000) detected at line 119 [][][] [79] Underfull \hbox (badness 10000) detected at line 181 [][][] [80] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 266 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] [81] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] [82] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 379 [][][] [83] Underfull \hbox (badness 10000) detected at line 411 [][][] [84]) (./class_iso_spec_1_1_marginal_trek.tex <./class_iso_spec_1_1_marginal_tr ek.pdf> [85] [86] [87] Underfull \hbox (badness 10000) detected at line 191 [][][] [88] Underfull \hbox (badness 10000) detected at line 215 [][][] ) (./class_iso_spec_1_1_order_marginals_by_size_decresing.tex) (./classpod__vector.tex [89] [90] [91] [92] [93] [94] [95]) (./class_iso_spec_1_1_precalculated_marginal.tex <./class_iso_spec_1_1_pr ecalculated_marginal.pdf> [96] [97] [98] Underfull \hbox (badness 10000) detected at line 167 [][][] [99] Underfull \hbox (badness 10000) detected at line 206 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 245 [][][] [100] Underfull \hbox (badness 10000) detected at line 267 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] [101] Underfull \hbox (badness 10000) detected at line 323 [][][] Underfull \hbox (badness 10000) detected at line 340 [][][] Underfull \hbox (badness 10000) detected at line 357 [][][] [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]) (./structws__match__res.tex [115]) [116] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [117]) (./btrd_8h_source.tex [118] [119] [120]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [121] [122] [123] [124] 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), [125] 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)))); [126]) (./cwrapper_8h_source.tex [127] [128]) (./dirty_allocator_8cpp_source.tex [129]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [130] [131] [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]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [165] [166] [167] [168]) (./fasta_8h_source.tex [169]) (./fixed_envelopes_8cpp_source.tex [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183]) (./fixed_envelopes_8h_source.tex [184] [185] [186]) (./iso_math_8cpp_source.tex [187] [188]) (./iso_math_8h_source.tex [189]) (./iso_spec_09_09_8cpp_source.tex [190] [191] [192] [193] [194] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [195] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [196] [197] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200]) (./iso_spec_09_09_8h_source.tex [201] [202] [203] [204] [205] [206]) (./marginal_trek_09_09_8cpp_source.tex [207] [208] [209] [210] [211] [212] [213] [214]) (./marginal_trek_09_09_8h_source.tex [215] [216] [217] [218]) (./misc_8cpp_source.tex [219]) (./misc_8h_source.tex [220] [221]) (./mman_8cpp_source.tex [222] [223]) (./mman_8h_source.tex [224]) (./operators_8cpp_source.tex [225]) (./operators_8h_source.tex [226] [227]) (./platform_8h_source.tex [228]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [229] [230] [231] [232] [233]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [234] [235]) (./unity-build_8cpp_source.tex) [236] (./refman.ind Overfull \hbox (28.18492pt too wide) in paragraph at lines 3--5 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp , Overfull \hbox (18.68105pt too wide) in paragraph at lines 5--7 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h, Overfull \hbox (31.09198pt too wide) in paragraph at lines 11--13 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.cpp, Overfull \hbox (21.5881pt too wide) in paragraph at lines 13--15 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h, Overfull \hbox (46.54446pt too wide) in paragraph at lines 15--17 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocato r.cpp, Overfull \hbox (37.04059pt too wide) in paragraph at lines 17--19 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocato r.h, Overfull \hbox (55.33754pt too wide) in paragraph at lines 19--21 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_table s.cpp, Overfull \hbox (45.83366pt too wide) in paragraph at lines 21--23 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_table s.h, Overfull \hbox (54.84283pt too wide) in paragraph at lines 27--29 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelope s.cpp, Overfull \hbox (45.33896pt too wide) in paragraph at lines 29--31 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelope s.h, Overfull \hbox (26.13304pt too wide) in paragraph at lines 31--33 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp, Overfull \hbox (16.62917pt too wide) in paragraph at lines 33--35 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h, Overfull \hbox (37.14894pt too wide) in paragraph at lines 35--37 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp , Overfull \hbox (27.64507pt too wide) in paragraph at lines 37--39 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h, Overfull \hbox (56.56161pt too wide) in paragraph at lines 39--41 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek+ +.cpp, Overfull \hbox (47.05774pt too wide) in paragraph at lines 41--43 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek+ +.h, Overfull \hbox (19.62622pt too wide) in paragraph at lines 47--49 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp, Overfull \hbox (32.41495pt too wide) in paragraph at lines 51--53 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp , Overfull \hbox (22.91107pt too wide) in paragraph at lines 53--55 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h, Overfull \hbox (17.58307pt too wide) in paragraph at lines 55--57 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h, Overfull \hbox (36.08676pt too wide) in paragraph at lines 57--59 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl .h, Overfull \hbox (28.96791pt too wide) in paragraph at lines 59--61 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h, Overfull \hbox (24.67503pt too wide) in paragraph at lines 63--65 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h, Underfull \hbox (badness 10000) in paragraph at lines 65--67 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/unity- [237] [238] [239] [240] [241] [242] Underfull \hbox (badness 870) in paragraph at lines 842--844 []| \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 , [243] Underfull \hbox (badness 870) in paragraph at lines 856--858 []| \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 , [244] [245] [246]) (./refman.aux) ) (see the transcript file for additional information) Output written on refman.pdf (262 pages, 1054870 bytes). 