Mon May 13 11:51:56 UTC 2024 I: starting to build isospec/unstable/amd64 on jenkins on '2024-05-13 11:51' Mon May 13 11:51:56 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_27/20516/console.log Mon May 13 11:51:56 UTC 2024 I: Downloading source for unstable/isospec=2.2.1-4.1 --2024-05-13 11:51:56-- http://deb.debian.org/debian/pool/main/i/isospec/isospec_2.2.1-4.1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2471 (2.4K) [text/prs.lines.tag] Saving to: ‘isospec_2.2.1-4.1.dsc’ 0K .. 100% 309M=0s 2024-05-13 11:51:56 (309 MB/s) - ‘isospec_2.2.1-4.1.dsc’ saved [2471/2471] Mon May 13 11:51:56 UTC 2024 I: isospec_2.2.1-4.1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: isospec Binary: libisospec++-dev, libisospec++2t64, python3-isospec, libisospec++-doc Architecture: any all Version: 2.2.1-4.1 Maintainer: The Debichem Group Uploaders: Filippo Rusconi Homepage: https://github.com/MatteoLacki/IsoSpec Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/debichem-team/isospec Vcs-Git: https://salsa.debian.org/debichem-team/isospec.git Build-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 Package-List: libisospec++-dev deb libdevel optional arch=any libisospec++-doc deb doc optional arch=all libisospec++2t64 deb libs optional arch=any python3-isospec deb python optional arch=any Checksums-Sha1: 6af6b92579bd20e907cef89f229815a78eef095e 2173213 isospec_2.2.1.orig.tar.gz 0cf29c35867d6bcfc8861edd72420022159549ff 33820 isospec_2.2.1-4.1.debian.tar.xz Checksums-Sha256: 3158f659953918c3eea867bf32afbb2a531187e3c2b504e869b70c7a5edc2383 2173213 isospec_2.2.1.orig.tar.gz bec1f71e66f509178ca846639ba460ecd684f42054b33229e4911dc4676e8c32 33820 isospec_2.2.1-4.1.debian.tar.xz Files: 647bdc19f31afe75d06e434b7ed8fa44 2173213 isospec_2.2.1.orig.tar.gz 40213f0f07cf97e9c2b94ba6329bf1f8 33820 isospec_2.2.1-4.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE496GmCL5m2y8NfJ5v322IrMDrIsFAmXfHi4RHHNseW9uQGRl Ymlhbi5vcmcACgkQv322IrMDrIvU3hAAzp/Pa2brMN80F0f3n0+wdi3BlYJczYQL DK0M24dfxZ6UtnDPJ/bMp0E7K87AynAJ2uyVxPdoYI1t3K2Jvj1Sy4SpL1/Gx0n3 JqWPIGMijjJh0I35itLANyQIles2PJ8DJa6mC9Q3zWBZPoZ1bhrUwq8ryxRHxnbc Th/zYDYo7CzJWKI/01ohrmuN6K3dJWFMH7kSFS48YEUeMMH2mJ6FYtiG0Vjg8dfj XAYxyLLctBmoQXGRITUlDhqiPPrFhPGDiIaenhzXY+XSWLQ/OnRpPHkPxklMVKL1 d7Vhs94ZUDMx2SwRu5IlodgXMGLmFFLPsvLRrCvg+yzWW1E/rrE/I/Nk71nczaxP VGty7mEL6ayHBtc8WOOkRyLE0nzrSK8W1XZr+djqiiyHBjGjqg/f561gv2aVwrg7 Sb907ESNlEX0K5dPc8eBjHgQneEP9uHIcDfqpNccU+GA597DdrF6KvoxDpE/lW+a clJCoB6cLG8nwyrnlKXQQb/DfUyzTqotf6McFZoFpIPbPEdv0xo3jn2whNn5P1qx 6U93/T6ZqE2/K926FshGvcOBr1ayykHj0iuMBoVurTnQCThqJUpjIBTOmxvYKvti cqJgyPWYFiZx4K4S0jzf/m5fkBOK+Aa64xbHUelBKCUG6nd5yuvz2M6rxLeEGXME s/c/miD0Iyc= =DsmR -----END PGP SIGNATURE----- Mon May 13 11:51:56 UTC 2024 I: Checking whether the package is not for us Mon May 13 11:51:56 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Mon May 13 11:51:56 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Mon May 13 12:07:19 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun May 12 23:51:59 -12 2024 I: pbuilder-time-stamp: 1715601119 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: 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/2347544/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ae4a9c572c7044d3ad7e0084dd76008a' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2347544' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.QIDHT3mi/pbuilderrc_qazn --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QIDHT3mi/b1 --logfile b1/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+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 13 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2347544/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 ... 19699 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} libbsd0{a} libcairo2{a} libclang-cpp16t64{a} libclang1-16t64{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} libfmt9{a} libfontbox-java{a} libfontconfig1{a} libfontenc1{a} libfreetype6{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} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} libjxl0.7{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libllvm16t64{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{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} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libsub-override-perl{a} libsynctex2{a} libteckit0{a} libtexlua53-5{a} libtiff6{a} libtool{a} libuchardet0{a} libuv1{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-cffi{a} python3-cffi-backend{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-ply{a} python3-pycparser{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} 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 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, 192 newly installed, 0 to remove and 0 not upgraded. Need to get 277 MB of archives. After unpacking 1028 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024a-4 [255 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 41 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.7.1-5 [441 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libuv1 amd64 1.48.0-2 [147 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.29.3-1 [2167 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.29.3-1 [10.7 MB] Get: 56 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.106 [10.9 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 dh-exec amd64 0.29 [25.4 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20240422 [107 