sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-05.freexian.com
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| isospec 2.2.1-4.1 (arm64) Sat, 16 Nov 2024 19:11:30 +0000 |
+==============================================================================+
Package: isospec
Version: 2.2.1-4.1
Source Version: 2.2.1-4.1
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: binary
I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/957781/system.tar.xz to /tmp/tmp.sbuild.Ku9s4y8VtP...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
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| Chroot Setup Commands |
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rm -f /etc/resolv.conf
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I: Finished running 'rm -f /etc/resolv.conf'.
Finished processing commands.
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Copying /tmp/debusine-fetch-exec-upload-_b_eafob/dpkg-dbgsym_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_b_eafob/dpkg_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_b_eafob/dselect-dbgsym_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_b_eafob/dselect_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_b_eafob/libdpkg-dev_1.22.12~1.gbp82cafd_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_b_eafob/dpkg-dev_1.22.12~1.gbp82cafd_all.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-_b_eafob/libdpkg-perl_1.22.12~1.gbp82cafd_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/isospec-dlPgc8/resolver-wjuRNw' with '<<RESOLVERDIR>>'
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| Update chroot |
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Get:1 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ InRelease
Ign:1 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ InRelease
Get:2 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ Release [606 B]
Get:2 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ Release [606 B]
Get:3 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ Release.gpg
Ign:3 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ Release.gpg
Get:4 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ Packages [9246 B]
Get:5 http://deb.debian.org/debian sid InRelease [202 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9951 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 Components [4911 kB]
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Reading package lists...
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Calculating upgrade...
The following packages will be upgraded:
apt bsdextrautils bsdutils debianutils dpkg dpkg-dev libapt-pkg6.0t64
libaudit-common libaudit1 libblkid1 libbrotli1 libcap-ng0 libdpkg-perl
libglib2.0-0t64 libmarkdown2 libmount1 libpcre2-8-0 libseccomp2 libselinux1
libsemanage2 libsmartcols1 libsystemd0 libudev1 libuuid1 libxml2 login
login.defs mount passwd util-linux
30 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 9274 kB/12.8 MB of archives.
After this operation, 603 kB disk space will be freed.
Get:1 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ dpkg 1.22.12~1.gbp82cafd [1513 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 bsdutils arm64 1:2.40.2-11 [104 kB]
Get:3 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ dpkg-dev 1.22.12~1.gbp82cafd [1337 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 debianutils arm64 5.21 [92.1 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 libsystemd0 arm64 257~rc2-3 [416 kB]
Get:6 file:/build/isospec-dlPgc8/resolver-gT2Bd2/apt_archive ./ libdpkg-perl 1.22.12~1.gbp82cafd [647 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 libudev1 arm64 257~rc2-3 [139 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.11 [921 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 libblkid1 arm64 2.40.2-11 [162 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libmount1 arm64 2.40.2-11 [190 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 libsmartcols1 arm64 2.40.2-11 [135 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 mount arm64 2.40.2-11 [153 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 libuuid1 arm64 2.40.2-11 [35.7 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 util-linux arm64 2.40.2-11 [1170 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libpcre2-8-0 arm64 10.44-4 [243 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libselinux1 arm64 3.7-3+b1 [72.1 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libseccomp2 arm64 2.5.5-1+b3 [46.8 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.11 [1287 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libaudit-common all 1:4.0.2-2 [12.7 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 libcap-ng0 arm64 0.8.5-3+b1 [17.0 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 libaudit1 arm64 1:4.0.2-2 [54.2 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 login arm64 1:4.16.0-2+really2.40.2-11 [80.0 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 login.defs all 1:4.16.0-5 [185 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libsemanage2 arm64 3.7-2+b1 [84.5 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 passwd arm64 1:4.16.0-5 [1210 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 libmarkdown2 arm64 2.2.7-2.1 [33.1 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Preparing to unpack .../9-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_arm64.deb ...
Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) over (2.12.7+dfsg+really2.9.14-0.1) ...
Setting up bsdextrautils (2.40.2-11) ...
Setting up login.defs (1:4.16.0-5) ...
Installing new version of config file /etc/login.defs ...
Setting up libbrotli1:arm64 (1.1.0-2+b6) ...
Setting up libglib2.0-0t64:arm64 (2.82.2-3) ...
No schema files found: doing nothing.
Setting up libdpkg-perl (1.22.12~1.gbp82cafd) ...
Setting up mount (2.40.2-11) ...
Setting up libsemanage2:arm64 (3.7-2+b1) ...
Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up libmarkdown2:arm64 (2.2.7-2.1) ...
Setting up login (1:4.16.0-2+really2.40.2-11) ...
Setting up dpkg-dev (1.22.12~1.gbp82cafd) ...
Setting up passwd (1:4.16.0-5) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for libc-bin (2.40-3) ...
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| Fetch source files |
+------------------------------------------------------------------------------+
Local sources
-------------
/tmp/debusine-fetch-exec-upload-_b_eafob/isospec_2.2.1-4.1.dsc exists in /tmp/debusine-fetch-exec-upload-_b_eafob; copying to chroot
I: NOTICE: Log filtering will replace 'build/isospec-dlPgc8/isospec-2.2.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/isospec-dlPgc8' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged 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, build-essential, fakeroot
Filtered 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, build-essential, fakeroot
dpkg-deb: warning: root directory has unusual owner or group 998:999.
Hint: either pass --root-owner-group, see dpkg-build-api(7) or add an explicit 'Rules-Requires-Root: no' in debian/control.
dpkg-deb: warning: ignoring 1 warning about the control file(s)
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
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Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [966 B]
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Reading package lists...