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[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf- dist/fonts/enc/dvips/base/8r.enc}] [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] 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[]_[][ ] [21] 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 ) [22] Chapter 6. (./class_iso_spec_1_1_allocator.tex [23]) (./class_iso_spec_1_1_conf_equal.tex [24]) (./class_iso_spec_1_1_conf_order.tex) (./class_iso_spec_1_1_conf_order_marginal.tex [25]) (./class_iso_spec_1_1_conf_order_marginal_descending.tex [26]) (./class_iso_spec_1_1_dirty_allocator.tex [27]) (./class_iso_spec_1_1_fixed_envelope.tex [28] 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[] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39]) (./class_iso_spec_1_1_iso.tex <./class_iso_spec_1_1_iso.pdf> [40] [41] [42] [43] [44] [45] [46] [47]) (./class_iso_spec_1_1_iso_generator.tex <./class_iso_spec_1_1_iso_generat or.pdf> [48] [49] [50] Underfull \hbox (badness 10000) detected at line 175 [][][] [51] Underfull \hbox (badness 10000) detected at line 206 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 211--212 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 227 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 232--233 []\T1/phv/m/n/10 Reimplemented in [], [], and []. Underfull \hbox (badness 10000) detected at line 248 [][][] Overfull \hbox (30.52501pt too wide) in paragraph at lines 253--254 []\T1/phv/m/n/10 Reimplemented in [], [], and []. [52]) (./class_iso_spec_1_1_iso_layered_generator.tex <./class_iso_spec_1_1_iso _layered_generator.pdf> [53] [54] [55] Underfull \hbox (badness 10000) detected at line 177 [][][] [56] Underfull \hbox (badness 10000) in paragraph at lines 192--193 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Layered []Generator[]::advance[]To[]Next[]Configuration[]Within[]Layer Underfull \hbox (badness 10000) in paragraph at lines 230--231 \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 236 [][][] Underfull \hbox (badness 10000) in paragraph at lines 251--252 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Layer ed[]Generator[]::mass ( ) const [inline], [final], [57] Underfull \hbox (badness 10000) detected at line 257 [][][] Underfull \hbox (badness 10000) in paragraph at lines 282--283 \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 288 [][][] ) (./class_iso_spec_1_1_iso_ordered_generator.tex <./class_iso_spec_1_1_iso_ord ered_generator.pdf> [58] [59] [60] [61] Underfull \hbox (badness 10000) detected at line 188 [][][] ) (./class_iso_spec_1_1_iso_stochastic_generator.tex <./class_iso_spec_1_1_iso_ stochastic_generator.pdf> [62] [63] [64] Underfull \hbox (badness 10000) in paragraph at lines 147--148 \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 153 [][][] [65] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) in paragraph at lines 217--218 \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 223 [][][] Underfull \hbox (badness 10000) in paragraph at lines 238--239 \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 244 [][][] ) (./class_iso_spec_1_1_iso_threshold_generator.tex <./class_iso_spec_1_1_iso_t hreshold_generator.pdf> [66] [67] [68] [69] Overfull \hbox (18.89209pt too wide) in paragraph at lines 195--196 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE bool Iso[]Spec[]::[]Iso[]Thresho ld[]Generator[]::advance[]To[]Next[]Configuration ( ) [inline], Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) in paragraph at lines 244--245 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::lprob ( ) const [inline], [final], [70] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) in paragraph at lines 265--266 \T1/pcr/m/n/8 ISOSPEC[]_[][]FORCE[]_[][]INLINE double Iso[]Spec[]::[]Iso[]Thres hold[]Generator[]::mass ( ) const [inline], [final], Underfull \hbox (badness 10000) detected at line 271 [][][] Underfull \hbox (badness 10000) in paragraph at lines 286--287 \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 292 [][][] [71]) (./class_iso_spec_1_1_key_hasher.tex) (./class_iso_spec_1_1_layered_marginal.tex [72] <./class_iso_spec_1_1_layered_marginal.pdf> [73] [74] Overfull \vbox (7.19118pt too high) has occurred while \output is active [75] Underfull \hbox (badness 10000) detected at line 168 [][][] [76] Underfull \hbox (badness 10000) detected at line 297 [][][] ) (./class_iso_spec_1_1_marginal.tex <./class_iso_spec_1_1_marginal.pdf> [77] [78] Underfull \hbox (badness 10000) detected at line 119 [][][] [79] Underfull \hbox (badness 10000) detected at line 181 [][][] [80] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 249 [][][] Underfull \hbox (badness 10000) detected at line 266 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] [81] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 331 [][][] [82] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 379 [][][] [83] Underfull \hbox (badness 10000) detected at line 411 [][][] [84]) (./class_iso_spec_1_1_marginal_trek.tex <./class_iso_spec_1_1_marginal_tr ek.pdf> [85] [86] [87] Underfull \hbox (badness 10000) detected at line 191 [][][] [88] Underfull \hbox (badness 10000) detected at line 215 [][][] ) (./class_iso_spec_1_1_order_marginals_by_size_decresing.tex) (./classpod__vector.tex [89] [90] [91] [92] [93] [94] [95]) (./class_iso_spec_1_1_precalculated_marginal.tex <./class_iso_spec_1_1_pr ecalculated_marginal.pdf> [96] [97] [98] Underfull \hbox (badness 10000) detected at line 167 [][][] [99] Underfull \hbox (badness 10000) detected at line 206 [][][] Underfull \hbox (badness 10000) detected at line 228 [][][] Underfull \hbox (badness 10000) detected at line 245 [][][] [100] Underfull \hbox (badness 10000) detected at line 267 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] [101] Underfull \hbox (badness 10000) detected at line 323 [][][] Underfull \hbox (badness 10000) detected at line 340 [][][] Underfull \hbox (badness 10000) detected at line 357 [][][] [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]) (./structws__match__res.tex [115]) [116] Chapter 7. (./allocator_8cpp_source.tex) (./allocator_8h_source.tex [117]) (./btrd_8h_source.tex [118] [119] [120]) (./conf_8h_source.tex) (./cwrapper_8cpp_source.tex [121] [122] [123] [124] 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), [125] 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)))); [126]) (./cwrapper_8h_source.tex [127] [128]) (./dirty_allocator_8cpp_source.tex [129]) (./dirty_allocator_8h_source.tex) (./element__tables_8cpp_source.tex [130] [131] [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]) (./element__tables_8h_source.tex) (./fasta_8cpp_source.tex [165] [166] [167] [168]) (./fasta_8h_source.tex [169]) (./fixed_envelopes_8cpp_source.tex [170] [171] [172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183]) (./fixed_envelopes_8h_source.tex [184] [185] [186]) (./iso_math_8cpp_source.tex [187] [188]) (./iso_math_8h_source.tex [189]) (./iso_spec_09_09_8cpp_source.tex [190] [191] [192] [193] [194] Overfull \hbox (15.15555pt too wide) in paragraph at lines 441--441 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [195] Overfull \hbox (15.15555pt too wide) in paragraph at lines 477--477 \T1/pcr/m/n/7 ----------------------------------------------------------------- -----------------------------------------[] [196] [197] Overfull \hbox (73.9555pt too wide) in paragraph at lines 654--654 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [198] [199] Overfull \hbox (73.9555pt too wide) in paragraph at lines 814--814 \T1/pcr/m/n/7 ----------------------------------------------------------------- -------------------------------------------------------[] [200]) (./iso_spec_09_09_8h_source.tex [201] [202] [203] [204] [205] [206]) (./marginal_trek_09_09_8cpp_source.tex [207] [208] [209] [210] [211] [212] [213] [214]) (./marginal_trek_09_09_8h_source.tex [215] [216] [217] [218]) (./misc_8cpp_source.tex [219]) (./misc_8h_source.tex [220] [221]) (./mman_8cpp_source.tex [222] [223]) (./mman_8h_source.tex [224]) (./operators_8cpp_source.tex [225]) (./operators_8h_source.tex [226] [227]) (./platform_8h_source.tex [228]) (./platform__incl_8h_source.tex) (./pod__vector_8h_source.tex [229] [230] [231] [232] [233]) (./python-build_8cpp_source.tex) (./summator_8h_source.tex [234] [235]) (./unity-build_8cpp_source.tex) [236] (./refman.ind Overfull \hbox (28.18492pt too wide) in paragraph at lines 3--5 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.cpp , Overfull \hbox (18.68105pt too wide) in paragraph at lines 5--7 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/allocator.h, Overfull \hbox (31.09198pt too wide) in paragraph at lines 11--13 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.cpp, Overfull \hbox (21.5881pt too wide) in paragraph at lines 13--15 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/cwrapper.h, Overfull \hbox (46.54446pt too wide) in paragraph at lines 15--17 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocato r.cpp, Overfull \hbox (37.04059pt too wide) in paragraph at lines 17--19 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/dirtyAllocato r.h, Overfull \hbox (55.33754pt too wide) in paragraph at lines 19--21 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_table s.cpp, Overfull \hbox (45.83366pt too wide) in paragraph at lines 21--23 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/element_table s.h, Overfull \hbox (54.84283pt too wide) in paragraph at lines 27--29 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelope s.cpp, Overfull \hbox (45.33896pt too wide) in paragraph at lines 29--31 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/fixedEnvelope s.h, Overfull \hbox (26.13304pt too wide) in paragraph at lines 31--33 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.cpp, Overfull \hbox (16.62917pt too wide) in paragraph at lines 33--35 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoMath.h, Overfull \hbox (37.14894pt too wide) in paragraph at lines 35--37 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.cpp , Overfull \hbox (27.64507pt too wide) in paragraph at lines 37--39 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/isoSpec++.h, Overfull \hbox (56.56161pt too wide) in paragraph at lines 39--41 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek+ +.cpp, Overfull \hbox (47.05774pt too wide) in paragraph at lines 41--43 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/marginalTrek+ +.h, Overfull \hbox (19.62622pt too wide) in paragraph at lines 47--49 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/mman.cpp, Overfull \hbox (32.41495pt too wide) in paragraph at lines 51--53 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.cpp , Overfull \hbox (22.91107pt too wide) in paragraph at lines 53--55 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/operators.h, Overfull \hbox (17.58307pt too wide) in paragraph at lines 55--57 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform.h, Overfull \hbox (36.08676pt too wide) in paragraph at lines 57--59 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/platform_incl .h, Overfull \hbox (28.96791pt too wide) in paragraph at lines 59--61 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/pod_vector.h, Overfull \hbox (24.67503pt too wide) in paragraph at lines 63--65 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/summator.h, Underfull \hbox (badness 10000) in paragraph at lines 65--67 []\T1/phv/m/n/10 /build/reproducible-path/isospec-2.2.1/IsoSpec++/unity- [237] [238] [239] [240] [241] [242] Underfull \hbox (badness 870) in paragraph at lines 842--844 []| \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 , [243] Underfull \hbox (badness 870) in paragraph at lines 856--858 []| \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 , [244] [245] [246]) (./refman.aux) ) (see the transcript file for additional information) Output written on refman.pdf (262 pages, 1054870 bytes). Transcript written on refman.log. make[6]: Leaving directory '/build/reproducible-path/isospec-2.2.1/man/latex' make[5]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' [100%] Built target pdf_doc make[4]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' # 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/reproducible-path/isospec-2.2.1/debian/tmp pybuild --install -i python{version} -p 3.12 --dest-dir /build/reproducible-path/isospec-2.2.1/debian/tmp I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/isospec-2.2.1/debian/python3-isospec running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py creating /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/__init__.