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libllvm16t64 amd64 1:16.0.6-27 [23.1 MB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libclang-cpp16t64 amd64 1:16.0.6-27 [11.5 MB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libclang1-16t64 amd64 1:16.0.6-27 [6581 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 libfmt9 amd64 9.1.0+ds1-2 [113 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 doxygen amd64 1.9.8+ds-2+b1 [4913 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 93 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libgs-common all 10.03.0~dfsg-1 [148 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 libgs10-common all 10.03.0~dfsg-1 [474 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-13+b2 [112 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-13+b2 [43.3 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.14.10-4+b1 [203 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-13+b2 [47.0 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.7-1.2+b1 [247 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libidn12 amd64 1.42-2 [80.4 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libijs-0.35 amd64 0.35-15.1+b1 [15.1 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b2 [64.3 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3 [167 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b1 [12.9 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1 [113 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1 [311 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.10-1+b1 [56.7 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1+b1 [33.6 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2 [187 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libgs10 amd64 10.03.0~dfsg-1 [2509 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 ghostscript amd64 10.03.0~dfsg-1 [50.1 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.4.1-1 [547 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.17.6-1+b2 [9856 B] Get: 129 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b1 [187 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.17.6-1+b2 [13.1 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.17.6-1+b2 [284 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libhwy1t64 amd64 1.0.7-8.1 [526 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libjxl0.7 amd64 0.7.0-10.2+b3 [1068 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1 [123 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libwmflite-0.2-7 amd64 0.2.13-1.1+b2 [75.4 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libgraphicsmagick-q16-3t64 amd64 1.4+really1.3.43-1 [1200 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 graphicsmagick amd64 1.4+really1.3.43-1 [1068 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 graphicsmagick-imagemagick-compat all 1.4+really1.3.43-1 [16.4 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 29-2 [5276 B] Get: 141 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-1 [114 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b1 [27.9 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.80.2-1 [1485 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 7.2.6-7 [150 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2023.20230311.66589-9+b2 [154 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b1 [9176 B] Get: 159 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b1 [25.2 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2023.20230311.66589-9+b2 [47.2 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 166 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2023.20230311.66589-9+b2 [62.2 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1 [339 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2023.20230311.66589-9+b2 [113 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b2 [58.7 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b1 [56.1 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.14-1+b2 [199 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.2+b1 [56.2 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.18 [32.5 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1 [350 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-cffi-backend amd64 1.16.0-2+b2 [112 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3-ply all 3.11-6 [63.7 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-pycparser all 2.22-1 [78.0 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-cffi all 1.16.0-2 [88.5 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2023.20230311.66589-9+b2 [8495 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2023.20240207-1 [22.0 MB] Get: 186 http://deb.debian.org/debian unstable/main amd64 texlive-font-utils all 2023.20240207-1 [7046 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2023.20240207-1 [4990 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2023.20240207-1 [1255 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 191 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2023.20240207-1 [19.7 MB] Get: 192 http://deb.debian.org/debian unstable/main amd64 texlive-plain-generic all 2023.20240207-1 [29.0 MB] Fetched 277 MB in 20s (13.7 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 ... 19699 files and directories currently installed.) Preparing to unpack .../poppler-data_0.4.12-1_all.deb ... Unpacking poppler-data (0.4.12-1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20549 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Not building database; man-db/auto-update is not 'true'. Setting up libclang-cpp16t64 (1:16.0.6-27) ... Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up doxygen (1.9.8+ds-2+b1) ... Setting up libpython3.11-dev:amd64 (3.11.9-1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2) ... Setting up cmake (3.29.3-1) ... Setting up libcups2t64:amd64 (2.4.7-1.2+b1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b2) ... Setting up libpython3-dev:amd64 (3.11.8-1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up python3.11-dev (3.11.9-1) ... Setting up preview-latex-style (13.2-1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up dh-exec (0.29) ... Setting up libxaw7:amd64 (2:1.0.14-1+b2) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up texlive-binaries (2023.20230311.66589-9+b2) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up python3-lib2to3 (3.12.3-1) ... Setting up texlive-base (2023.20240207-1) ... 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 python3-cffi-backend:amd64 (1.16.0-2+b2) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.12.3-1) ... Setting up libgs10-common (10.03.0~dfsg-1) ... Setting up python3-setuptools (68.1.2-2) ... Setting up python3-ply (3.11-6) ... Setting up texlive-plain-generic (2023.20240207-1) ... Setting up texlive-font-utils (2023.20240207-1) ... Setting up python3-pycparser (2.22-1) ... Setting up texlive-latex-base (2023.20240207-1) ... Setting up python3-dev (3.11.8-1) ... Setting up texlive-latex-recommended (2023.20240207-1) ... Setting up texlive-pictures (2023.20240207-1) ... Setting up texlive-fonts-recommended (2023.20240207-1) ... Setting up libgs10:amd64 (10.03.0~dfsg-1) ... Setting up dh-python (6.20240422) ... Setting up python3-cffi (1.16.0-2) ... Setting up texlive-latex-extra (2023.20240207-1) ... Setting up ghostscript (10.03.0~dfsg-1) ... Setting up libheif-plugin-dav1d:amd64 (1.17.6-1+b2) ... Setting up libheif-plugin-libde265:amd64 (1.17.6-1+b2) ... Setting up libheif1:amd64 (1.17.6-1+b2) ... Setting up libgraphicsmagick-q16-3t64 (1.4+really1.3.43-1) ... Setting up graphicsmagick (1.4+really1.3.43-1) ... Setting up graphicsmagick-imagemagick-compat (1.4+really1.3.43-1) ... Processing triggers for libc-bin (2.38-11) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.34-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/isospec-2.2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 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 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- 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 (4.3s) -- 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 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 (1.5s) -- 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 3.11 I: pybuild base:311: python3.11 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 3.11 I: pybuild base:311: python3.11 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' 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 -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++-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++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.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 -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++-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 [ 50%] 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 [ 75%] 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' [ 75%] Built target IsoSpec++-shared [100%] 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' [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 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 (1.9s) -- Generating done (0.0s) -- 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[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++-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 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". 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]: 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]: 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++-static.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 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 (1.8s) -- 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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[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. 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, 940760 bytes). Transcript written on refman.log. makeindex refman.idx This is makeindex, version 2.17 [TeX Live 2023] (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_generator.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_m arginal.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_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, 1051221 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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(/usr/share/texlive/texmf-dist/tex/latex/caption/caption.sty (/usr/share/texlive/texmf-dist/tex/latex/caption/caption3.sty) (/usr/share/texlive/texmf-dist/tex/latex/caption/ltcaption.sty)) (/usr/share/texlive/texmf-dist/tex/latex/etoc/etoc.sty) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./refman.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (./refman.out) (./refman.out) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}{/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_generator.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_m arginal.