Created attachment 374670 [details] work/shogun-3.2.0_build/CMakeFiles/CMakeOutput.log 'emerge shogun' fails with: ... -- Looking for clapack_dpotrf in ATLAS_LAPACK-NOTFOUND CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: ATLAS_LAPACK linked by target "cmTryCompileExec3274824850" in directory /var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0_build/CMakeFiles/CMakeTmp CMake Error: Internal CMake error, TryCompile configure of cmake failed ... Compiler flags: C -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated -g -march=native -O2 -pipe -fopenmp C++ -std=c++11 -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated -g -march=native -O2 -pipe -fopenmp Linker flags: Executable -Wl,-O1 -Wl,--as-needed Module -Wl,-O1 -Wl,--as-needed Shared -Wl,-O1 -Wl,--as-needed -- Configuring incomplete, errors occurred! See also "/var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0_build/CMakeFiles/CMakeOutput.log". See also "/var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0_build/CMakeFiles/CMakeError.log". * ERROR: sci-libs/shogun-3.2.0::gentoo failed (configure phase): * cmake failed root@lynx2:/usr/local/portage/dev-lang(51)# emerge --info '=sci-libs/shogun-3.2.0::gentoo' Portage 2.2.10 (default/linux/amd64/13.0/desktop, gcc-4.8.2, glibc-2.19, 3.14.0-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.14.0-gentoo-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T7500_@_2.20GHz-with-gentoo-2.2 KiB Mem: 3972248 total, 436388 free KiB Swap: 12582908 total, 12362756 free Timestamp of tree: Thu, 10 Apr 2014 02:30:01 +0000 ld GNU ld (GNU Binutils) 2.24 app-shells/bash: 4.2_p46-r1 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.6, 3.3.5, 3.4.0 dev-util/cmake: 2.8.12.2 dev-util/pkgconfig: 0.28-r1 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.9.6-r3, 1.10.3, 1.11.6, 1.14.1 sys-devel/binutils: 2.24-r2 sys-devel/gcc: 4.8.2 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 4.0-r1 sys-kernel/linux-headers: 3.14 (virtual/os-headers) sys-libs/glibc: 2.19 Repositories: gentoo sunrise science x-portage g-cpan g-octave 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 /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php5/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 /etc/udev/rules.d" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-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="-march=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" 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" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage_lynx2" PORTDIR_OVERLAY="/var/lib/layman/sunrise /var/lib/layman/science /usr/local/portage /var/lib/cpan /var/lib/g-octave" USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cgi chm cli cmake consolekit cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fuse g3dvl garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print 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 id3 id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java jbig john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libkms libnotify libsamplerate libxml2 lirc live lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi 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 openexr opengl openmp openvg pam pango pcre pda pdf perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rhythmbox rle romio rpc rrdcgi rrdtool samba sasl schroedinger science sdk sdl 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 sse sse2 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb userlocales utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib 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" 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" CURL_SSL="nss" DVB_CARDS="usb-wt220u" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev synaptics void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de 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="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="intel 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON root@lynx2:/usr/local/portage/dev-lang(52)# emerge -pqv '=sci-libs/shogun-3.2.0::gentoo' [ebuild U ] sci-libs/shogun-3.2.0 [2.0.0] USE="R doc examples lua mono octave python -ruby -static-libs {-test} (-arpack%*) (-bzip2%*) (-eigen%) (-glpk%*) (-gzip%) (-hdf5%*) (-java%*) (-json%) (-lapack%*) (-lpsolve%) (-lzma%*) (-lzo%*) (-nlopt%) (-readline%*) (-smp%*) (-snappy%) (-superlu%) (-xml%*)" PYTHON_SINGLE_TARGET="python2_7%* -python3_3%" PYTHON_TARGETS="python2_7%* python3_3%*"
Created attachment 374672 [details] work/shogun-3.2.0_build/CMakeFiles/CMakeError.log
BTW. atlas is installed: root@lynx2:/usr/local/portage/dev-lang(56)# genlop -t atlas * sci-libs/atlas Thu Dec 13 10:16:37 2012 >>> sci-libs/atlas-3.10.0 merge time: 14 minutes and 49 seconds. Thu Dec 13 10:43:10 2012 >>> sci-libs/atlas-3.10.0 merge time: 16 minutes and 20 seconds. Sat Dec 15 21:23:39 2012 >>> sci-libs/atlas-3.10.0 merge time: 16 minutes. Sun Dec 16 06:45:54 2012 >>> sci-libs/atlas-3.10.0 merge time: 15 minutes and 27 seconds. Thu Dec 27 08:35:05 2012 >>> sci-libs/atlas-3.10.0 merge time: 15 minutes and 13 seconds. Fri Feb 1 13:55:43 2013 >>> sci-libs/atlas-3.10.1 merge time: 15 minutes and 28 seconds. Thu Feb 21 17:24:14 2013 >>> sci-libs/atlas-3.10.1-r1 merge time: 15 minutes and 57 seconds. Mon Feb 3 00:26:58 2014 >>> sci-libs/atlas-3.10.1-r2 merge time: 22 minutes and 18 seconds.