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Ign:3 file:/<<BUILDDIR>>/resolver-gT2Bd2/apt_archive ./ Release.gpg
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev build-essential cmake cmake-data
cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu d-shlibs debhelper
dh-autoreconf dh-exec dh-python dh-strip-nondeterminism doxygen dwz fakeroot
fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern
fonts-mathjax fonts-urw-base35 g++ g++-14 g++-14-aarch64-linux-gnu
g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu
gcc-aarch64-linux-gnu ghostscript graphicsmagick
graphicsmagick-imagemagick-compat libapache-pom-java libarchive13t64
libasan8 libavahi-client3 libavahi-common-data libavahi-common3 libc-dev-bin
libc6-dev libcairo2 libcc1-0 libclang-cpp19 libclang1-19
libcommons-logging-java libcommons-parent-java libcrypt-dev libcups2t64
libcurl4t64 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0
libedit2 libelf1t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfmt10 libfontbox-java libfontconfig1
libfontenc1 libfreetype6 libgcc-14-dev libgif7 libgraphicsmagick-q16-3t64
libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b
libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhwasan0 libhwy1t64
libice6 libidn12 libijs-0.35 libimath-3-1-29t64 libisl23 libitm1 libjbig0
libjbig2dec0 libjpeg62-turbo libjs-jquery libjs-mathjax libjs-sphinxdoc
libjs-underscore libjsoncpp26 libjxl0.9 libkpathsea6 liblcms2-2 liblerc4
libllvm19 liblsan0 libmpc3 libmpfi0 libmpfr6 libncursesw6 libnsl2
libopenexr-3-1-30 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java
libpixman-1-0 libpng16-16t64 libpotrace0 libproc2-0 libptexenc1
libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal
libpython3.12-stdlib libpython3.12t64 librhash1 libsharpyuv0 libsm6
libstdc++-14-dev libsynctex2 libteckit0 libtexlua53-5 libtiff6
libtirpc-common libtirpc3t64 libtool libtsan2 libubsan1 libuv1t64 libwebp7
libwebpmux3 libwmflite-0.2-7 libx11-6 libx11-data libxapian30 libxau6
libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxmu6
libxpm4 libxrender1 libxt6t64 libz3-4 libzzip-0-13t64 linux-libc-dev m4
media-types po-debconf poppler-data preview-latex-style procps python3
python3-autocommand python3-cffi python3-cffi-backend python3-dev
python3-inflect python3-jaraco.context python3-jaraco.functools
python3-jaraco.text python3-minimal python3-more-itertools
python3-pkg-resources python3-ply python3-pycparser python3-setuptools
python3-typeguard python3-typing-extensions python3-zipp python3.12
python3.12-dev python3.12-minimal rpcsvc-proto tex-common texlive-base
texlive-binaries texlive-font-utils texlive-fonts-recommended
texlive-latex-base texlive-latex-extra texlive-latex-recommended
texlive-pictures texlive-plain-generic x11-common xdg-utils xfonts-encodings
xfonts-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
elpa-cmake-mode ninja-build cpp-doc gcc-14-locales cpp-14-doc dh-make flit
python3-build python3-installer python3-wheel doxygen-latex doxygen-doc
doxygen-gui graphviz fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre
gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
gdb-aarch64-linux-gnu graphicsmagick-dbg lrzip libc-devtools glibc-doc
libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java
cups-common libheif-plugin-ffmpegdec libheif-plugin-jpegdec
libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc
libheif-plugin-kvazaar libheif-plugin-rav1e libheif-plugin-svtenc
fonts-mathjax-extras fonts-stix libjs-mathjax-doc liblcms2-utils libmpfi-doc
libstdc++-14-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
xapian-tools m4-doc libmail-box-perl poppler-utils fonts-japanese-mincho
| fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic
fonts-arphic-ukai fonts-arphic-uming fonts-nanum python3-doc python3-tk
python3-venv python-ply-doc python-setuptools-doc python3.12-venv
python3.12-doc binfmt-support perl-tk xpdf | pdf-viewer xzdec
texlive-binaries-sse2 hintview lcdf-typetools psutils
texlive-fonts-recommended-doc texlive-latex-base-doc wp2latex
python3-pygments icc-profiles libfile-which-perl texlive-latex-extra-doc
texlive-science texlive-latex-recommended-doc texlive-luatex
texlive-pstricks dot2tex prerex texlive-pictures-doc vprerex
default-jre-headless
Recommended packages:
manpages manpages-dev dbus libarchive-cpio-perl fonts-droid-fallback
libheif-plugin-x265 libheif-plugin-aomenc javascript-common libgpm2
libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults lmodern
dvisvgm ps2eps tex-gyre tipa default-jre libspreadsheet-parseexcel-perl ruby
tk libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev build-essential cmake cmake-data
cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu d-shlibs debhelper
dh-autoreconf dh-exec dh-python dh-strip-nondeterminism doxygen dwz fakeroot
fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern
fonts-mathjax fonts-urw-base35 g++ g++-14 g++-14-aarch64-linux-gnu
g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu
gcc-aarch64-linux-gnu ghostscript graphicsmagick
graphicsmagick-imagemagick-compat libapache-pom-java libarchive13t64
libasan8 libavahi-client3 libavahi-common-data libavahi-common3 libc-dev-bin
libc6-dev libcairo2 libcc1-0 libclang-cpp19 libclang1-19
libcommons-logging-java libcommons-parent-java libcrypt-dev libcups2t64
libcurl4t64 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0
libedit2 libelf1t64 libexpat1 libexpat1-dev libfakeroot
libfile-stripnondeterminism-perl libfmt10 libfontbox-java libfontconfig1
libfontenc1 libfreetype6 libgcc-14-dev libgif7 libgraphicsmagick-q16-3t64
libgraphite2-3 libgs-common libgs10 libgs10-common libharfbuzz0b
libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhwasan0 libhwy1t64
libice6 libidn12 libijs-0.35 libimath-3-1-29t64 libisl23 libitm1 libjbig0
libjbig2dec0 libjpeg62-turbo libjs-jquery libjs-mathjax libjs-sphinxdoc
libjs-underscore libjsoncpp26 libjxl0.9 libkpathsea6 liblcms2-2 liblerc4
libllvm19 liblsan0 libmpc3 libmpfi0 libmpfr6 libncursesw6 libnsl2
libopenexr-3-1-30 libopenjp2-7 libpaper-utils libpaper1 libpdfbox-java
libpixman-1-0 libpng16-16t64 libpotrace0 libproc2-0 libptexenc1
libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal
libpython3.12-stdlib libpython3.12t64 librhash1 libsharpyuv0 libsm6
libstdc++-14-dev libsynctex2 libteckit0 libtexlua53-5 libtiff6
libtirpc-common libtirpc3t64 libtool libtsan2 libubsan1 libuv1t64 libwebp7
libwebpmux3 libwmflite-0.2-7 libx11-6 libx11-data libxapian30 libxau6
libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxmu6
libxpm4 libxrender1 libxt6t64 libz3-4 libzzip-0-13t64 linux-libc-dev m4
media-types po-debconf poppler-data preview-latex-style procps python3
python3-autocommand python3-cffi python3-cffi-backend python3-dev
python3-inflect python3-jaraco.context python3-jaraco.functools
python3-jaraco.text python3-minimal python3-more-itertools
python3-pkg-resources python3-ply python3-pycparser python3-setuptools
python3-typeguard python3-typing-extensions python3-zipp python3.12
python3.12-dev python3.12-minimal rpcsvc-proto
sbuild-build-depends-main-dummy tex-common texlive-base texlive-binaries
texlive-font-utils texlive-fonts-recommended texlive-latex-base
texlive-latex-extra texlive-latex-recommended texlive-pictures
texlive-plain-generic x11-common xdg-utils xfonts-encodings xfonts-utils
zlib1g-dev
0 upgraded, 203 newly installed, 0 to remove and 0 not upgraded.
Need to get 319 MB of archives.
After this operation, 1223 MB of additional disk space will be used.