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_precalcu lated_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, 1050915 bytes). Transcript written on refman.log. makeindex refman.idx This is makeindex, version 2.17 [TeX Live 2023] (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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[1{/var/lib/texmf/fo nts/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_generator.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_m arginal.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_precalcu lated_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, 1050915 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-HuVj4Ne0 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 3.11 I: pybuild base:311: python3.11 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++-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". 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++-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 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++-static.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++-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 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 (3.9s) -- Generating done (0.7s) -- 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++-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". 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++-static.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++-shared.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 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 (2.1s) -- 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... 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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/fo nts/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_i so_generator.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_m arginal.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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[87] Underfull \hbox (badness 10000) detected at line 191 [][][] Package longtable Warning: Column widths have changed (longtable) in table 6.11 on input line 214. [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_precalcu lated_marginal.pdf> [96] [97] [98] Package longtable Warning: Column widths have changed (longtable) in table 6.12 on input line 166. Underfull \hbox (badness 10000) detected at line 167 [][][] [99] Package longtable Warning: Column widths have changed (longtable) in table 6.13 on input line 205. Underfull \hbox (badness 10000) detected at line 206 [][][] Package longtable Warning: Column widths have changed (longtable) in table 6.14 on input line 227. 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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, 940760 bytes). Transcript written on refman.log. makeindex refman.idx This is makeindex, version 2.17 [TeX Live 2023] (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_generator.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, 1051221 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_m arginal.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_precalcu lated_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, 1050915 bytes). 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[1{/var/lib/texmf/fo nts/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_generator.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_m arginal.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_precalcu lated_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, 1050915 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 3.11 --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_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/__init__.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/isoFFI.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/Distributions.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/Formulas.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/Advanced.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/PeriodicTbl.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/IsoSpecPy.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/confs_passthrough.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/IsoSpecPyOld.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy copying IsoSpecPy/approximations.py -> /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy running build_ext building 'IsoSpecCppPy' extension creating build creating build/temp.linux-x86_64-cpython-311 creating build/temp.linux-x86_64-cpython-311/IsoSpec++ x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -Werror=implicit-function-declaration -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -O2 -Werror=implicit-function-declaration -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/python3.11 -c IsoSpec++/python-build.cpp -o build/temp.linux-x86_64-cpython-311/IsoSpec++/python-build.o -O3 -std=c++17 cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -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-311/IsoSpec++/python-build.o -L/usr/lib/x86_64-linux-gnu -o /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecCppPy.cpython-311-x86_64-linux-gnu.so running install_lib creating /build/reproducible-path/isospec-2.2.1/debian/python3-isospec creating /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr creating /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib creating /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11 creating /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages creating /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/__init__.