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/isoFFI.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/Distributions.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/Formulas.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/Advanced.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/PeriodicTbl.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/IsoSpecPy.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/confs_passthrough.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/IsoSpecPyOld.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy copying IsoSpecPy/approximations.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy running build_ext building 'IsoSpecCppPy' extension creating build/temp.linux-x86_64-cpython-312/IsoSpec++ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/isospec-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c IsoSpec++/python-build.cpp -o build/temp.linux-x86_64-cpython-312/IsoSpec++/python-build.o -O3 -std=c++17 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/isospec-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/isospec-2.2.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/IsoSpec++/python-build.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecCppPy.cpython-312-x86_64-linux-gnu.so running install_lib creating /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecCppPy.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages creating /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/__init__.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/isoFFI.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/Distributions.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/Formulas.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/Advanced.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/PeriodicTbl.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/IsoSpecPy.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/confs_passthrough.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/IsoSpecPyOld.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.12_isospec/build/IsoSpecPy/approximations.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/isoFFI.py to isoFFI.cpython-312.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/Distributions.py to Distributions.cpython-312.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/Formulas.py to Formulas.cpython-312.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/Advanced.py to Advanced.cpython-312.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/PeriodicTbl.py to PeriodicTbl.cpython-312.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/IsoSpecPy.py to IsoSpecPy.cpython-312.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/confs_passthrough.py to confs_passthrough.cpython-312.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/IsoSpecPyOld.py to IsoSpecPyOld.cpython-312.pyc /usr/lib/python3.12/dist-packages/IsoSpecPy/IsoSpecPyOld.py:98: SyntaxWarning: invalid escape sequence '\D' /usr/lib/python3.12/dist-packages/IsoSpecPy/IsoSpecPyOld.py:99: SyntaxWarning: invalid escape sequence '\d' byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/dist-packages/IsoSpecPy/approximations.py to approximations.cpython-312.pyc /usr/lib/python3.12/dist-packages/IsoSpecPy/approximations.py:38: SyntaxWarning: invalid escape sequence '\s' /usr/lib/python3.12/dist-packages/IsoSpecPy/approximations.py:53: SyntaxWarning: invalid escape sequence '\s' 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/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.12/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/reproducible-path/isospec-2.2.1/debian/tmp cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/isospec-2.2.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/isospec-2.2.1 -B/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/isospec++/FindIsoSpec++.cmake -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/isospec++/IsoSpec++Config.cmake -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libisospec++.pc -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/logo2_high.pdf -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/isospec_logo2_high_versioned.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/logo2_long.pdf -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/isospec_logo2_high_versioned.svg -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/isospec_logo2_long_versioned.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/images/isospec_logo2_long_versioned.svg -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/platform__incl_8h_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/plus.svg -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/dirty_allocator_8h_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_allocator-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_layered_marginal.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/classes.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_conf_order_marginal-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_threshold_generator.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_conf_order.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_t_summator-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/iso_spec_09_09_8cpp_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/fixed_envelopes_8cpp_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_key_hasher-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/namespace_iso_spec.