Created attachment 537358 [details] build.log 'MAKEOPTS=-j1 emerge -v1 sage' fails with: ... Updating Cython code.... /usr/lib64/python2.7/site-packages/cysignals/signals.pxd: cannot find cimported module 'cysignals.__init__' sage/rings/complex_double.pyx: cannot find cimported module 'gmpy2' ... [139/489] Cythonizing sage/groups/perm_gps/partn_ref/refinement_graphs.pyx [140/489] Cythonizing sage/groups/perm_gps/partn_ref/refinementwarning: sage/libs/gap/element.pyx:150:24: local variable 'result' referenced before assignment warning: sage/libs/gap/element.pyx:152:11: local variable 'result' referenced before assignment ... [296/489] Cythonizing sage/modular/arithgroup/farey_symbol.pyx [297/489] Cythonizing sage/modular/warning: sage/numerical/backends/gurobi_backend.pyx:90:10: Compatible but non-identical C method 'add_variable' not redeclared in definition part of extension type 'GurobiBackend'. This may cause incorrect vtables to be generated. warning: sage/numerical/backends/generic_backend.pxd:13:26: Previous declaration is here warning: sage/numerical/backends/interactivelp_backend.pyx:179:10: Compatible but non-identical C method 'add_variable' not redeclared in definition part of extension type 'InteractiveLPBackend'. This may cause incorrect vtables to be generated. warning: sage/numerical/backends/generic_backend.pxd:13:26: Previous declaration is here Error compiling Cython file: ------------------------------------------------------------ ... from .real_double cimport RealDoubleElement, double_repr, double_str from .real_double import RDF from sage.rings.integer_ring import ZZ IF HAVE_GMPY2: cimport gmpy2 ... sage/rings/complex_double.pyx:112:9: cimported module has no attribute 'import_gmpy2' Error compiling Cython file: ... CompileError: sage/rings/complex_double.pyx ************************************************************************ Error building the Sage library ************************************************************************ * ERROR: sci-mathematics/sage-8.2-r1::sage-on-gentoo failed (compile phase): root@lynx:/root(14)# emerge --info '=sci-mathematics/sage-8.2-r1::sage-on-gentoo' Portage 2.3.40 (python 3.6.5-final-0, default/linux/amd64/17.0/desktop, gcc-7.3.0, glibc-2.27-r5, 4.17.2-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.17.2-gentoo-x86_64-Intel-R-_Core-TM-_i7-6700HQ_CPU_@_2.60GHz-with-gentoo-2.6 KiB Mem: 15905260 total, 2918136 free KiB Swap: 50331644 total, 50311500 free Timestamp of repository gentoo: Tue, 26 Jun 2018 20:00:01 +0000 Head commit of repository gentoo: 2a44c2ce8dff33d5381fbaa1f39740f612145712 sh bash 4.4_p23 ld GNU ld (Gentoo 2.30 p3) 2.30.0 distcc[13794] (dcc_trace_version) distcc 3.2rc1 x86_64-pc-linux-gnu; built Mar 21 2018 07:00:29 [disabled] app-shells/bash: 4.4_p23::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.26.2::gentoo dev-lang/python: 2.7.15::gentoo, 3.5.5-r1::gentoo, 3.6.5-r1::gentoo dev-util/cmake: 3.11.4::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, 1.13.4-r2::gentoo, 1.15.1-r2::gentoo, 1.16.1-r1::gentoo sys-devel/binutils: 2.30-r3::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: 4.17::gentoo (virtual/os-headers) sys-libs/glibc: 2.27-r5::gentoo Repositories: gentoo location: /usr/portage_lynx 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-metamanifest: yes sync-rsync-verify-jobs: 1 local 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 ago location: /var/lib/layman/ago masters: gentoo priority: 50 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 tlp location: /var/lib/layman/tlp 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=broadwell -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=broadwell -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="-march=broadwell -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="-j9" 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 branding btrfs bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg 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 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 hdaps hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap 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 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 neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg 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 qt3support 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 thinkpad 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 wifi 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="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 plan sheets stage words" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog sensors thermal" CPU_FLAGS_X86="aes avx avx2 fma3 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 synaptics void" 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" LIRC_DEVICES="devinput" LLVM_TARGETS="NVPTX 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 postgres10" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7 python3_5 python3_6" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby23" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" 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@lynx:/root(15)# emerge -pqv '=sci-mathematics/sage-8.2-r1::sage-on-gentoo' [ebuild U ] sci-mathematics/sage-8.2-r1 [8.1-r3] USE="X doc-html-bin latex sagenb -bliss -debug -doc-html -doc-pdf -doc-pdf-bin -jmol% -libbraiding -libhomfly -modular_decomposition -testsuite" L10N="de en fr ru -ca -es -hu -it -ja -pt -tr" PYTHON_TARGETS="python2_7 python3_6"
What gmpy do you have installed if any?
(In reply to François Bissey from comment #1) > What gmpy do you have installed if any? gmpy-2.1.0_alpha2 is installed, which is a dependency of mpmath-1.0.0, if the gmp USE flag is set. mpmath-1.0.0 is a dependency of astropy-2.0.1, sympy-1.1.1-r4 and sage-8.1-r3.
BTW.: gmpy-2.1.0_alpha2 is from sage-on-gentoo overlay.
If I remove gmp US from mpmath and remove gmpy 'emerge sage' fails with: ... >>> Installing (1 of 1) sci-mathematics/sage-8.2-r1::sage-on-gentoo * checking 28441 files for package collisions 27441 files remaining ... ... 441 files remaining ... * Package 'sci-mathematics/sage-8.2-r1' has one or more collisions * between symlinks and directories, which is explicitly forbidden by PMS * section 13.4 (see bug #326685): * * /usr/share/doc/sage/html/_static/localization * /usr/share/doc/sage/html/_static/fonts * /usr/share/doc/sage/html/_static/config * /usr/share/doc/sage/html/_static/extensions * /usr/share/doc/sage/html/_static/unpacked * /usr/share/doc/sage/html/_static/jax * * This package will overwrite one or more files that may belong to other * packages (see list below). You can use a command such as `portageq ... * Package 'sci-mathematics/sage-8.2-r1' NOT merged since it has one or * more collisions between symlinks and directories, which is explicitly * forbidden by PMS section 13.4 (see bug #326685). If necessary, refer * to your elog messages for the whole content of the above message. >>> Failed to install sci-mathematics/sage-8.2-r1, Log file:
I should mask that version of gmpy-2. It is just trouble.
I am somewhat surprised those dependencies of gmpy works with the version I have in my overlay. This is an alpha release that breaks a lot of things. It is now masked in the overlay which means you should downgrade to the version in the main tree. If the problem persist I will have to do something a little bit better to fix this autodetection upstream. Not everyone is happy with that code I must say.
I do a better treatment of gmpy2 from sage 8.2 onwards. This problem should be fixed now.
I got confirmation that this completely fixed on github.
