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Bug 625890 - sci-mathematics/sage-7.6 [sage-on-gentoo] with cython-0.26 - InternalError: Internal compiler error: 'cysignals/memory.pxi' not found
Summary: sci-mathematics/sage-7.6 [sage-on-gentoo] with cython-0.26 - InternalError: I...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Keywording (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: François Bissey
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2017-07-21 19:08 UTC by Juergen Rose
Modified: 2017-08-01 07:45 UTC (History)
2 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (build.log,314.53 KB, text/x-log)
2017-07-21 19:08 UTC, Juergen Rose
no flags Details

Note You need to log in before you can comment on or make changes to this bug.
Description Juergen Rose 2017-07-21 19:08:58 UTC
Created attachment 486406 [details]
build.log

'MAKEOPTS=-j1 emerge -v1 sage' fails with:
...
copying sage/parallel/use_fork.py -> /var/tmp/portage/sci-mathematics/sage-7.6/work/sage-7.6/src-python2_7/build/lib/sage/parallel
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
Updating Cython code....
Enabling Cython debugging support
************************************************************************
Traceback (most recent call last):
  File "setup.py", line 764, in <module>
    ext_modules = ext_modules)
  File "/usr/lib64/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/usr/lib64/python2.7/distutils/command/build.py", line 127, in run
    self.run_command(cmd_name)
  File "/usr/lib64/python2.7/distutils/cmd.py", line 326, in run_command
    self.distribution.run_command(command)
  File "/usr/lib64/python2.7/distutils/dist.py", line 971, in run_command
    cmd_obj.ensure_finalized()
  File "/usr/lib64/python2.7/distutils/cmd.py", line 109, in ensure_finalized
    self.finalize_options()
  File "setup.py", line 343, in finalize_options
    self.run_cython()
  File "setup.py", line 417, in run_cython
    cache=False,
  File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 897, in cythonize
    aliases=aliases)
  File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 782, in create_extension_list
    kwds = deps.distutils_info(file, aliases, base).values
  File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 637, in distutils_info
    return (self.transitive_merge(filename, self.distutils_info0, DistutilsInfo.merge)
  File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 647, in transitive_merge
    node, extract, merge, seen, {}, self.cimported_files)[0]
  File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 652, in transitive_merge_helper
    deps = extract(node)
  File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 619, in distutils_info0
    cimports, externs, incdirs = self.cimports_externs_incdirs(filename)
  File "/usr/lib64/python2.7/site-packages/Cython/Utils.py", line 44, in wrapper
    res = cache[args] = f(self, *args)
  File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 524, in cimports_externs_incdirs
    for include in self.included_files(filename):
  File "/usr/lib64/python2.7/site-packages/Cython/Utils.py", line 44, in wrapper
    res = cache[args] = f(self, *args)
  File "/usr/lib64/python2.7/site-packages/Cython/Build/Dependencies.py", line 506, in included_files
    include_path = self.context.find_include_file(include, None)
  File "/usr/lib64/python2.7/site-packages/Cython/Compiler/Main.py", line 274, in find_include_file
    error(pos, "'%s' not found" % filename)
  File "/usr/lib64/python2.7/site-packages/Cython/Compiler/Errors.py", line 177, in error
    raise InternalError(message)
InternalError: Internal compiler error: 'cysignals/memory.pxi' not found
************************************************************************
Error building the Sage library
************************************************************************





root@cheetahnew:/root(13)# emerge --info '=sci-mathematics/sage-7.6::sage-on-gentoo'
Portage 2.3.6 (python 3.4.6-final-0, default/linux/amd64/13.0/desktop, gcc-5.4.0, glibc-2.24-r3, 4.12.2-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.12.2-gentoo-x86_64-Intel-R-_Core-TM-_i3-2120_CPU_@_3.30GHz-with-gentoo-2.4.1
KiB Mem:     7863316 total,   1907544 free
KiB Swap:   25165820 total,  25143028 free
Timestamp of repository gentoo: Fri, 21 Jul 2017 17:30:01 +0000
sh bash 4.4_p12
ld GNU ld (Gentoo 2.28 p1.2) 2.28
distcc[29160] (dcc_trace_version) distcc 3.2rc1 x86_64-pc-linux-gnu; built Oct  2 2016 20:26:57 [disabled]
app-shells/bash:          4.4_p12::gentoo
dev-java/java-config:     2.2.0-r3::gentoo
dev-lang/perl:            5.24.2::gentoo
dev-lang/python:          2.7.13-r100::sage-on-gentoo, 3.4.6::gentoo, 3.5.3::gentoo, 3.6.1-r1::gentoo
dev-util/cmake:           3.9.0::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.4.1::gentoo
sys-apps/openrc:          0.28::gentoo
sys-apps/sandbox:         2.10-r4::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r3::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.15.1::gentoo
sys-devel/binutils:       2.28-r2::gentoo
sys-devel/gcc:            5.4.0-r3::gentoo, 6.3.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r4::gentoo
sys-devel/make:           4.2.1-r1::gentoo
sys-kernel/linux-headers: 4.10::gentoo (virtual/os-headers)
sys-libs/glibc:           2.24-r3::gentoo
Repositories:

gentoo
    location: /usr/portage_cheetahnew
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