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/isoFFI.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/Distributions.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/Formulas.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/Advanced.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/PeriodicTbl.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/IsoSpecPy.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/confs_passthrough.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/IsoSpecPyOld.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecPy/approximations.py -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy copying /build/reproducible-path/isospec-2.2.1/.pybuild/cpython3_3.11_isospec/build/IsoSpecCppPy.cpython-311-x86_64-linux-gnu.so -> /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/__init__.py to __init__.cpython-311.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/isoFFI.py to isoFFI.cpython-311.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/Distributions.py to Distributions.cpython-311.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/Formulas.py to Formulas.cpython-311.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/Advanced.py to Advanced.cpython-311.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/PeriodicTbl.py to PeriodicTbl.cpython-311.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/IsoSpecPy.py to IsoSpecPy.cpython-311.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/confs_passthrough.py to confs_passthrough.cpython-311.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/IsoSpecPyOld.py to IsoSpecPyOld.cpython-311.pyc byte-compiling /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy/approximations.py to approximations.cpython-311.pyc running install_egg_info running egg_info creating IsoSpecPy.egg-info writing IsoSpecPy.egg-info/PKG-INFO writing dependency_links to IsoSpecPy.egg-info/dependency_links.txt writing requirements to IsoSpecPy.egg-info/requires.txt writing top-level names to IsoSpecPy.egg-info/top_level.txt writing manifest file 'IsoSpecPy.egg-info/SOURCES.txt' reading manifest file 'IsoSpecPy.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'IsoSpecPy/*.dll' adding license file 'LICENCE' writing manifest file 'IsoSpecPy.egg-info/SOURCES.txt' Copying IsoSpecPy.egg-info to /build/reproducible-path/isospec-2.2.1/debian/python3-isospec/usr/lib/python3.11/dist-packages/IsoSpecPy-2.2.1.egg-info Skipping SOURCES.txt running install_scripts # Install the C++ library dh_auto_install -O--buildsystem=cmake install -m0755 -d /build/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: 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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/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\+\+-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\+\+-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 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 dh_installman install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_Allocator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Allocator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ConfEqual.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfEqual.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ConfOrder.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrder.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginal.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ConfOrderMarginalDescending.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_DirtyAllocator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_DirtyAllocator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_FixedEnvelope.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_FixedEnvelope.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_Iso.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Iso.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoLayeredGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoOrderedGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoStochasticGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_IsoThresholdGenerator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_KeyHasher.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_KeyHasher.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_LayeredMarginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_LayeredMarginal.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_Marginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Marginal.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_MarginalTrek.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_MarginalTrek.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_OrderMarginalsBySizeDecresing.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ProbAndConfPtr.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_ReverseOrder.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_ReverseOrder.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_SSummator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_SSummator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_Summator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Summator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_TableOrder.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TableOrder.