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Get:2 http://deb.debian.org/debian sid/main arm64 poppler-data all 0.4.12-1 [1601 kB]
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Get:9 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
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Get:11 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB]
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Get:17 http://deb.debian.org/debian sid/main arm64 procps arm64 2:4.0.4-6 [872 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:21 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.7-1 [2454 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
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Get:35 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-8 [42.2 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-8 [24.2 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-8 [2579 kB]
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Get:40 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-8 [1039 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-8 [1442 kB]
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Get:43 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8 [17.7 MB]
Get:44 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-8 [519 kB]
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Get:51 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:52 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:53 http://deb.debian.org/debian sid/main arm64 cmake-data all 3.31.0-1 [2265 kB]
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Get:80 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.21.0-1 [10.6 kB]
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Get:91 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:92 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:93 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:94 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB]
Get:96 http://deb.debian.org/debian sid/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get:98 http://deb.debian.org/debian sid/main arm64 x11-common all 1:7.7+23.1 [216 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get:102 http://deb.debian.org/debian sid/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB]
Get:103 http://deb.debian.org/debian sid/main arm64 fonts-lmodern all 2.005-1 [4540 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 libgs-common all 10.04.0~dfsg-1 [148 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 libgs10-common all 10.04.0~dfsg-1 [474 kB]
Get:107 http://deb.debian.org/debian sid/main arm64 libavahi-common-data arm64 0.8-13+b3 [112 kB]
Get:108 http://deb.debian.org/debian sid/main arm64 libavahi-common3 arm64 0.8-13+b3 [42.3 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 libdbus-1-3 arm64 1.14.10-6 [196 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 libavahi-client3 arm64 0.8-13+b3 [46.0 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 libcups2t64 arm64 2.4.10-2 [235 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 libidn12 arm64 1.42-2+b1 [80.2 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 libijs-0.35 arm64 0.35-15.1+b2 [14.9 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 libjbig2dec0 arm64 0.20-1+b3 [60.1 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 liblcms2-2 arm64 2.16-2 [151 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 libpaper1 arm64 1.1.29+b2 [13.0 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB]
Get:125 http://deb.debian.org/debian sid/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3+b2 [24.4 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 libx11-data all 2:1.8.10-2 [337 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB]
Get:132 http://deb.debian.org/debian sid/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b1 [173 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 libgs10 arm64 10.04.0~dfsg-1 [2351 kB]
Get:135 http://deb.debian.org/debian sid/main arm64 ghostscript arm64 10.04.0~dfsg-1 [50.5 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 libdav1d7 arm64 1.5.0-1+b1 [248 kB]
Get:137 http://deb.debian.org/debian sid/main arm64 libheif-plugin-dav1d arm64 1.19.3-1 [11.2 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 libde265-0 arm64 1.0.15-1+b2 [153 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 libheif-plugin-libde265 arm64 1.19.3-1 [14.9 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 libheif1 arm64 1.19.3-1 [419 kB]
Get:141 http://deb.debian.org/debian sid/main arm64 libgif7 arm64 5.2.2-1+b1 [44.2 kB]
Get:142 http://deb.debian.org/debian sid/main arm64 libhwy1t64 arm64 1.2.0-2+b1 [500 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 libimath-3-1-29t64 arm64 3.1.12-1+b1 [38.3 kB]
Get:144 http://deb.debian.org/debian sid/main arm64 libopenexr-3-1-30 arm64 3.1.5-5.1+b3 [856 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 libjxl0.9 arm64 0.9.2-10+b1 [811 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 libwmflite-0.2-7 arm64 0.2.13-1.1+b3 [72.0 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB]
Get:149 http://deb.debian.org/debian sid/main arm64 libgraphicsmagick-q16-3t64 arm64 1.4+really1.3.45-1+b1 [1078 kB]
Get:150 http://deb.debian.org/debian sid/main arm64 graphicsmagick arm64 1.4+really1.3.45-1+b1 [1080 kB]
Get:151 http://deb.debian.org/debian sid/main arm64 graphicsmagick-imagemagick-compat all 1.4+really1.3.45-1 [22.1 kB]
Get:152 http://deb.debian.org/debian sid/main arm64 libapache-pom-java all 33-2 [5852 B]
Get:153 http://deb.debian.org/debian sid/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB]
Get:154 http://deb.debian.org/debian sid/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB]
Get:155 http://deb.debian.org/debian sid/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB]
Get:156 http://deb.debian.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB]
Get:157 http://deb.debian.org/debian sid/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get:158 http://deb.debian.org/debian sid/main arm64 libcommons-parent-java all 56-1 [10.8 kB]
Get:159 http://deb.debian.org/debian sid/main arm64 libcommons-logging-java all 1.3.0-1 [68.6 kB]
Get:160 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.4-1 [143 kB]
Get:161 http://deb.debian.org/debian sid/main arm64 libfontbox-java all 1:1.8.16-5 [211 kB]
Get:162 http://deb.debian.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB]
Get:163 http://deb.debian.org/debian sid/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB]
Get:164 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:165 http://deb.debian.org/debian sid/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB]
Get:166 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:167 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
Get:168 http://deb.debian.org/debian sid/main arm64 libkpathsea6 arm64 2024.20240313.70630+ds-5 [153 kB]
Get:169 http://deb.debian.org/debian sid/main arm64 libmpfi0 arm64 1.5.4+ds-4 [34.5 kB]
Get:170 http://deb.debian.org/debian sid/main arm64 libpaper-utils arm64 1.1.29+b2 [9128 B]
Get:171 http://deb.debian.org/debian sid/main arm64 libpdfbox-java all 1:1.8.16-5 [5527 kB]
Get:172 http://deb.debian.org/debian sid/main arm64 libpotrace0 arm64 1.16-2+b2 [23.4 kB]
Get:173 http://deb.debian.org/debian sid/main arm64 libptexenc1 arm64 2024.20240313.70630+ds-5 [47.9 kB]
Get:174 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-3 [1982 kB]
Get:175 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get:176 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-3 [4792 kB]
Get:177 http://deb.debian.org/debian sid/main arm64 libpython3-dev arm64 3.12.7-1 [9980 B]
Get:178 http://deb.debian.org/debian sid/main arm64 libsynctex2 arm64 2024.20240313.70630+ds-5 [60.3 kB]
Get:179 http://deb.debian.org/debian sid/main arm64 libteckit0 arm64 2.5.12+ds1-1+b1 [303 kB]
Get:180 http://deb.debian.org/debian sid/main arm64 libtexlua53-5 arm64 2024.20240313.70630+ds-5 [106 kB]
Get:181 http://deb.debian.org/debian sid/main arm64 libxmu6 arm64 2:1.1.3-3+b3 [55.6 kB]
Get:182 http://deb.debian.org/debian sid/main arm64 libxpm4 arm64 1:3.5.17-1+b2 [53.2 kB]
Get:183 http://deb.debian.org/debian sid/main arm64 libxaw7 arm64 2:1.0.16-1 [195 kB]
Get:184 http://deb.debian.org/debian sid/main arm64 libxi6 arm64 2:1.8.2-1 [77.8 kB]
Get:185 http://deb.debian.org/debian sid/main arm64 libzzip-0-13t64 arm64 0.13.72+dfsg.1-1.3 [56.6 kB]
Get:186 http://deb.debian.org/debian sid/main arm64 tex-common all 6.18 [32.5 kB]
Get:187 http://deb.debian.org/debian sid/main arm64 preview-latex-style all 13.2-1 [350 kB]
Get:188 http://deb.debian.org/debian sid/main arm64 python3-cffi-backend arm64 1.17.1-2+b1 [94.8 kB]
Get:189 http://deb.debian.org/debian sid/main arm64 python3-ply all 3.11-7 [62.6 kB]
Get:190 http://deb.debian.org/debian sid/main arm64 python3-pycparser all 2.22-2 [78.0 kB]
Get:191 http://deb.debian.org/debian sid/main arm64 python3-cffi all 1.17.1-2 [89.4 kB]
Get:192 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-3 [505 kB]
Get:193 http://deb.debian.org/debian sid/main arm64 python3-dev arm64 3.12.7-1 [26.1 kB]
Get:194 http://deb.debian.org/debian sid/main arm64 texlive-binaries arm64 2024.20240313.70630+ds-5 [7358 kB]
Get:195 http://deb.debian.org/debian sid/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:196 http://deb.debian.org/debian sid/main arm64 texlive-base all 2024.20241102-1 [22.7 MB]
Get:197 http://deb.debian.org/debian sid/main arm64 texlive-font-utils all 2024.20241102-1 [6982 kB]
Get:198 http://deb.debian.org/debian sid/main arm64 texlive-fonts-recommended all 2024.20241102-1 [4991 kB]
Get:199 http://deb.debian.org/debian sid/main arm64 texlive-latex-base all 2024.20241102-1 [1278 kB]
Get:200 http://deb.debian.org/debian sid/main arm64 texlive-latex-recommended all 2024.20241102-1 [8757 kB]
Get:201 http://deb.debian.org/debian sid/main arm64 texlive-pictures all 2024.20241102-1 [17.0 MB]
Get:202 http://deb.debian.org/debian sid/main arm64 texlive-latex-extra all 2024.20241102-1 [24.6 MB]
Get:203 http://deb.debian.org/debian sid/main arm64 texlive-plain-generic all 2024.20241102-1 [28.6 MB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking poppler-data (0.4.12-1) ...