Any news?
I still have the same issue.
Created attachment 381442 [details, diff] Patch which enables the recognition of atlas-3.10.1-r2
Created attachment 381444 [details, diff] Patch for generation of the include directories of octave
With the attached FindAtlas and the FindOctave patch the configuration finishes successfully. 'MAKEOPTS=-j1 emerge -v shogun' fails then with: cd /var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0_build/src/interfaces/octave_static && /usr/bin/x86_64-pc-linux-gnu-g++ -Doctave_static_EXPORTS -DNDEBUG -std=c++11 -Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated -g -march=native -O2 -pipe -fopenmp -fPIC -I/var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0/src -I/var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0/src/shogun -I/var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0_build/src -I/var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0_build/src/shogun -I/usr/include/octave-3.8.1/octave -I/usr/include/octave-3.8.1 -o CMakeFiles/octave_static.dir/OctaveInterface.cpp.o -c /var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0/src/interfaces/octave_static/OctaveInterface.cpp /var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0/src/interfaces/octave_static/OctaveInterface.cpp: In static member function ‘static void COctaveInterface::run_octave_exit()’: /var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0/src/interfaces/octave_static/OctaveInterface.cpp:646:19: error: ‘do_octave_atexit’ was not declared in this scope do_octave_atexit(); It looks, if there is no more a do_octave_atexit function with octave-3.8.1-r1. Without the octave USE flag emerge fails then with: root@lynx:/usr/local/portage/sci-libs(46)# MAKEOPTS=-j1 USE=-octave emerge -v shogun ... Creating modshogun.dll cd /var/tmp/portage/sci-libs/shogun-3.2.0/work/shogun-3.2.0_build/src/interfaces/csharp_modular && /usr/bin/mcs /t:library *.cs /out:modshogun.dll modshogunPINVOKE.cs(9036,141): error CS0100: The parameter name `rows' is a duplicate .... modshogunPINVOKE.cs(29466,165): error CS0100: The parameter name `size' is a duplicate Compilation failed: 129 error(s), 0 warnings src/interfaces/csharp_modular/CMakeFiles/csharp_modular.dir/build.make:372: recipe for target 'src/interfaces/csharp_modular/libmodshogun.so' failed make[2]: *** [src/interfaces/csharp_modular/libmodshogun.so] Error 1 Without the octave and the mono USE flag emerge fails with: root@lynx:/usr/local/portage/sci-libs(47)# MAKEOPTS=-j1 USE="-octave -mono" emerge -v shogun ... Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Gentoo" -- Installing: /var/tmp/portage/sci-libs/shogun-3.2.0/image/usr/lib64/python2.7/site-packages/_modshogun.so -- Removed runtime path from "/var/tmp/portage/sci-libs/shogun-3.2.0/image//usr/lib64/python2.7/site-packages/_modshogun.so" -- Installing: /var/tmp/portage/sci-libs/shogun-3.2.0/image/usr/lib64/python2.7/site-packages/modshogun.py ... -- Installing: /var/tmp/portage/sci-libs/shogun-3.2.0/image/usr/lib64/R/library/shogun/libs/modshogun.so -- Installing: /var/tmp/portage/sci-libs/shogun-3.2.0/image/usr/lib64/R/library/shogun/R/modshogun.RData * ACCESS DENIED: mkdir: /usr/lib64/R/library/shogun * ISE:write_logfile: unable to append logfile: /var/log/sandbox/sandbox-9160.log ... Makefile:65: recipe for target 'install' failed make: *** [install] Aborted * ERROR: sci-libs/shogun-3.2.0::local failed (install phase):
ping!
+ 25 Jan 2015; Justin Lecher <jlec@gentoo.org> shogun-3.2.0.ebuild, + +files/shogun-3.2.0-atlas.patch, metadata.xml: + Fix buildproblems with atlas detection, #507304; be multilib friendly, + #531034; do not fetch gmock for tests, #528566 +