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

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/chromium/policies/managed/chrome-gnome-shell.json /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/opt/chrome/policies/managed/chrome-gnome-shell.json /etc/php/apache2-php7.1/ext-active/ /etc/php/cgi-php7.1/ext-active/ /etc/php/cli-php7.1/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"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs clean-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync 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"
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 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 cracklib 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 evo examples excel exif expat extensions extra extras faac faad fam 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 qt3support qt4 qt5 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool rtlsdr sage samba sasl schroedinger science sdk sdl seccomp secure-delete semantic-desktop 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 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="kexi words flow plan sheets stage tables krita karbon braindump author" 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" CURL_SSL="nss" 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" LINGUAS="de en fr ru" 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" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_4" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby21 ruby22" 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_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

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

sci-mathematics/sage-7.6::sage-on-gentoo was built with the following:
USE="X doc-html-bin latex sagenb -bliss -debug -doc-html -doc-pdf -doc-pdf-bin -libbraiding -libhomfly -modular_decomposition -testsuite" ABI_X86="(64)" L10N="de en fr ru -ca -hu -it -ja -pt -tr" PYTHON_TARGETS="python2_7"


root@cheetahnew:/root(120)# emerge -pqv '=sci-mathematics/sage-7.6::sage-on-gentoo'
[ebuild   R   ] sci-mathematics/sage-7.6  USE="X doc-html-bin latex sagenb -bliss -debug -doc-html -doc-pdf -doc-pdf-bin -libbraiding -libhomfly -modular_decomposition -testsuite" L10N="de en fr ru -ca -hu -it -ja -pt -tr" PYTHON_TARGETS="python2_7"
Comment 1 François Bissey 2017-07-21 22:52:39 UTC
Hi Juergen,

That's a good way to know that cython 0.26 has landed in the tree. HAve you rebuild cysignals after the cython upgrade? Furthermore which version of cysignals are you using? I may have to block the latest one I pushed yesterday for 7.6. sage 8.0 has just been released and I think everything will be ok with that one but I am needing a few hours to bump everything properly and prepare the binary doc.
Comment 2 Juergen Rose 2017-07-22 04:35:17 UTC
(In reply to François Bissey from comment #1)
> Hi Juergen,
> 
> That's a good way to know that cython 0.26 has landed in the tree. HAve you
> rebuild cysignals after the cython upgrade? Furthermore which version of
> cysignals are you using? I may have to block the latest one I pushed
> yesterday for 7.6. sage 8.0 has just been released and I think everything
> will be ok with that one but I am needing a few hours to bump everything
> properly and prepare the binary doc.

I compiled now cysignals after cython. But 'emerge sage' still fails:

root@lynx:/etc(74)# genlop -t cython | tail

     Tue Mar 28 21:44:10 2017 >>> dev-python/cython-0.25.2-r2
       merge time: 2 minutes and 53 seconds.

     Sat Apr 22 23:03:01 2017 >>> dev-python/cython-0.25.2-r3
       merge time: 2 minutes and 47 seconds.

     Fri Jul 21 18:53:03 2017 >>> dev-python/cython-0.26
       merge time: 5 minutes and 53 seconds.

root@lynx:/etc(75)# genlop -t cysignals | tail

     Sun Mar 26 13:01:19 2017 >>> dev-python/cysignals-1.4.0
       merge time: 27 seconds.

     Mon Apr 24 18:00:17 2017 >>> dev-python/cysignals-1.4.0
       merge time: 34 seconds.

     Sat Jul 22 03:50:38 2017 >>> dev-python/cysignals-1.4.0
       merge time: 40 seconds.
Comment 3 François Bissey 2017-07-22 04:47:50 UTC
Right. Now that I think about the stuff that has gone in cython 0.26, it is quite possible that sage 7.6 won't build with it.

I think sage 8.0 will be ok with it but I may want to backport a small patch from upstream before release.
Comment 4 François Bissey 2017-07-22 05:39:41 UTC
OK, sage 8.0 has hit the overlay. I made it use cython 0.26. I'll be waiting for feedback, I haven't had time to test the release on a "production" system, only in a development environment. Sometimes I forget some bits in the development environment that need to be moved to a more consumable form.
Comment 5 François Bissey 2017-08-01 07:45:58 UTC
In your case I guess no feedback is a sign that things work.