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Unpacking libpython3.12-minimal:arm64 (3.12.7-3) ...
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Unpacking libexpat1:arm64 (2.6.4-1) ...
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Unpacking python3.12-minimal (3.12.7-3) ...
Setting up libpython3.12-minimal:arm64 (3.12.7-3) ...
Setting up libexpat1:arm64 (2.6.4-1) ...
Setting up python3.12-minimal (3.12.7-3) ...
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Unpacking python3-minimal (3.12.7-1) ...
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Unpacking libtirpc-common (1.3.4+ds-1.3) ...
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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ...
Selecting previously unselected package libnsl2:arm64.
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Unpacking libnsl2:arm64 (1.3.0-3+b3) ...
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Unpacking libpython3.12-stdlib:arm64 (3.12.7-3) ...
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Unpacking python3.12 (3.12.7-3) ...
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Unpacking libpython3-stdlib:arm64 (3.12.7-1) ...
Setting up python3-minimal (3.12.7-1) ...
Selecting previously unselected package python3.
(Reading database ... 18445 files and directories currently installed.)
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Unpacking python3 (3.12.7-1) ...
Selecting previously unselected package libproc2-0:arm64.
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Unpacking libproc2-0:arm64 (2:4.0.4-6) ...
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Unpacking procps (2:4.0.4-6) ...
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Unpacking m4 (1.4.19-4) ...
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Unpacking autotools-dev (20220109.1) ...
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Unpacking automake (1:1.16.5-1.3) ...
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Unpacking autopoint (0.22.5-2) ...
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Unpacking libc-dev-bin (2.40-3) ...
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Unpacking libcrypt-dev:arm64 (1:4.4.36-5) ...
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Unpacking rpcsvc-proto (1.4.3-1+b1) ...
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Unpacking libc6-dev:arm64 (2.40-3) ...
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Unpacking libisl23:arm64 (0.27-1) ...
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Unpacking libmpfr6:arm64 (4.2.1-1+b2) ...
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Unpacking libmpc3:arm64 (1.3.1-1+b3) ...
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Unpacking cpp (4:14.2.0-1) ...
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Unpacking libtsan2:arm64 (14.2.0-8) ...
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (arm64 included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.12~1.gbp82cafd g++-14_14.2.0-8 gcc-14_14.2.0-8 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 linux-libc-dev_6.11.7-1
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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
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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 <debichem-devel@lists.alioth.debian.org>
Uploaders: Filippo Rusconi <lopippo@debian.org>
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
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-----END PGP SIGNATURE-----
gpgv: Signature made Wed Feb 28 11:51:10 2024 UTC
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 /<<PKGBUILDDIR>>
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
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=debusine-worker
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -b -rfakeroot
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 <slyon@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
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 -j8 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf IsoSpecPy.egg-info build dist
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
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_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 ..
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
[1;31mConfiguring build for project IsoSpec[m
-- [1;32mCMAKE_CXX_COMPILER: /usr/bin/c++[m
-- [1;32mSetting definition -Wno-unknown-pragmas.[m
-- [1;32mSetting definition -Wall.[m
-- [1;32mSetting definition -Wextra.[m
-- [1;32mSetting definition -pedantic.[m
-- [1;32mCMAKE_SOURCE_DIR: /<<PKGBUILDDIR>>[m
-- [1;32mCMAKE_BINARY_DIR: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu[m
[1;31mUNIX non APPLE environment[m
~~~~~~ Instructions ~~~~~~
On UNIX/GNU-Linux, please run the configuration like this:
cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=<Debug | Release> -DCMAKE_INSTALL_PREFIX=</usr | your_dir> ../development
-- [1;32mStarting configuration for the doc material for IsoSpec [m
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).
-- [1;32mFinished configuration of the doc material.[m
-- [1;32mStarting configuration for the example material for IsoSpec [m
-- [1;32mFinished configuration for the example material.[m
[1;31mThe build toolchain is: Linux
[m
-- [1;33mCMAKE_BUILD_TYPE: None.[m
-- [1;33mCMAKE_INSTALL_PREFIX: /usr.[m
[1;31m"Now configuring IsoSpec++/ for IsoSpec"[m
-- Configuring done (1.6s)
-- 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: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu
dh_auto_configure -O--buildsystem=cmake -- \
-DCMAKE_INSTALL_PREFIX=/usr \
-DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2
cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 ..
[1;31mConfiguring build for project IsoSpec[m
-- [1;32mCMAKE_CXX_COMPILER: /usr/bin/c++[m
-- [1;32mSetting definition -Wno-unknown-pragmas.[m
-- [1;32mSetting definition -Wall.[m
-- [1;32mSetting definition -Wextra.[m
-- [1;32mSetting definition -pedantic.[m
-- [1;32mCMAKE_SOURCE_DIR: /<<PKGBUILDDIR>>[m
-- [1;32mCMAKE_BINARY_DIR: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu[m
[1;31mUNIX non APPLE environment[m
~~~~~~ Instructions ~~~~~~
On UNIX/GNU-Linux, please run the configuration like this:
cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=<Debug | Release> -DCMAKE_INSTALL_PREFIX=</usr | your_dir> ../development
-- [1;32mStarting configuration for the doc material for IsoSpec [m
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).
-- [1;32mFinished configuration of the doc material.[m
-- [1;32mStarting configuration for the example material for IsoSpec [m
-- [1;32mFinished configuration for the example material.[m
[1;31mThe build toolchain is: Linux
[m
-- [1;33mCMAKE_BUILD_TYPE: None.[m
-- [1;33mCMAKE_INSTALL_PREFIX: /usr.[m
[1;31m"Now configuring IsoSpec++/ for IsoSpec"[m
-- Configuring done (0.6s)
-- Generating done (0.0s)
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu
dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=.
pybuild --configure -i python{version} -p 3.12
I: pybuild base:311: python3.12 setup.py config
running config
dh override_dh_auto_configure --with python3
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
dpkg-query: no packages found matching r-base-dev
dpkg-query: no packages found matching r-base-core
dh_auto_configure -O--buildsystem=pybuild -O--system=distutils --sourcedirectory=.
pybuild --configure -i python{version} -p 3.12
I: pybuild base:311: python3.12 setup.py config
running config
dh_auto_build -O--buildsystem=cmake -O--system=distutils --sourcedirectory=.
cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/IsoSpec++ /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/IsoSpec++ /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-static.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 25%] Building CXX object IsoSpec++/CMakeFiles/IsoSpec++-static.dir/unity-build.cpp.o
[ 50%] Building CXX object IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/unity-build.cpp.o
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ && /usr/bin/c++ -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ -I/<<PKGBUILDDIR>>/IsoSpec++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/IsoSpec++/unity-build.cpp
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ && /usr/bin/c++ -DIsoSpec___shared_EXPORTS -I/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ -I/<<PKGBUILDDIR>>/IsoSpec++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 /<<PKGBUILDDIR>>/IsoSpec++/unity-build.cpp
In file included from /<<PKGBUILDDIR>>/IsoSpec++/unity-build.cpp:30:
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp: In constructor ‘IsoSpec::Iso::Iso()’:
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp:53:25: warning: allocation of insufficient size ‘0’ for type ‘int’ with size ‘4’ [-Walloc-size]
53 | isotopeNumbers(new int[0]),
| ^
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp:54:21: warning: allocation of insufficient size ‘0’ for type ‘int’ with size ‘4’ [-Walloc-size]
54 | atomCounts(new int[0]),
| ^
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp:57:26: warning: allocation of insufficient size ‘0’ for type ‘IsoSpec::Marginal*’ with size ‘8’ [-Walloc-size]
57 | marginals(new Marginal*[0])
| ^
In file included from /<<PKGBUILDDIR>>/IsoSpec++/unity-build.cpp:30:
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp: In constructor ‘IsoSpec::Iso::Iso()’:
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp:53:25: warning: allocation of insufficient size ‘0’ for type ‘int’ with size ‘4’ [-Walloc-size]
53 | isotopeNumbers(new int[0]),
| ^
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp:54:21: warning: allocation of insufficient size ‘0’ for type ‘int’ with size ‘4’ [-Walloc-size]
54 | atomCounts(new int[0]),
| ^
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp:57:26: warning: allocation of insufficient size ‘0’ for type ‘IsoSpec::Marginal*’ with size ‘8’ [-Walloc-size]
57 | marginals(new Marginal*[0])
| ^
In file included from /<<PKGBUILDDIR>>/IsoSpec++/unity-build.cpp:37:
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.cpp: In lambda function:
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.cpp:427:31: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
427 | auto next = [&]() -> std::pair<double, double> {
| ^~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/IsoSpec++/unity-build.cpp:37:
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.cpp: In lambda function:
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.cpp:427:31: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
427 | auto next = [&]() -> std::pair<double, double> {
| ^~~~~~~~~~~~~~~~~~~~
[ 75%] Linking CXX shared library libIsoSpec++.so
cd /<<PKGBUILDDIR>>/obj-aarch64-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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--dependency-file,CMakeFiles/IsoSpec++-shared.dir/link.d -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 /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ && /usr/bin/cmake -E cmake_symlink_library libIsoSpec++.so.2.2.1 libIsoSpec++.so.2 libIsoSpec++.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 75%] Built target IsoSpec++-shared
[100%] Linking CXX static library libIsoSpec++.a
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ && /usr/bin/cmake -P CMakeFiles/IsoSpec++-static.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[100%] Built target IsoSpec++-static
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
dh_auto_configure -O--buildsystem=cmake -- \
-DCMAKE_INSTALL_PREFIX=/usr \
-DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2
cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 ..
[1;31mConfiguring build for project IsoSpec[m
-- [1;32mCMAKE_CXX_COMPILER: /usr/bin/c++[m
-- [1;32mSetting definition -Wno-unknown-pragmas.[m
-- [1;32mSetting definition -Wall.[m
-- [1;32mSetting definition -Wextra.[m
-- [1;32mSetting definition -pedantic.[m
-- [1;32mCMAKE_SOURCE_DIR: /<<PKGBUILDDIR>>[m
-- [1;32mCMAKE_BINARY_DIR: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu[m
[1;31mUNIX non APPLE environment[m
~~~~~~ Instructions ~~~~~~
On UNIX/GNU-Linux, please run the configuration like this:
cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=<Debug | Release> -DCMAKE_INSTALL_PREFIX=</usr | your_dir> ../development
-- [1;32mStarting configuration for the doc material for IsoSpec [m
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).
-- [1;32mFinished configuration of the doc material.[m
-- [1;32mStarting configuration for the example material for IsoSpec [m
-- [1;32mFinished configuration for the example material.[m
[1;31mThe build toolchain is: Linux
[m
-- [1;33mCMAKE_BUILD_TYPE: None.[m
-- [1;33mCMAKE_INSTALL_PREFIX: /usr.[m
[1;31m"Now configuring IsoSpec++/ for IsoSpec"[m
-- Configuring done (0.6s)
-- Generating done (0.0s)
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu
dh_auto_build -O--buildsystem=cmake
cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-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 '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/IsoSpec++ /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/IsoSpec++ /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++ /<<PKGBUILDDIR>>/obj-aarch64-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 "/<<PKGBUILDDIR>>/obj-aarch64-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 "/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/compiler_depend.internal".
Dependencies file "IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/link.d" is newer than depends file "/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/compiler_depend.internal".
Consolidate compiler generated dependencies of target IsoSpec++-static
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[4]: Nothing to be done for 'IsoSpec++/CMakeFiles/IsoSpec++-static.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
Consolidate compiler generated dependencies of target IsoSpec++-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build.make IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[4]: Nothing to be done for 'IsoSpec++/CMakeFiles/IsoSpec++-shared.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 50%] Built target IsoSpec++-static
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make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
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dh_auto_configure -O--buildsystem=cmake -- \
-DCMAKE_INSTALL_PREFIX=/usr \
-DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2
cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DCMAKE_INSTALL_PREFIX=/usr -DISOSPEC_LIB_VERSION=2.1.0 -DISOSPEC_LIB_SOVERSION=2 ..
[1;31mConfiguring build for project IsoSpec[m
-- [1;32mCMAKE_CXX_COMPILER: /usr/bin/c++[m
-- [1;32mSetting definition -Wno-unknown-pragmas.[m
-- [1;32mSetting definition -Wall.[m
-- [1;32mSetting definition -Wextra.[m
-- [1;32mSetting definition -pedantic.[m
-- [1;32mCMAKE_SOURCE_DIR: /<<PKGBUILDDIR>>[m
-- [1;32mCMAKE_BINARY_DIR: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu[m
[1;31mUNIX non APPLE environment[m
~~~~~~ Instructions ~~~~~~
On UNIX/GNU-Linux, please run the configuration like this:
cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=<Debug | Release> -DCMAKE_INSTALL_PREFIX=</usr | your_dir> ../development
-- [1;32mStarting configuration for the doc material for IsoSpec [m
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).
-- [1;32mFinished configuration of the doc material.[m
-- [1;32mStarting configuration for the example material for IsoSpec [m
-- [1;32mFinished configuration for the example material.[m
[1;31mThe build toolchain is: Linux
[m
-- [1;33mCMAKE_BUILD_TYPE: None.[m
-- [1;33mCMAKE_INSTALL_PREFIX: /usr.[m
[1;31m"Now configuring IsoSpec++/ for IsoSpec"[m
-- Configuring done (0.6s)
-- Generating done (0.0s)
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-aarch64-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-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" html_doc VERBOSE=1
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make -f CMakeFiles/Makefile2 html_doc
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make -f CMakeFiles/Makefile2 man/CMakeFiles/html_doc.dir/all
make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/depend
make[5]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/man /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/man /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/man/CMakeFiles/html_doc.dir/DependInfo.cmake "--color="
make[5]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make -f man/CMakeFiles/html_doc.dir/build.make man/CMakeFiles/html_doc.dir/build
make[5]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[100%] Doxygen-based developer html documentation generation
cd /<<PKGBUILDDIR>>/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.
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warning: Tag 'HTML_TIMESTAMP' at line 1256 of file 'doxyfile' has become obsolete.
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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 /<<PKGBUILDDIR>>/IsoSpec++
Reading and parsing tag files
Parsing files
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/allocator.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/allocator.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/allocator.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/allocator.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/btrd.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/btrd.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/conf.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/conf.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/cwrapper.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/cwrapper.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/cwrapper.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/cwrapper.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/element_tables.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/element_tables.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/fasta.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/fasta.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/fasta.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/fasta.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/isoMath.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/isoMath.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/misc.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/misc.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/misc.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/misc.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/mman.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/mman.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/mman.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/mman.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/operators.cpp...