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/IsoSpec_TSummator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TSummator.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/pod_vector.3 debian/libisospec\+\+-dev/usr/share/man/man3/pod_vector.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/unsafe_pod_vector.3 debian/libisospec\+\+-dev/usr/share/man/man3/unsafe_pod_vector.3 install -m0755 -d debian/libisospec\+\+-dev/usr/share/man/man3/ install -p -m0644 debian/tmp/usr/share/man/man3/ws_match_res.3 debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_Allocator.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_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_DirtyAllocator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_FixedEnvelope.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_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_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_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_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_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_OrderMarginalsBySizeDecresing.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_PrecalculatedMarginal.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_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_TSummator.3 debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_TableOrder.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/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_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/pod_vector.3 debian/libisospec\+\+-dev/usr/share/man/man3/unsafe_pod_vector.3 man-recode --to-code UTF-8 --suffix .dh-new debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3.dh-new debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3 chmod 0644 -- debian/libisospec\+\+-dev/usr/share/man/man3/ws_match_res.3 mv debian/libisospec\+\+-dev/usr/share/man/man3/IsoSpec_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.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_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/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_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_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_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/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_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_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_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_python3:179: version: 6.20240422 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=None) D: dh_python3 dh_python3:182: supported Python versions: 3.11,3.12 (default=3.11) 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_python3:204: processing package python3-isospec... D: dh_python3 fs:50: moving files from debian/python3-isospec/usr/lib/python3.11/dist-packages to debian/python3-isospec/usr/lib/python3/dist-packages/ D: dh_python3 fs:335: 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('3.11')}, 'ext_no_version': set()} D: dh_python3 depends:103: generating dependencies for package python3-isospec D: dh_python3 pydist:173: trying to find dependency for cffi (python=None) D: dh_python3 pydist:207: dependency: module seems to be installed D: dh_python3 pydist:218: dependency: requirement already has hardcoded version D: dh_python3 depends:253: D={'python3-cffi-backend-api-min (<= 9729), python3-cffi-backend-api-max (>= 9729)', 'python3 (>= 3.11~)', 'python3 (<< 3.12)', 'python3:any'}; 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/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/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/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/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/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_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/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/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/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/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/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/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/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/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/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.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/tab_h.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/class_iso_spec_1_1_iso_generator.png using File::StripNondeterminism::handlers::png Normalizing debian/libisospec++-doc/usr/share/doc/isospec/html/open.png using File::StripNondeterminism::handlers::png dh_compress cd debian/libisospec++2t64 cd debian/python3-isospec cd debian/libisospec++-dev cd debian/libisospec++-doc chmod a-x usr/share/doc/libisospec\+\+2t64/changelog usr/share/doc/libisospec\+\+2t64/changelog.Debian gzip -9nf 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/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 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/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/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' cd '/build/reproducible-path/isospec-2.2.1' dh_fixperms find debian/python3-isospec -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/libisospec++2t64 -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++-doc -true -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 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 ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libisospec\+\+-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/libisospec\+\+-doc ! -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/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\+\+-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/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\+\+2t64/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libisospec\+\+-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/python3-isospec/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/libisospec\+\+2t64/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/libisospec\+\+-dev/usr/share/man debian/libisospec\+\+-dev/usr/include -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-isospec -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 -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/libisospec\+\+-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 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/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/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w 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-311-x86_64-linux-gnu.so dh_strip -a strip --strip-debug --remove-section=.comment --remove-section=.note --enable-deterministic-archives -R .gnu.lto_\* -R .gnu.debuglto_\* -N __gnu_lto_slim -N __gnu_lto_v1 debian/libisospec\+\+-dev/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.a install -m0755 -d debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/78 objcopy --only-keep-debug --compress-debug-sections debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-311-x86_64-linux-gnu.so debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/78/08744fe8bdb547694256d0b99b43db32172eb6.debug install -m0755 -d debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/lib/debug/.build-id/55 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/55/ad5937539d835176784477cfb83d467f547419.debug chmod 0644 -- debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/lib/debug/.build-id/55/ad5937539d835176784477cfb83d467f547419.debug chown 0:0 -- debian/.debhelper/libisospec\+\+2t64/dbgsym-root/usr/lib/debug/.build-id/55/ad5937539d835176784477cfb83d467f547419.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/55/ad5937539d835176784477cfb83d467f547419.debug debian/libisospec\+\+2t64/usr/lib/x86_64-linux-gnu/libIsoSpec\+\+.so.2.2.1 chmod 0644 -- debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/78/08744fe8bdb547694256d0b99b43db32172eb6.debug chown 0:0 -- debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/78/08744fe8bdb547694256d0b99b43db32172eb6.debug strip --remove-section=.comment --remove-section=.note --strip-unneeded debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-311-x86_64-linux-gnu.so 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 objcopy --add-gnu-debuglink debian/.debhelper/python3-isospec/dbgsym-root/usr/lib/debug/.build-id/78/08744fe8bdb547694256d0b99b43db32172eb6.debug debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-311-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/python3-isospec/DEBIAN dpkg-shlibdeps -Tdebian/python3-isospec.substvars debian/python3-isospec/usr/lib/python3/dist-packages/IsoSpecCppPy.cpython-311-x86_64-linux-gnu.so 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 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/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=7808744fe8bdb547694256d0b99b43db32172eb6 -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=55ad5937539d835176784477cfb83d467f547419 -DSection=debug -UReplaces -UBreaks 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 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/.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/libisospec\+\+-dev/DEBIAN/control chown 0:0 -- debian/libisospec\+\+-dev/DEBIAN/control chmod 0644 -- debian/libisospec\+\+-doc/DEBIAN/control chown 0:0 -- debian/libisospec\+\+-doc/DEBIAN/control chmod 0644 -- debian/libisospec\+\+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 dh_md5sums install -m0755 -d debian/libisospec\+\+-dev/DEBIAN install -m0755 -d debian/libisospec\+\+2t64/DEBIAN install -m0755 -d debian/python3-isospec/DEBIAN install -m0755 -d debian/libisospec\+\+-doc/DEBIAN cd debian/libisospec++2t64 >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libisospec++-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/libisospec\+\+-dev/DEBIAN/md5sums chown 0:0 -- debian/libisospec\+\+-dev/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/python3-isospec >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libisospec++-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/.debhelper/libisospec++2t64/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/python3-isospec/DEBIAN/md5sums chown 0:0 -- debian/python3-isospec/DEBIAN/md5sums install -m0755 -d debian/.debhelper/python3-isospec/dbgsym-root/DEBIAN cd debian/.debhelper/python3-isospec/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/python3-isospec/dbgsym-root/DEBIAN/md5sums chown 0:0 -- debian/.debhelper/python3-isospec/dbgsym-root/DEBIAN/md5sums chmod 0644 -- debian/libisospec\+\+-doc/DEBIAN/md5sums chown 0:0 -- debian/libisospec\+\+-doc/DEBIAN/md5sums dh_builddeb dpkg-deb --build debian/libisospec\+\+2t64 .. dpkg-deb --build debian/libisospec\+\+-dev .. dpkg-deb --root-owner-group --build