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_generator.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/folderopend.svg -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/tab_ad.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_precalculated_marginal.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/namespaces.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_marginal.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/nav_f.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/folderclosedd.svg -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/nav_fd.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_table_order-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_b.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_2.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/variables_3.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_10.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_a.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_1.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_c.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_4.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/close.svg -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_4.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_f.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_2.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_9.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/searchdata.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_11.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/variables_1.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_4.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_5.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_a.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/search.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_7.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_13.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/namespaces_0.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_3.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_f.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/search.css -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_3.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_c.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_c.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/mag_sel.svg -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_3.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_8.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_d.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_b.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_9.js -- Installing: 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Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_10.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/variables_0.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/mag_d.svg -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/functions_e.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/all_e.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/variables_4.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/classes_0.js -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/search/variables_5.js -- Installing: 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/build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/doxygen.css -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/splitbar.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/annotated.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/classpod__vector-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_layered_generator.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_threshold_generator-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/iso_math_8h_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/marginal_trek_09_09_8h_source.html -- Installing: 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/build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/structws__match__res-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/mman_8h_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/fasta_8cpp_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_table_order.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/tab_h.png -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/fasta_8h_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/pod__vector_8h_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_order_marginals_by_size_decresing.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/unity-build_8cpp_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_threshold_generator.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_conf_order_marginal_descending-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_marginal_trek.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/dirty_allocator_8cpp_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_s_summator-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/misc_8cpp_source.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/namespacemembers_func.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/index.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_summator.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/class_iso_spec_1_1_conf_equal.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/html/struct_iso_spec_1_1_prob_and_conf_ptr-members.html -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/pdf/refman.pdf -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_Allocator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ConfEqual.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ConfOrder.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_DirtyAllocator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_FixedEnvelope.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_Iso.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoGenerator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_KeyHasher.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_LayeredMarginal.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_Marginal.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_MarginalTrek.