Parsing file /buil/<<PKGBUILDDIR>>/IsoSpec++/allocator.h:33: warning: Compound IsoSpec::Allocator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:53: warning: Compound IsoSpec::ConfEqual is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:75: warning: Compound IsoSpec::ConfOrder is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:87: warning: Compound IsoSpec::ConfOrderMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:102: warning: Compound IsoSpec::ConfOrderMarginalDescending is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.h:25: warning: Compound IsoSpec::DirtyAllocator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:40: warning: Compound IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:439: warning: Compound IsoSpec::IsoLayeredGenerator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:542: warning: Compound IsoSpec::IsoStochasticGenerator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:28: warning: Compound IsoSpec::KeyHasher is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:141: warning: Compound IsoSpec::OrderMarginalsBySizeDecresing is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/conf.h:24: warning: Compound IsoSpec::ProbAndConfPtr is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:117: warning: Compound IsoSpec::ReverseOrder is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:26: warning: Compound IsoSpec::SSummator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:76: warning: Compound IsoSpec::Summator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:99: warning: Compound IsoSpec::TSummator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:124: warning: Compound IsoSpec::TableOrder is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:32: warning: Compound pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/cwrapper.h:146: warning: Compound ws_match_res is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command
d/isospec-dlPgc8/isospec-2.2.1/IsoSpec++/operators.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/operators.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/operators.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/platform.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/platform.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/platform_incl.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/platform_incl.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/python-build.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/python-build.cpp...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/summator.h...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/summator.h...
Preprocessing /<<PKGBUILDDIR>>/IsoSpec++/unity-build.cpp...
Parsing file /<<PKGBUILDDIR>>/IsoSpec++/unity-build.cpp...
Building macro definition list...
Building group list...
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Building namespace list...
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Computing nesting relations for classes...
Associating documentation with classes...
Associating documentation with concepts...
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Building example list...
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Building interface member list...
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Computing class inheritance relations...
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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...
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Computing page relations...
Determining the scope of groups...
Computing module relations...
Sorting lists...
Determining which enums are documented
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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...
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Resolving user defined references...
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Transferring function references...
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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 /<<PKGBUILDDIR>>/IsoSpec++/allocator.cpp...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/allocator.h...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/btrd.h...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/conf.h...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/cwrapper.cpp...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/cwrapper.h...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.cpp...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.h...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/element_tables.h...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/fasta.cpp...
Generating code for file /<<BUILDDIR>>/isos/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:194: warning: Member iterator (typedef) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:195: warning: Member const_iterator (typedef) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:196: warning: Member value_type (typedef) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:197: warning: Member size_type (typedef) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:198: warning: Member reference (typedef) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:199: warning: Member const_reference (typedef) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:39: warning: Member pod_vector(size_t initial_size=16) (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:54: warning: Member operator=(pod_vector< T > &&other) (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:64: warning: Member pod_vector(pod_vector< T > &&other) (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:74: warning: Member pod_vector(unsafe_pod_vector< T > &&other) (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:82: warning: Member fast_reserve(size_t n) (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:94: warning: Member reserve(size_t n) (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:100: warning: Member resize(size_t new_size) (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:114: warning: Member resize_and_wipe(size_t new_size) (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:122: warning: Member nocheck_push_back(const T &val) noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:129: warning: Member push_back(const T &val) (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:137: warning: Member operator[](size_t n) noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:143: warning: Member operator[](size_t n) const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:149: warning: Member size() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:154: warning: Member capacity() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:159: warning: Member data() noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:164: warning: Member data() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:169: warning: Member empty() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:174: warning: Member back() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:180: warning: Member pop_back() noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:187: warning: Member swap(pod_vector< T > &other) noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:201: warning: Member begin() noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:202: warning: Member begin() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:203: warning: Member cbegin() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:204: warning: Member end() noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:205: warning: Member end() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:206: warning: Member cend() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:208: warning: Member front() const noexcept (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:214: warning: Member clear() (function) of class pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:372: warning: Member iterator (typedef) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:373: warning: Member const_iterator (typedef) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:374: warning: Member value_type (typedef) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:375: warning: Member size_type (typedef) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:376: warning: Member reference (typedef) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:377: warning: Member const_reference (typedef) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:234: warning: Member init() (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:242: warning: Member init(size_t initial_size) (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:261: warning: Member fast_reserve(size_t n) (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:272: warning: Member reserve(size_t n) (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:278: warning: Member resize(size_t new_size) (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:292: warning: Member resize_and_wipe(size_t new_size) (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:300: warning: Member nocheck_push_back(const T &val) noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:307: warning: Member push_back(const T &val) (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:315: warning: Member operator[](size_t n) noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:321: warning: Member operator[](size_t n) const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:327: warning: Member size() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:332: warning: Member capacity() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:337: warning: Member data() noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:342: warning: Member data() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:347: warning: Member empty() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:352: warning: Member back() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:358: warning: Member pop_back() noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:365: warning: Member swap(pod_vector< T > &other) noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:379: warning: Member begin() noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:380: warning: Member begin() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:381: warning: Member cbegin() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:382: warning: Member end() noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:383: warning: Member end() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:384: warning: Member cend() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:386: warning: Member front() const noexcept (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/pod_vector.h:392: warning: Member clear() (function) of class unsafe_pod_vector is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/cwrapper.h:147: warning: Member res1 (variable) of struct ws_match_res is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/cwrapper.h:148: warning: Member res2 (variable) of struct ws_match_res is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/cwrapper.h:149: warning: Member flow (variable) of struct ws_match_res is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/btrd.h:27: warning: Member RealType (typedef) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/btrd.h:28: warning: Member IntType (typedef) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/conf.h:22: warning: Member Conf (typedef) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/allocator.h:26: warning: Member copyConf(const T *source, T *destination, int dim) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/btrd.h:160: warning: Member invert(IntType t, RealType p, std::mt19937 &urng=random_gen) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/fasta.h:33: warning: Member parse_fasta(const char *fasta, int atomCounts[6]) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:23: warning: Member release_g_lfact_table() (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:32: warning: Member alloc_lfact_table() (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:47: warning: Member RationalApproximation(double t) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:57: warning: Member NormalCDFInverse(double p) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:65: warning: Member NormalCDFInverse(double p, double mean, double stdev) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:70: warning: Member NormalCDF(double x, double mean, double stdev) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:95: warning: Member NormalPDF(double x, double mean, double stdev) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:104: warning: Member LowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:131: warning: Member InverseLowerIncompleteGamma2(int a, double x) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:150: warning: Member random_gen(random_dev()) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:151: warning: Member stdunif(0.0, 1.0) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:153: warning: Member rdvariate_binom(size_t tries, double succ_prob, std::mt19937 &rgen) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.h:68: warning: Member InverseChiSquareCDF2(int k, double x) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.h:76: warning: Member rdvariate_beta_1_b(double b, std::mt19937 &rgen=random_gen) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.cpp:149: warning: Member get_loggamma_nominator(int x) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.cpp:156: warning: Member verify_atom_cnt(int atomCnt) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.cpp:28: warning: Member quickselect(void **array, int n, int start, int end) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:29: warning: Member combinedSum(const int *conf, const std::vector< double > **valuesContainer, int dimNumber) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:38: warning: Member combinedSum(const int *conf, const pod_vector< double > **valuesContainer, int dimNumber) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:47: warning: Member getConf(void *conf) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:54: warning: Member getLProb(void *conf) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:61: warning: Member unnormalized_logProb(const int *conf, const double *logProbs, int dim) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:71: warning: Member calc_mass(const int *conf, const double *masses, int dim) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:85: warning: Member printArray(const T *array, int size, const char *prefix="") (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:94: warning: Member printVector(const std::vector< T > &vec) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:108: warning: Member printNestedArray(const T **array, const int *shape, int size) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:133: warning: Member dealloc_table(T *tbl, int dim) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:142: warning: Member realloc_append(T **array, T what, size_t old_array_size) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:151: warning: Member get_order(T *order_array, size_t N) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/misc.h:162: warning: Member get_inverse_order(T *order_array, size_t N) (function) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:26: warning: Member isospec_number_of_isotopic_entries (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:28: warning: Member elem_table_ID[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:325: warning: Member elem_table_atomicNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:621: warning: Member elem_table_mass[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:917: warning: Member elem_table_massNo[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:1213: warning: Member elem_table_extraNeutrons[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:1509: warning: Member elem_table_element[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:1805: warning: Member elem_table_symbol[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:2101: warning: Member elem_table_Radioactive[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:2397: warning: Member elem_table_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/element_tables.cpp:2693: warning: Member elem_table_log_probability[ISOSPEC_NUMBER_OF_ISOTOPIC_ENTRIES] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fasta.cpp:25: warning: Member aa_isotope_numbers[6] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fasta.cpp:27: warning: Member aa_elem_masses[19] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fasta.cpp:37: warning: Member aa_elem_nominal_masses[19] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fasta.cpp:47: warning: Member aa_elem_probabilities[19] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fasta.cpp:57: warning: Member aa_symbol_to_elem_counts[256 *6] (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:44: warning: Member g_lfact_table (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:102: warning: Member sqrt_pi (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp:149: warning: Member random_dev (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.h:53: warning: Member pi (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.h:54: warning: Member logpi (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.h:73: warning: Member random_gen (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoMath.h:74: warning: Member stdunif (variable) of namespace IsoSpec is not documented.