debian/.debhelper/python3-isospec/dbgsym-root .. dpkg-deb --build debian/libisospec\+\+-doc .. dpkg-deb --build debian/python3-isospec .. dpkg-deb --root-owner-group --build debian/.debhelper/libisospec\+\+2t64/dbgsym-root .. dpkg-deb: building package 'libisospec++2t64' in '../libisospec++2t64_2.2.1-4.1_amd64.deb'. dpkg-deb: building package 'libisospec++-dev' in '../libisospec++-dev_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-deb: building package 'libisospec++-doc' in '../libisospec++-doc_2.2.1-4.1_all.deb'. dpkg-deb: building package 'libisospec++2t64-dbgsym' in '../libisospec++2t64-dbgsym_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: 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/2347544 and its subdirectories I: Current time: Mon May 13 00:07:18 -12 2024 I: pbuilder-time-stamp: 1715602038 Mon May 13 12:07:20 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Mon May 13 12:07:20 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Mon May 13 12:12:10 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Mon May 13 12:12:11 UTC 2024 I: isospec_2.2.1-4.1_amd64.changes: Format: 1.8 Date: Wed, 28 Feb 2024 11:50:05 +0000 Source: isospec Binary: libisospec++-dev libisospec++-doc libisospec++2t64 libisospec++2t64-dbgsym python3-isospec python3-isospec-dbgsym Architecture: amd64 all Version: 2.2.1-4.1 Distribution: unstable Urgency: medium Maintainer: The Debichem Group Changed-By: Lukas Märdian Description: libisospec++-dev - Isotopic fine structure calculator (C++ development files) libisospec++-doc - Isotopic fine structure calculator (C++ API documentation) libisospec++2t64 - Isotopic fine structure calculator (C++ runtime) python3-isospec - Isotopic fine structure calculator for Python 3 Closes: 1062459 Changes: isospec (2.2.1-4.1) unstable; urgency=medium . * Non-maintainer upload. * Rename libraries for 64-bit time_t transition. Closes: #1062459 Checksums-Sha1: d654421021867cd4f4a6af4380d7972fe381ff8b 12002 isospec_2.2.1-4.1_amd64.buildinfo da06011a73e5c83f72a8d3ac846a5c575bf18568 127656 libisospec++-dev_2.2.1-4.1_amd64.deb 63ccee42711eb4ee30b4db802b702060788b182c 1552200 libisospec++-doc_2.2.1-4.1_all.deb 183454c29241059eb904bd4703f4127bd78293fc 294356 libisospec++2t64-dbgsym_2.2.1-4.1_amd64.deb 3e51f26fce4e1bcae6b7815c509fece9d893b3e5 67052 libisospec++2t64_2.2.1-4.1_amd64.deb 6bd3d1c1f1b976f2f1dc5a3dea83303e34549aa2 307928 python3-isospec-dbgsym_2.2.1-4.1_amd64.deb 442776bae9ea71c8c176167ed1e2525dd34719c8 85772 python3-isospec_2.2.1-4.1_amd64.deb Checksums-Sha256: c11612a34b2811417cc15b6b7c7790c1b0ac4dff09214c66c10ec31b3a6bf066 12002 isospec_2.2.1-4.1_amd64.buildinfo 63e926b8b75d31b99187257a2e3090b8225f40e45a57ebfdc0c953725cdaa304 127656 libisospec++-dev_2.2.1-4.1_amd64.deb 23889c88c2f9ccfc8c3a9895f4bf2ec9a201c90b1d6d7a7bd62aa9e6d15b7737 1552200 libisospec++-doc_2.2.1-4.1_all.deb 59c96e74410f33649a57e07f8421379d99d58c747e1dd99e34f6baa49d464216 294356 libisospec++2t64-dbgsym_2.2.1-4.1_amd64.deb 88b1a105440ead6028985deab7a1c022da195eef80c2b2665cd1102a70d57fae 67052 libisospec++2t64_2.2.1-4.1_amd64.deb 438099deb6dae521623b47fcc9a3c4ced9fe982b91b4b96c9f9a0d56616baa97 307928 python3-isospec-dbgsym_2.2.1-4.1_amd64.deb 5348330a05f6820b1b551cc54c27d0d82cc04587638809dc193dd903e2066517 85772 python3-isospec_2.2.1-4.1_amd64.deb Files: 1ccf7270e3e0d8b5041b78f8d60f8a72 12002 science optional isospec_2.2.1-4.1_amd64.buildinfo 6a2a0e6a16c5463fc46ef98638cf15e3 127656 libdevel optional libisospec++-dev_2.2.1-4.1_amd64.deb dbeb5e663d3f67bee158dc331cc40de1 1552200 doc optional libisospec++-doc_2.2.1-4.1_all.deb da3a04c5effa8fe859090a8b236d8fd0 294356 debug optional libisospec++2t64-dbgsym_2.2.1-4.1_amd64.deb f9aa99e3dca79dca445282b96f08a879 67052 libs optional libisospec++2t64_2.2.1-4.1_amd64.deb 533d683ab3ccc6b51482744e75231bd8 307928 debug optional python3-isospec-dbgsym_2.2.1-4.1_amd64.deb 1673dc64cf2538656f61192fc7dd94e2 85772 python optional python3-isospec_2.2.1-4.1_amd64.deb Mon May 13 12:12:13 UTC 2024 I: diffoscope 266 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_27-20516.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QIDHT3mi/isospec_2.2.1-4.1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QIDHT3mi/isospec_2.2.1-4.1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QIDHT3mi/isospec_2.2.1-4.1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QIDHT3mi/b1/isospec_2.2.1-4.1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QIDHT3mi/b2/isospec_2.2.1-4.1_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.871s) 0.871s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.220s) 0.220s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 1.206s CPU time consumed: 1.100s Mon May 13 12:12:14 UTC 2024 I: diffoscope 266 found no differences in the changes files, and a .buildinfo file also exists. Mon May 13 12:12:14 UTC 2024 I: isospec from unstable built successfully and reproducibly on amd64. Mon May 13 12:12:16 UTC 2024 I: Submitting .buildinfo files to external archives: Mon May 13 12:12:16 UTC 2024 I: Submitting 16K b1/isospec_2.2.1-4.1_amd64.buildinfo.asc Mon May 13 12:12:17 UTC 2024 I: Submitting 16K b2/isospec_2.2.1-4.1_amd64.buildinfo.asc Mon May 13 12:12:17 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 13 12:12:17 UTC 2024 I: Done submitting .buildinfo files. Mon May 13 12:12:17 UTC 2024 I: Removing signed isospec_2.2.1-4.1_amd64.buildinfo.asc files: removed './b1/isospec_2.2.1-4.1_amd64.buildinfo.asc' removed './b2/isospec_2.2.1-4.1_amd64.buildinfo.asc'