Bug 657066 – dev-python/notebook-5.2.1 (with sphinx-1.7.1::sage-on-gentoo) - Exception occurred "/usr/lib64/python3.5/site-packages/nbsphinx.py", line 1177

• Product: Gentoo Linux
• Status: RESOLVED NEEDINFO

[Description Juergen Rose 2018-06-01 19:55:52 UTC]

Created attachment 534428 [details]
build.log

'MAKEOPTS=-j1 emerge -v1 notebook' fails with:
...
writing output... [100%] ui_components

/var/tmp/portage/dev-python/notebook-5.2.1/work/notebook-5.2.1/docs/source/extending/frontend_extensions.rst:210: WARNING: undefined label: jupyter_path (if the link has no caption the label must precede a section header)
/var/tmp/portage/dev-python/notebook-5.2.1/work/notebook-5.2.1/docs/source/notebook.rst:25: WARNING: undefined label: jupyter:install (if the link has no caption the label must precede a section header)
/var/tmp/portage/dev-python/notebook-5.2.1/work/notebook-5.2.1/docs/source/notebook.rst:83: WARNING: undefined label: nbformat:notebook_file_format (if the link has no caption the label must precede a section header)
/var/tmp/portage/dev-python/notebook-5.2.1/work/notebook-5.2.1/docs/source/notebook.rst:153: WARNING: undefined label: magics_explained (if the link has no caption the label must precede a section header)
/var/tmp/portage/dev-python/notebook-5.2.1/work/notebook-5.2.1/docs/source/notebook.rst:168: WARNING: undefined label: magics_explained (if the link has no caption the label must precede a section header)
/var/tmp/portage/dev-python/notebook-5.2.1/work/notebook-5.2.1/docs/source/notebook.rst:174: WARNING: undefined label: ipythonzmq (if the link has no caption the label must precede a section header)
/var/tmp/portage/dev-python/notebook-5.2.1/work/notebook-5.2.1/docs/source/notebook.rst:226: WARNING: undefined label: magics_explained (if the link has no caption the label must precede a section header)
/var/tmp/portage/dev-python/notebook-5.2.1/work/notebook-5.2.1/docs/source/public_server.rst:7: WARNING: undefined label: ipython:ipythonzmq (if the link has no caption the label must precede a section header)
generating indices... genindex

Exception occurred:
  File "/usr/lib64/python3.5/site-packages/nbsphinx.py", line 1177, in html_collect_pages
    for file in app.status_iterator(files, 'copying linked files... ',
AttributeError: 'Sphinx' object has no attribute 'status_iterator'
The full traceback has been saved in /var/tmp/portage/dev-python/notebook-5.2.1/temp/sphinx-err-k8f9bh0n.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
make: *** [Makefile:57: html] Error 2



root@cheetahnew:/root(34)# emerge --info '=dev-python/notebook-5.2.1::gentoo'
Portage 2.3.40 (python 3.5.5-final-0, default/linux/amd64/17.0, gcc-7.3.0, glibc-2.26-r7, 4.16.10-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.16.10-gentoo-x86_64-Intel-R-_Core-TM-_i3-2120_CPU_@_3.30GHz-with-gentoo-2.6
KiB Mem:     7857220 total,   1244896 free
KiB Swap:   50331640 total,  48989676 free
Timestamp of repository gentoo: Fri, 01 Jun 2018 16:30:01 +0000
Head commit of repository gentoo: f91ea2e2d841e7ac2a36385701aef34662d3d1fb
sh bash 4.4_p19
ld GNU ld (Gentoo 2.30 p2) 2.30.0
distcc[19542] (dcc_trace_version) distcc 3.2rc1 x86_64-pc-linux-gnu; built Jan 22 2018 18:55:17 [disabled]
app-shells/bash:          4.4_p19::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.26.2::gentoo
dev-lang/python:          2.7.14-r101::sage-on-gentoo, 3.4.8-r1::gentoo, 3.5.5-r1::gentoo, 3.6.5-r1::gentoo
dev-util/cmake:           3.11.3::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.9.6-r5::gentoo, 1.11.6-r3::gentoo, 1.15.1-r2::gentoo, 1.16.1-r1::gentoo
sys-devel/binutils:       2.30-r2::gentoo
sys-devel/gcc:            7.3.0-r3::gentoo
sys-devel/gcc-config:     1.9.1::gentoo
sys-devel/libtool:        2.4.6-r5::gentoo
sys-devel/make:           4.2.1-r3::gentoo
sys-kernel/linux-headers: 4.16-r1::gentoo (virtual/os-headers)
sys-libs/glibc:           2.26-r7::gentoo
Repositories:

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

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

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

g-octave
    location: /var/lib/g-octave
    masters: gentoo
    priority: 2

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

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

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/cgi-php7.2/ext-active/ /etc/php/cli-php7.2/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 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-logs clean-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de en fr ru"
MAKEOPTS="-j5"
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 audiofile aufs automap automount barcode bash-completion berkdb blas blast bluetooth bluray boost btrfs bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cilk clang cli cmake collada 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 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 gstreamer gtk gtk3 gudev guile hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 ithreads jadetex java jbig jit john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libgda libkms libnotify libsamplerate live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses 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 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 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 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 xa xattr xcb xen xetex xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zsh-completion zvbi" ABI_X86="64" ALSA_CARDS="hda-intel" 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 plan sheets stage words" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog sensors thermal" CPU_FLAGS_X86="avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 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 hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd SureElec" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="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 php7-0" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7 python3_5" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby23" USERLAND="GNU" VIDEO_CARDS="intel" 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




root@cheetahnew:/usr/local/portage/media-video(59)# emerge -pqv '=dev-python/notebook-5.2.1::gentoo'
[ebuild     U ] dev-python/notebook-5.2.1 [5.0.0] USE="doc {-test}" PYTHON_TARGETS="python2_7 python3_4 python3_5 -python3_6"

[Comment 1 Jonas Stein 2018-06-02 21:04:29 UTC]

Please test, if the problem remains, if you use only the official gentoo packages.
My first guess is, that the problem is located in the overlay, but you should try to collect some more details so that we can assign the ticket properly.

[Comment 2 Juergen Rose 2018-06-06 18:33:04 UTC]

After downgrading to dev-python/sphinx-1.6.7::gentoo 'emerge notebook' works again.