/<<PKGBUILDDIR>>/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'
/<<PKGBUILDDIR>>/IsoSpec++/allocator.h:42: warning: Member Allocator(const int dim, const int tabSize=10000) (function) of class IsoSpec::Allocator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/allocator.h:48: warning: Member shiftTables() (function) of class IsoSpec::Allocator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/allocator.h:50: warning: Member newConf() (function) of class IsoSpec::Allocator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/allocator.h:60: warning: Member makeCopy(const T *conf) (function) of class IsoSpec::Allocator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:59: warning: Member ConfEqual(int dim) (function) of class IsoSpec::ConfEqual is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:61: warning: Member operator()(const int *conf1, const int *conf2) const (function) of class IsoSpec::ConfEqual is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:79: warning: Member operator()(void *conf1, void *conf2) const (function) of class IsoSpec::ConfOrder is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:93: warning: Member ConfOrderMarginal(const double *logProbs, int dim) (function) of class IsoSpec::ConfOrderMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:95: warning: Member operator()(const Conf conf1, const Conf conf2) (function) of class IsoSpec::ConfOrderMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:108: warning: Member ConfOrderMarginalDescending(const double *logProbs, int dim) (function) of class IsoSpec::ConfOrderMarginalDescending is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:110: warning: Member operator()(const Conf conf1, const Conf conf2) (function) of class IsoSpec::ConfOrderMarginalDescending is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.h:36: warning: Member DirtyAllocator(const int dim, const int tabSize=10000) (function) of class IsoSpec::DirtyAllocator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.h:42: warning: Member shiftTables() (function) of class IsoSpec::DirtyAllocator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/dirtyAllocator.h:44: warning: Member newConf() (function) of class IsoSpec::DirtyAllocator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:70: warning: Member FixedEnvelope(const FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:71: warning: Member FixedEnvelope(FixedEnvelope &&other) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:82: warning: Member operator+(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:83: warning: Member operator*(const FixedEnvelope &other) const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:85: warning: Member confs_no() const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:86: warning: Member getAllDim() const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:88: warning: Member masses() const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:89: warning: Member probs() const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:90: warning: Member confs() const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:92: warning: Member release_masses() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:93: warning: Member release_probs() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:94: warning: Member release_confs() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:95: warning: Member release_everything() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:98: warning: Member mass(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:99: warning: Member prob(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:100: warning: Member conf(size_t i) const (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:102: warning: Member sort_by_mass() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:103: warning: Member sort_by_prob() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:105: warning: Member get_total_prob() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:106: warning: Member scale(double factor) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:107: warning: Member normalize() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:108: warning: Member shift_mass(double shift) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:109: warning: Member resample(size_t ionic_current, double beta_bias=1.0) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:111: warning: Member empiric_average_mass() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:112: warning: Member empiric_variance() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:113: warning: Member empiric_stddev() (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:115: warning: Member WassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:116: warning: Member OrientedWassersteinDistance(FixedEnvelope &other) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:125: warning: Member bin(double bin_width=1.0, double middle=0.0) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:170: warning: Member threshold_init(Iso &&iso, double threshold, bool absolute) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:172: warning: Member addConfILG(const GenType &generator) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:181: warning: Member total_prob_init(Iso &&iso, double target_prob, bool trim) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:183: warning: Member FromThreshold(Iso &&iso, double threshold, bool absolute, bool tgetConfs=false) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:132: warning: Member store_conf(const T &generator) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:139: warning: Member store_conf(double _mass, double _prob) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:166: warning: Member reallocate_memory(size_t new_size) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:167: warning: Member slow_reallocate_memory(size_t new_size) (function) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:42: warning: Member _masses (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:43: warning: Member _probs (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:44: warning: Member _confs (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:45: warning: Member _confs_no (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:46: warning: Member allDim (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:47: warning: Member sorted_by_mass (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:48: warning: Member sorted_by_prob (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:49: warning: Member total_prob (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:50: warning: Member current_size (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:51: warning: Member tmasses (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:52: warning: Member tprobs (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:53: warning: Member tconfs (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h:54: warning: Member allDimSizeofInt (variable) of class IsoSpec::FixedEnvelope is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:110: warning: Found unknown command '\use_nominal_masses'
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:111: warning: Found unknown command '\add_water'
/<<PKGBUILDDIR>>/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'
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:483: warning: Member get_currentLThreshold() const (function) of class IsoSpec::IsoLayeredGenerator is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:499: warning: Member advanceToNextConfigurationWithinLayer() (function) of class IsoSpec::IsoLayeredGenerator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:534: warning: Member nextLayer(double offset) (function) of class IsoSpec::IsoLayeredGenerator is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:555: warning: Member count() const (function) of class IsoSpec::IsoStochasticGenerator is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:186: warning: Member mode_lprob (variable) of class IsoSpec::IsoGenerator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/isoSpec++.h:70: warning: Member doMarginalsNeedSorting() const (function) of class IsoSpec::Iso is not documented.
/<<PKGBUILDDIR>>/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)
/<<PKGBUILDDIR>>/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)
/<<PKGBUILDDIR>>/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'
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:34: warning: Member KeyHasher(int dim) (function) of class IsoSpec::KeyHasher is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:36: warning: Member operator()(const int *conf) const noexcept (function) of class IsoSpec::KeyHasher is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/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'
/<<PKGBUILDDIR>>/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'
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:386: warning: unable to resolve reference to 'PrecalculatedMarginal::get_eProb' for \ref command
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:59: warning: found documented return type for IsoSpec::Marginal::Marginal that does not return anything
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:233: warning: Member conf_lprobs() const (function) of class IsoSpec::MarginalTrek is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:234: warning: Member conf_masses() const (function) of class IsoSpec::MarginalTrek is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:235: warning: Member confs() const (function) of class IsoSpec::MarginalTrek is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/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'
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:145: warning: Member OrderMarginalsBySizeDecresing(T const *const *const MT_) (function) of class IsoSpec::OrderMarginalsBySizeDecresing is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:146: warning: Member operator()(int m1, int m2) (function) of class IsoSpec::OrderMarginalsBySizeDecresing is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:90: warning: Member get_lProbs() const (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:168: warning: Member ensureModeConf() (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:254: warning: Member configurations (variable) of class IsoSpec::PrecalculatedMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:255: warning: Member confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:256: warning: Member no_confs (variable) of class IsoSpec::PrecalculatedMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:257: warning: Member masses (variable) of class IsoSpec::PrecalculatedMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:258: warning: Member lProbs (variable) of class IsoSpec::PrecalculatedMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:259: warning: Member probs (variable) of class IsoSpec::PrecalculatedMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:260: warning: Member allocator (variable) of class IsoSpec::PrecalculatedMarginal is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:160: warning: Member logProb(Conf conf) const (function) of class IsoSpec::Marginal is not documented.
