Bug 678308 – media-libs/vigra-1.11.1-r1[doc,python] with dev-python/sphinx-1.8.3 - src_compile(): Could not import extension sphinx.ext.pngmath (exception: No module named pngmath)

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Juergen Rose 2019-02-18 18:09:56 UTC]

Created attachment 565728 [details]
build.log

'MAKEOPTS=-j1 emerge -v1 vigra' fails with cd /var/tmp/portage/media-libs/vigra-1.11.1-r1/work/vigra-1.11.1-python2_7/vigranumpy/docsrc && /usr/bin/sphinx-build -b html -d /var/tmp/portage/media-libs/vigra-1.11.1-r1/work/vigra-1.11.1-python2_7/doc/vigranumpy/doctrees -D latex_paper_size=a4 -c /var/tmp/portage/media-libs/vigra-1.11.1-r1/work/vigra-1.11.1-python2_7/vigranumpy/docsrc /var/tmp/portage/media-libs/vigra-1.11.1-r1/work/vigra-1.11.1/vigranumpy/docsrc /var/tmp/portage/media-libs/vigra-1.11.1-r1/work/vigra-1.11.1-python2_7/doc/vigranumpy
Running Sphinx v1.8.3
Working directory: /var/tmp/portage/media-libs/vigra-1.11.1-r1/work/vigra-1.11.1-python2_7/vigranumpy
vigraimpex path: /var/tmp/portage/media-libs/vigra-1.11.1-r1/work/vigra-1.11.1-python2_7/src/impex

Extension error:
Could not import extension sphinx.ext.pngmath (exception: No module named pngmath)
make[3]: *** [vigranumpy/docsrc/CMakeFiles/doc_python.dir/build.make:59: vigranumpy/docsrc/CMakeFiles/doc_python] Error 2



root@condor:/root(58)# emerge --info '=media-libs/vigra-1.11.1-r1::gentoo'
Portage 2.3.60 (python 3.6.6-final-0, default/linux/amd64/17.0/desktop, gcc-8.2.0, glibc-2.28-r5, 4.20.5-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.20.5-gentoo-x86_64-Intel-R-_Core-TM-2_CPU_6600_@_2.40GHz-with-gentoo-2.6
KiB Mem:     7060700 total,   3536560 free
KiB Swap:   50347860 total,  47676928 free
Timestamp of repository gentoo: Mon, 18 Feb 2019 15:30:01 +0000
Head commit of repository gentoo: 76bf33070ea260d53dd8934c04fd2daf41fb5df7
sh bash 5.0_p2
ld GNU ld (Gentoo 2.31.1 p5) 2.31.1
distcc 3.3.2 x86_64-pc-linux-gnu [disabled]
app-shells/bash:          5.0_p2::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.28.0::gentoo
dev-lang/python:          2.7.15-r100::sage-on-gentoo, 3.6.6::gentoo, 3.7.0::gentoo
dev-util/cmake:           3.11.4-r1::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/sandbox:         2.15::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.11.6-r3::gentoo, 1.16.1-r1::gentoo
sys-devel/binutils:       2.31.1-r4::gentoo
sys-devel/gcc:            8.2.0-r6::gentoo
sys-devel/gcc-config:     2.0::gentoo
sys-devel/libtool:        2.4.6-r5::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 4.20::gentoo (virtual/os-headers)
sys-libs/glibc:           2.28-r5::gentoo
Repositories:

gentoo
    location: /usr/portage_condor
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-metamanifest: yes
    sync-rsync-extra-opts: 
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-max-age: 24

local
    location: /usr/local/portage
    masters: gentoo
    priority: 0

g-cpan
    location: /var/lib/cpan
    masters: gentoo
    priority: 1

sage-on-gentoo
    location: /var/lib/layman/sage-on-gentoo
    masters: gentoo science
    priority: 50

science
    location: /var/lib/layman/science
    masters: gentoo
    priority: 50