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_ReverseOrder.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_SSummator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_Summator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_TSummator.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/IsoSpec_TableOrder.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/pod_vector.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/unsafe_pod_vector.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/man/man3/ws_match_res.3 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/C++ -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/C++/radiolabelling.cpp -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/C++/water.cpp -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/C++/COMPILING -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python/water.py -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python/radiolabelling.py -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python/fasta.py -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/Python/custom_elements.py -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/R -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/R/radiolabelling.R -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/share/doc/isospec/examples/R/water.R -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/lib/x86_64-linux-gnu/libIsoSpec++.so.2.2.1 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/lib/x86_64-linux-gnu/libIsoSpec++.so.2 -- Installing: /build/reproducible-path/isospec-2.2.1/debian/tmp/usr/lib/x86_64-linux-gnu/libIsoSpec++.a make[2]: Leaving directory '/build/reproducible-path/isospec-2.2.1/obj-x86_64-linux-gnu' # 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]: Leaving directory '/build/reproducible-path/isospec-2.2.1' dh_install install -m0755 -d debian/libisospec\+\+-dev//usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.a debian/libisospec\+\+-dev//usr/lib/x86_64-linux-gnu/ install -m0755 -d debian/libisospec\+\+-dev//usr/lib/x86_64-linux-gnu/cmake cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/cmake/isospec\+\+ debian/libisospec\+\+-dev//usr/lib/x86_64-linux-gnu/cmake/ install -m0755 -d debian/libisospec\+\+-dev//usr/lib/x86_64-linux-gnu/pkgconfig cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/libisospec\+\+.pc debian/libisospec\+\+-dev//usr/lib/x86_64-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\+\+2t64//usr/lib/x86_64-linux-gnu cp --reflink=auto -a debian/tmp/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so.2.2.1 debian/libisospec\+\+2t64//usr/lib/x86_64-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\+\+2t64/usr/share/doc/libisospec\+\+2t64 install -p -m0644 debian/copyright debian/libisospec\+\+2t64/usr/share/doc/libisospec\+\+2t64/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\+\+-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/libisospec\+\+2t64/usr/share/doc/libisospec\+\+2t64 install -p -m0644 debian/.debhelper/generated/libisospec\+\+2t64/dh_installchangelogs.dch.trimmed debian/libisospec\+\+2t64/usr/share/doc/libisospec\+\+2t64/changelog.Debian install -p -m0644 ./CHANGELOG debian/libisospec\+\+2t64/usr/share/doc/libisospec\+\+2t64/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_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_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.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_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_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_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_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_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/ws_match_res.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/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/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 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_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_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_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/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_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_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_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_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 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/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_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_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_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 dh_python3 D: dh_python3 dh_python3:180: version: 6.20241024 D: dh_python3 dh_python3:181: argv: ['/usr/bin/dh_python3'] D: dh_python3 dh_python3:182: 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_python3:183: supported Python versions: 3.12 (default=3.12) D: dh_python3 debhelper:166: skipping package libisospec++-dev (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:166: skipping package libisospec++2t64 (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:166: skipping package libisospec++-doc (missing ${python3:Depends} in Depends/Recommends) D: dh_python3 debhelper:174: source=isospec, binary packages=['python3-isospec'] D: dh_python3 dh_python3:205: processing package python3-isospec... D: dh_python3 fs:50: moving files from debian/python3-isospec/usr/lib/python3.12/dist-packages to debian/python3-isospec/usr/lib/python3/dist-packages/ D: dh_python3 fs:338: package python3-isospec details = {'requires.txt': {'debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecPy-2.2.1.egg-info/requires.txt'}, 'egg-info': {'debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecPy-2.2.1.egg-info/PKG-INFO'}, 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': {Version('3.12')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-isospec D: dh_python3 pydist:175: trying to find dependency for cffi (python=None) D: dh_python3 pydist:209: dependency: module seems to be installed D: dh_python3 pydist:220: dependency: requirement already has hardcoded version D: dh_python3 depends:253: D={'python3-cffi-backend-api-min (<= 9729), python3-cffi-backend-api-max (>= 9729)', 'python3 (>= 3.12~)', 'python3:any', 'python3 (<< 3.13)'}; R=[]; S=[]; E=[], B=[]; RT=[] dh_lintian install -m0755 -d debian/libisospec\+\+2t64/usr/share/lintian/overrides install -p -m0644 debian/libisospec\+\+2t64.lintian-overrides debian/libisospec\+\+2t64/usr/share/lintian/overrides/libisospec\+\+2t64 dh_perl dh_link install -m0755 -d debian/libisospec\+\+-dev/usr/lib/x86_64-linux-gnu rm -f debian/libisospec\+\+-dev/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so ln -s libIsoSpec\+\+.so.2.2.1 debian/libisospec\+\+-dev/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so install -m0755 -d debian/libisospec\+\+2t64/usr/lib/x86_64-linux-gnu rm -f debian/libisospec\+\+2t64/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so.2 ln -s libIsoSpec\+\+.so.2.2.1 debian/libisospec\+\+2t64/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so.2 dh_strip_nondeterminism Using 1709121005 as canonical time 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/class_iso_spec_1_1_iso_threshold_generator.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/images/isospec_logo2_long_versioned.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/bc_sd.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/nav_f.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/nav_fd.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/tab_ad.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/tab_hd.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/nav_hd.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/isospec_logo2_high_versioned.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/tab_sd.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/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_precalculated_marginal.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/tab_s.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/splitbard.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/tab_bd.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/class_iso_spec_1_1_iso_ordered_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/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_generator.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/class_iso_spec_1_1_iso.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/tab_h.png using File::StripNondeterminism::handlers::png dh_compress cd debian/libisospec++2t64 cd debian/libisospec++-dev cd debian/libisospec++-doc cd debian/python3-isospec chmod a-x usr/share/doc/libisospec\+\+2t64/changelog usr/share/doc/libisospec\+\+2t64/changelog.Debian chmod a-x usr/share/doc/python3-isospec/changelog usr/share/doc/python3-isospec/changelog.Debian gzip -9nf usr/share/doc/libisospec\+\+2t64/changelog usr/share/doc/libisospec\+\+2t64/changelog.Debian gzip -9nf usr/share/doc/python3-isospec/changelog usr/share/doc/python3-isospec/changelog.Debian cd '/build/reproducible-path/isospec-2.2.1' cd '/build/reproducible-path/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 cd '/build/reproducible-path/isospec-2.2.1' 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/reproducible-path/isospec-2.2.1' dh_fixperms find debian/libisospec++2t64 -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/python3-isospec -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libisospec++-dev -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libisospec\+\+2t64 ! -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\+\+2t64/usr/share/doc -type f -a -true -a ! -regex 'debian/libisospec++2t64/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libisospec\+\+2t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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\+\+2t64/usr/share/lintian/overrides -type f -a -true -a -true -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\+\+2t64 -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/python3-isospec/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\+\+2t64/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w 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/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/libisospec\+\+-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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/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\+\+-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 f -a -true -a ! -regex 'debian/libisospec++-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 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\+\+2t64/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so.2.2.1 dwz -- debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-312-x86_64-linux-gnu.so dh_strip -a install -m0755 -d debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/lib/debug/.build-id/f5 objcopy --only-keep-debug --compress-debug-sections debian/libisospec\+\+2t64/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so.2.2.1 debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/lib/debug/.build-id/f5/6f3635dc5c3d11f7c43637f1f44a48b44587d3.debug chmod 0644 -- debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/lib/debug/.build-id/f5/6f3635dc5c3d11f7c43637f1f44a48b44587d3.debug chown 0:0 -- debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/lib/debug/.build-id/f5/6f3635dc5c3d11f7c43637f1f44a48b44587d3.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/libisospec\+\+2t64/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so.2.2.1 objcopy --add-gnu-debuglink debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/lib/debug/.build-id/f5/6f3635dc5c3d11f7c43637f1f44a48b44587d3.debug debian/libisospec\+\+2t64/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so.2.2.1 install -m0755 -d debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/share/doc ln -s libisospec\+\+2t64 debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/share/doc/libisospec\+\+2t64-dbgsym install -m0755 -d debian/.debhelper/libisospec\+\+2t64 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/x86_64-linux-gnu/libIsoSpec\+\+.a install -m0755 -d debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/aa objcopy --only-keep-debug --compress-debug-sections debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-312-x86_64-linux-gnu.so debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/aa/cff8e6581ba52e1884574c1f7333221f907f2a.debug chmod 0644 -- debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/aa/cff8e6581ba52e1884574c1f7333221f907f2a.debug chown 0:0 -- debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/aa/cff8e6581ba52e1884574c1f7333221f907f2a.