'MAKEOPTS=-j1 emerge -v1 sage' fails with: ... * sage ... [ ok ] * Applying sage-8.4-neutering.patch ... [ ok ] * Applying sage-8.2-gmpy2_option.patch ... [ ok ] * Applying sage-8.2-tachyon_default.patch ... 2 out of 4 hunks FAILED -- saving rejects to file sage/graphs/generic_graph.py.rej [ !! ] * ERROR: sci-mathematics/sage-8.6::sage-on-gentoo failed (prepare phase): * patch -p1 failed with /var/tmp/portage/sci-mathematics/sage-8.6/files/sage-8.2-tachyon_default.patch root@lynx:/root(16)# emerge --info '=sci-mathematics/sage-8.6::sage-on-gentoo' Portage 2.3.56 (python 3.6.6-final-0, default/linux/amd64/17.0/desktop, gcc-8.2.0, glibc-2.28-r5, 4.20.2-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.20.2-gentoo-x86_64-Intel-R-_Core-TM-_i7-6700HQ_CPU_@_2.60GHz-with-gentoo-2.6 KiB Mem: 15904032 total, 2594232 free KiB Swap: 50331644 total, 50329076 free Timestamp of repository gentoo: Wed, 16 Jan 2019 11:30:01 +0000 Head commit of repository gentoo: 8d2ad1b6e0feb6dd673533a6914f7e3cef680070 sh bash 5.0 ld GNU ld (Gentoo 2.31.1 p5) 2.31.1 distcc[4801] (dcc_trace_version) distcc 3.3.2 x86_64-pc-linux-gnu; built Dec 10 2018 00:43:48 [disabled] app-shells/bash: 5.0::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, 1.13.4-r2::gentoo, 1.15.1-r2::gentoo, 1.16.1-r1::gentoo sys-devel/binutils: 2.31.1-r3::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_lynx 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 haskell location: /var/lib/layman/haskell masters: gentoo priority: 0 local location: /usr/local/portage masters: gentoo priority: 1 g-cpan location: /var/lib/cpan masters: gentoo priority: 2 ago location: /var/lib/layman/ago masters: gentoo priority: 50 imaging location: /var/lib/layman/imaging masters: gentoo priority: 50 octave location: /var/lib/layman/octave 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 torbrowser location: /var/lib/layman/torbrowser 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/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=broadwell -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=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 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 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 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 live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mng mod mono motif mozilla mp3 mp4 mpeg 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 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 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 plan sheets 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 framebuffer glcd 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 php7-1" 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="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(19)# emerge -pqv '=sci-mathematics/sage-8.6::sage-on-gentoo' [ebuild U ] sci-mathematics/sage-8.6 [8.5-r1] USE="X doc-html-bin latex sagenb -bliss -debug -doc-html -doc-pdf -doc-pdf-bin -gmpy2 -jmol -modular_decomposition -testsuite" L10N="de en fr ru -ca -es -hu -it -ja -pt -tr" PYTHON_TARGETS="python2_7 python3_6"
If I comment the lines with the sage-8.2-tachyon_default.patch in the ebuild (as in the attached ebuild) I can again emerge sage.
Created attachment 561434 [details] sage-8.6-r1.ebuild An ebuild-4.6 version whithout tachyon patch.
I tried to test some functionality of gap described at: http://www.gap-system.org/Manuals/doc/tut/chap2.html#X7A3C7AE07D6848E3 Some worked, some did not work, see the attached screenshot.
Created attachment 561438 [details] screenshot of sage with some gap commands
If I use the sage commands without the sage notebook, directly in the gap_console inside the sage console everthing seems to be fine: sage: gap_console() ┌───────┐ GAP 4.10.0 of 01-Nov-2018 │ GAP │ https://www.gap-system.org └───────┘ Architecture: amd64 Configuration: gmp 6.1.2, readline Loading the library and packages ... Packages: Alnuth 3.1.0, AtlasRep 1.5.1, AutoDoc 2018.09.20, AutPGrp 1.10, CRISP 1.4.4, CTblLib 1.2.2, FactInt 1.6.2, FGA 1.4.0, GAPDoc 1.6.2, IRREDSOL 1.4, LAGUNA 3.9.0, Polenta 1.3.8, Polycyclic 2.14, PrimGrp 3.3.2, RadiRoot 2.8, ResClasses 4.7.1, SmallGrp 1.3, Sophus 1.24, TomLib 1.2.7, TransGrp 2.0.4, utils 0.59 Try '??help' for help. See also '?copyright', '?cite' and '?authors' gap> (9 - 7) * (5 + 6); 22 gap> 12345/25; 2469/5 gap> -3; 17 - 23; -3 -6 gap> 3^132; 955004950796825236893190701774414011919935138974343129836853841 gap> (9 - 7) * 5 = 9 - 7 * 5; false gap> 10^5 < 10^4; false gap> 10 > 0 and 10 < 100; true gap> (1,2,3) * (1,2); (2,3) gap>
OK the problem with the tachyon patch is embarrassing. I had fixed it in 8.5 already it shouldn't have affected 8.6 and 9999. So fixed. The gap problem is a separate issue, when you talk about the sage notebook, are you talking about the jupyter notebook or "sagenb" the historic notebook that comes with the ebuild "sage-notebook"?
(In reply to François Bissey from comment #6) > OK the problem with the tachyon patch is embarrassing. I had fixed it in 8.5 > already it shouldn't have affected 8.6 and 9999. > So fixed. > > The gap problem is a separate issue, when you talk about the sage notebook, > are you talking about the jupyter notebook or "sagenb" the historic notebook > that comes with the ebuild "sage-notebook"? I am not really what notebook I am using. I suppose it is the sageb notebook: rose@lynx:/home/rose(1)$ sage ┌────────────────────────────────────────────────────────────────────┐ │ SageMath version 8.6, Release Date: 2019-01-15 │ │ Using Python 2.7.15. Type "help()" for help. │ └────────────────────────────────────────────────────────────────────┘ sage: notebook(); ('The notebook files are stored in:', 'sage_notebook.sagenb') Another Sage Notebook server is running, PID 28302. Opening web browser at http://localhost:8080/ ... The related installed packages are: root@lynx:/usr/local/portage/sci-mathematics/sage(48)# qlist -Iv notebook jupyter sagenb dev-python/jupyter_client-5.2.3 dev-python/jupyter_core-4.4.0 dev-python/notebook-5.7.0 sci-mathematics/sage-notebook-1.1.0
You are using the legacy notebook sagenb not the newer one at the moment. I would have to check if your particular issue happens with a vanilla install - if it does that's an upstream bug.
For the record try with jupyter notebook by starting sage with sage --notebook=jupyter