x11
    location: /var/lib/layman/x11
    masters: gentoo
    priority: 50

Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php7.2/ext-active/ /etc/php/apache2-php7.3/ext-active/ /etc/php/cgi-php7.2/ext-active/ /etc/php/cgi-php7.3/ext-active/ /etc/php/cli-php7.2/ext-active/ /etc/php/cli-php7.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs clean-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ rsync://ftp.fi.muni.cz/pub/linux/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo rsync://gd.tuwien.ac.at/opsys/linux/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo http://gentoo.oregonstate.edu"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de en fr ru"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 amr ao apache2 apng applet archive armadillo arpack asf aspell assistant atlas audacious audiofile aufs automap automount barcode bash-completion berkdb blas blast bluetooth bluray boost branding btrfs bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cilk clang cli cmake collada consolekit contrib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia digitalradio djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evdev evo examples excel exif expat extensions extra extras faac faad fam fbcon fbcondecor ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx ftp fuse gcj gd gdal gdbm gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap initramfs inotify introspection ipod ipv6 irda ithreads jadetex java jbig jit john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libgda libkms libnotify libsamplerate libtirpc lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mng mod mono motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg opencl opencv openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds ppp preview-latex proj projectm pstricks pulseaudio python q16 q32 qemu qhull qml qt5 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool rtlsdr sage samba sasl schroedinger science sdk sdl seccomp secure-delete server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite ssl startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tbb tcl tcpd tex tex4ht theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l v4l2 vaapi vala valgrind vdpau video vim-syntax virt-network virtualbox visio vorbis vpx vtk wav wayland webdav webdav-serf webkit wmf wxwidgets x264 x265 xa xattr xcb xen xetex xft xine xml xmlreader xmlrpc xpm xps xv xvid xvmc yaml youtube zlib zsh-completion zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="karbon sheets words" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog sensors thermal" CPU_FLAGS_X86="mmx mmxext sse sse2 sse3 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="aivdm ashtech earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 navcom ntrip oceanserver oncore rtcm104v2 rtcm104v3 sirf superstar2 tnt tripmate tsip ublox nmea0183 nmea2000 passthrough" GRUB_PLATFORMS="emu efi-64 pc xen" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" L10N="de en fr ru" LCD_DEVICES="cfontz framebuffer glcd hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd SureElec" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="AMDGPU X86" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-1" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby24" USERLAND="GNU" VIDEO_CARDS="radeon radeonsi" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

=================================================================
                        Package Settings
=================================================================

media-libs/vigra-1.11.1-r1::gentoo was built with the following:
USE="doc fftw hdf5 jpeg mpi openexr png python tiff valgrind -test" ABI_X86="(64)" PYTHON_TARGETS="python2_7"



root@condor:/root(59)# emerge -pqv '=media-libs/vigra-1.11.1-r1::gentoo'
[ebuild   R   ] media-libs/vigra-1.11.1-r1  USE="doc fftw hdf5 jpeg mpi openexr png python tiff valgrind -test" PYTHON_TARGETS="python2_7"

[Comment 1 Juergen Rose 2019-02-18 18:42:11 UTC]

'USE=-doc MAKEOPTS=-j1 emerge -v1 vigra' works.

[Comment 2 Jeroen Roovers (RETIRED) 2019-02-18 20:11:20 UTC]

Where did dev-python/sphinx-1.8.3 come from?

[Comment 3 Juergen Rose 2019-02-23 10:10:14 UTC]

(In reply to Jeroen Roovers from comment #2)
> Where did dev-python/sphinx-1.8.3 come from?

It comes from the sage-on-gentoo overlay.

[Comment 4 Marek Szuba 2019-03-27 10:44:39 UTC]

Well, sphinx.ext.pngmath _has_ been deprecated for quite a while now... Fortunately sphinx.ext.imgmath is a drop-in replacement for it, as far as Gentoo is concerned anyway (one needs a TeX distribution which includes the module anyfontsize, which TeX Live 2017 does; I have recently run into problems with pngmath->imgmath transition on RHEL7 though).

Anyway, there is an upstream issue pertaining to this. Maybe they will finally make a new release.

[Comment 5 Andreas Sturmlechner 2019-11-26 21:30:27 UTC]

Builds fine using dev-python/sphinx-2.0.1 though.

[Comment 6 Larry the Git Cow 2019-11-27 00:13:04 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7de4915e9c99fba07343fc33c4bf50c85b2b7c76

commit 7de4915e9c99fba07343fc33c4bf50c85b2b7c76
Author:     Andreas Sturmlechner <[e-mail]>
AuthorDate: 2019-11-26 22:23:53 +0000
Commit:     Andreas Sturmlechner <[e-mail]>
CommitDate: 2019-11-27 00:12:47 +0000

    media-libs/vigra: Fix build with sphinx-2
    
    See also: https://github.com/ukoethe/vigra/issues/462
    
    Closes: https://bugs.gentoo.org/678308
    Package-Manager: Portage-2.3.79, Repoman-2.3.18
    Signed-off-by: Andreas Sturmlechner <[e-mail]>

 .../files/vigra-1.11.1-sphinx.ext.pngmath.patch    | 27 ++++++++++++++++++++++
 media-libs/vigra/vigra-1.11.1-r2.ebuild            |  1 +
 media-libs/vigra/vigra-9999.ebuild                 |  6 ++++-
 3 files changed, 33 insertions(+), 1 deletion(-)