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-312-x86_64-linux-gnu.so objcopy --add-gnu-debuglink debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/aa/cff8e6581ba52e1884574c1f7333221f907f2a.debug debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-312-x86_64-linux-gnu.so 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\+\+2t64/DEBIAN/shlibs install -m0755 -d debian/libisospec\+\+2t64/DEBIAN echo "libIsoSpec++ 2 libisospec++2t64 (>= 2.2.1)" >> debian/libisospec\+\+2t64/DEBIAN/shlibs chmod 0644 -- debian/libisospec\+\+2t64/DEBIAN/shlibs chown 0:0 -- debian/libisospec\+\+2t64/DEBIAN/shlibs mv debian/.debhelper/generated/libisospec\+\+2t64/triggers.new debian/.debhelper/generated/libisospec\+\+2t64/triggers mv debian/libisospec\+\+2t64.substvars.new debian/libisospec\+\+2t64.substvars rm -f debian/python3-isospec/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/libisospec\+\+2t64/DEBIAN dpkg-shlibdeps -Tdebian/libisospec\+\+2t64.substvars debian/libisospec\+\+2t64/usr/lib/x86_64-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-312-x86_64-linux-gnu.so dh_installdeb install -m0755 -d debian/libisospec\+\+-dev/DEBIAN install -m0755 -d debian/libisospec\+\+2t64/DEBIAN install -p -m0644 debian/.debhelper/generated/libisospec\+\+2t64/triggers debian/libisospec\+\+2t64/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 -cdebian/control -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 -cdebian/control -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 -cdebian/control -Pdebian/.debhelper/python3-isospec/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=python3-isospec-dbgsym "-DDepends=python3-isospec (= \${binary:Version})" "-DDescription=debug symbols for python3-isospec" -DBuild-Ids=aacff8e6581ba52e1884574c1f7333221f907f2a -DSection=debug -UMulti-Arch -UReplaces -UBreaks install -m0755 -d debian/libisospec\+\+2t64/DEBIAN echo misc:Depends= >> debian/libisospec++2t64.substvars echo misc:Pre-Depends= >> debian/libisospec++2t64.substvars install -m0755 -d debian/.debhelper/libisospec\+\+2t64/dbgsym-root/DEBIAN dpkg-gencontrol -plibisospec\+\+2t64 -ldebian/changelog -Tdebian/libisospec\+\+2t64.substvars -cdebian/control -Pdebian/.debhelper/libisospec\+\+2t64/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=libisospec\+\+2t64-dbgsym "-DDepends=libisospec++2t64 (= \${binary:Version})" "-DDescription=debug symbols for libisospec++2t64" -DBuild-Ids=f56f3635dc5c3d11f7c43637f1f44a48b44587d3 -DSection=debug -UReplaces -UBreaks 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 -cdebian/control -Pdebian/python3-isospec chmod 0644 -- debian/.debhelper/libisospec\+\+2t64/dbgsym-root/DEBIAN/control chown 0:0 -- debian/.debhelper/libisospec\+\+2t64/dbgsym-root/DEBIAN/control dpkg-gencontrol -plibisospec\+\+2t64 -ldebian/changelog -Tdebian/libisospec\+\+2t64.substvars -cdebian/control -Pdebian/libisospec\+\+2t64 chmod 0644 -- debian/libisospec\+\+-dev/DEBIAN/control chown 0:0 -- debian/libisospec\+\+-dev/DEBIAN/control chmod 0644 -- debian/libisospec\+\+2t64/DEBIAN/control chown 0:0 -- debian/libisospec\+\+2t64/DEBIAN/control chmod 0644 -- debian/python3-isospec/DEBIAN/control chown 0:0 -- debian/python3-isospec/DEBIAN/control chmod 0644 -- debian/libisospec\+\+-doc/DEBIAN/control chown 0:0 -- debian/libisospec\+\+-doc/DEBIAN/control dh_md5sums install -m0755 -d debian/libisospec\+\+-dev/DEBIAN install -m0755 -d debian/libisospec\+\+-doc/DEBIAN install -m0755 -d debian/libisospec\+\+2t64/DEBIAN install -m0755 -d debian/python3-isospec/DEBIAN cd debian/libisospec++2t64 >/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 chmod 0644 -- debian/libisospec\+\+2t64/DEBIAN/md5sums chown 0:0 -- debian/libisospec\+\+2t64/DEBIAN/md5sums install -m0755 -d debian/.debhelper/libisospec\+\+2t64/dbgsym-root/DEBIAN cd debian/libisospec++-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums 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 cd debian/libisospec++-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libisospec\+\+-dev/DEBIAN/md5sums chown 0:0 -- debian/libisospec\+\+-dev/DEBIAN/md5sums chmod 0644 -- debian/libisospec\+\+-doc/DEBIAN/md5sums chown 0:0 -- debian/libisospec\+\+-doc/DEBIAN/md5sums cd debian/.debhelper/libisospec++2t64/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\+\+2t64/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/libisospec\+\+2t64/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 dh_builddeb dpkg-deb --build debian/libisospec\+\+-dev .. dpkg-deb --build debian/libisospec\+\+2t64 .. dpkg-deb --root-owner-group --build debian/.debhelper/libisospec\+\+2t64/dbgsym-root .. dpkg-deb --build debian/libisospec\+\+-doc .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-isospec/dbgsym-root .. dpkg-deb: building package 'libisospec++-dev' in '../libisospec++-dev_2.2.1-4.1_amd64.deb'. dpkg-deb --build debian/python3-isospec .. dpkg-deb: building package 'libisospec++2t64-dbgsym' in '../libisospec++2t64-dbgsym_2.2.1-4.1_amd64.deb'. dpkg-deb: building package 'libisospec++-doc' in '../libisospec++-doc_2.2.1-4.1_all.deb'. dpkg-deb: building package 'libisospec++2t64' in '../libisospec++2t64_2.2.1-4.1_amd64.deb'. dpkg-deb: building package 'python3-isospec-dbgsym' in '../python3-isospec-dbgsym_2.2.1-4.1_amd64.deb'. dpkg-deb: building package 'python3-isospec' in '../python3-isospec_2.2.1-4.1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../isospec_2.2.1-4.1_amd64.buildinfo dpkg-genchanges --build=binary -O../isospec_2.2.1-4.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3091672/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3091672/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/3091672 and its subdirectories I: Current time: Sat Dec 14 00:46:30 +14 2024 I: pbuilder-time-stamp: 1734086790