/<<PKGBUILDDIR>>/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)
/<<PKGBUILDDIR>>/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'
/<<PKGBUILDDIR>>/IsoSpec++/marginalTrek++.h:264: warning: found documented return type for IsoSpec::PrecalculatedMarginal::PrecalculatedMarginal that does not return anything
/<<PKGBUILDDIR>>/IsoSpec++/conf.h:30: warning: Member ProbAndConfPtr(double p, Conf c) (function) of struct IsoSpec::ProbAndConfPtr is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/conf.h:32: warning: Member operator<(const ProbAndConfPtr &other) const (function) of struct IsoSpec::ProbAndConfPtr is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/conf.h:27: warning: Member first (variable) of struct IsoSpec::ProbAndConfPtr is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/conf.h:28: warning: Member second (variable) of struct IsoSpec::ProbAndConfPtr is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:121: warning: Member operator()(const T a, const T b) const (function) of class IsoSpec::ReverseOrder is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:35: warning: Member SSummator(const SSummator &other) (function) of class IsoSpec::SSummator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:39: warning: Member add(double x) (function) of class IsoSpec::SSummator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:61: warning: Member get() (function) of class IsoSpec::SSummator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:85: warning: Member add(double what) (function) of class IsoSpec::Summator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:93: warning: Member get() (function) of class IsoSpec::Summator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:128: warning: Member TableOrder(const T *_tbl) (function) of class IsoSpec::TableOrder is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/operators.h:129: warning: Member operator()(unsigned int i, unsigned int j) (function) of class IsoSpec::TableOrder is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:107: warning: Member add(double what) (function) of class IsoSpec::TSummator is not documented.
/<<PKGBUILDDIR>>/IsoSpec++/summator.h:111: warning: Member get() (function) of class IsoSpec::TSummator is not documented.
pec-2.2.1/IsoSpec++/fasta.h...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.cpp...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/fixedEnvelopes.h...
Generating code for file /<<PKGBUILDDIR>>/IsoSpec++/isoMath.cpp...
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Chapter 3.
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Chapter 4.
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Chapter 5.
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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
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(/usr/share/texlive/texmf-dist/metafont/config/mf.ini
(/usr/share/texlive/texmf-dist/metafont/base/plain.mf
Preloading the plain base, version 2.71: preliminaries,
basic constants and mathematical macros,
macros for converting from device-independent units to pixels,
macros and tables for various modes of operation,
macros for drawing and filling,
macros for proof labels and rules,
macros for character and font administration,
and a few last-minute items.)
(/usr/share/texlive/texmf-dist/fonts/source/public/modes/modes.mf) )
Beginning to dump on file mf.base
(preloaded base=mf 2024.11.16)
2241 strings of total length 30242
12001 memory locations dumped; current usage is 3694&7945
1013 symbolic tokens
Transcript written on mf.log.
mktexfmt [INFO]: log file copied to: /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/web2c/metafont/mf.log
mktexfmt [INFO]: /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/web2c/metafont/mf.base installed.
mktexfmt [INFO]: successfully rebuilt formats: 1
mktexfmt [INFO]: not selected formats: 16
mktexfmt [INFO]: total formats: 17
mktexfmt [INFO]:
*************************************************************
* *
* WARNING: you are switching to fmtutil's per-user formats. *
* Please read the following warnings! *
* *
*************************************************************
You have run fmtutil-user (as opposed to fmtutil-sys) for the first time;
this has created format files which are local to your personal account.
From now on, any changes in system formats will *not* be automatically
reflected in your files; furthermore, running fmtutil-sys will no longer
have any effect for you.
As a consequence, you yourself have to rerun fmtutil-user after any
change in the system directories. For example, when one of the LaTeX or
other format source files changes, which happens frequently.
See https://tug.org/texlive/scripts-sys-user.html for details.
If you want to undo this, remove the files mentioned above.
Run mktexfmt --help for full documentation of fmtutil.
mktexfmt [INFO]: exiting with status 0
mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+120/600; nonstopmode; input cmmi12
This is METAFONT, Version 2.71828182 (TeX Live 2025/dev/Debian) (preloaded base=mf)
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/cmmi12.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/cmbase.mf)
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/mathit.mf
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romanu.mf [65] [66]
[67] [68] [69] [70] [71] [72] [73] [74] [75] [76] [77] [78] [79] [80] [81]
[82] [83] [84] [85] [86] [87] [88] [89] [90])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/itall.mf [97] [98]
[99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111]
[112] [113] [114] [115] [116] [117] [118] [119] [120] [121] [122])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/greeku.mf [0] [1]
[2] [3] [4] [5] [6] [7] [8] [9] [10])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/greekl.mf [11] [12]
[13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27]
[28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/italms.mf [64] [96]
[123] [124] [125] [126] [127])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/olddig.mf [48] [49]
[50] [51] [52] [53] [54] [55] [56] [57])
(/usr/share/texlive/texmf-dist/fonts/source/public/cm/romms.mf [40] [41]
[42] [43] [44] [45] [46] [47] [58] [59] [60] [61] [62] [63] [91] [92] [93]
[94] [95]) ) )
Font metrics written on cmmi12.tfm.
Output written on cmmi12.720gf (128 characters, 34900 bytes).
Transcript written on cmmi12.log.
mktexpk: /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/fonts/pk/ljfour/public/cm/cmmi12.720pk: successfully generated.
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) </<<BUILDDIR>>/iso
spec-2.2.1/debian/.debhelper/generated/_source/home/.texlive2024/texmf-var/font
s/pk/ljfour/public/cm/cmmi12.720pk>
kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 0+420/600 --dpi 420 pcrr8r
gsftopk: fatal: map file `psfonts.map' not found.
mktexpk: don't know how to create bitmap font for pcrr8r.
mktexpk: perhaps pcrr8r is missing from the map file.
kpathsea: Appending font creation commands to missfont.log.
!pdfTeX error: pdflatex (file pcrr8r): Font pcrr8r at 420 not found
==> Fatal error occurred, no output PDF file produced!
make[6]: *** [Makefile:12: refman.pdf] Error 1
make[6]: Leaving directory '/<<PKGBUILDDIR>>/man/latex'
make[5]: *** [man/CMakeFiles/pdf_doc.dir/build.make:74: man/CMakeFiles/pdf_doc] Error 2
make[5]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[4]: *** [CMakeFiles/Makefile2:190: man/CMakeFiles/pdf_doc.dir/all] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[3]: *** [CMakeFiles/Makefile2:197: man/CMakeFiles/pdf_doc.dir/rule] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[2]: *** [Makefile:185: pdf_doc] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
dh_auto_build: error: cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" pdf_doc VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:81: build_cpp_library_doc] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:29: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-11-16T19:13:52Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: arm64
Build Type: binary
Build-Space: 28776
Build-Time: 38
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 67
Job: /tmp/debusine-fetch-exec-upload-_b_eafob/isospec_2.2.1-4.1.dsc
Machine Architecture: arm64
Package: isospec
Package-Time: 142
Source-Version: 2.2.1-4.1
Space: 28776
Status: attempted
Version: 2.2.1-4.1
--------------------------------------------------------------------------------
Finished at 2024-11-16T19:13:52Z
Build needed 00:02:22, 28776k disk space