Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 335908 - dev-python/numpy-1.5.0: automagic dependency on fortran compilers
Summary: dev-python/numpy-1.5.0: automagic dependency on fortran compilers
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Gentoo Science Related Packages
Depends on:
Reported: 2010-09-04 03:58 UTC by Benjamin Schulz
Modified: 2010-09-16 04:37 UTC (History)
3 users (show)

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

build log (build.log,134.03 KB, text/plain)
2010-09-07 00:28 UTC, Benjamin Schulz
enforce gnu compiler (numpy-1.5.0-r1.diff,424 bytes, patch)
2010-09-08 09:48 UTC, Kacper Kowalik (Xarthisius) (RETIRED)
Details | Diff

Note You need to log in before you can comment on or make changes to this bug.
Description Benjamin Schulz 2010-09-04 03:58:52 UTC
C compiler: x86_64-pc-linux-gnu-gcc -pthread -march=native -O2 -pipe -fomit-frame-pointer -fPIC

creating build-2.6/temp.linux-x86_64-2.6/numpy/fft
compile options: '-Inumpy/core/include -Ibuild-2.6/src.linux-x86_64-2.6/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -Ibuild-2.6/src.linux-x86_64-2.6/numpy/core/src/multiarray -Ibuild-2.6/src.linux-x86_64-2.6/numpy/core/src/umath -c'
x86_64-pc-linux-gnu-gcc: numpy/fft/fftpack.c
x86_64-pc-linux-gnu-gcc: numpy/fft/fftpack_litemodule.c
x86_64-pc-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,--as-needed -shared -march=native -O2 -pipe -fomit-frame-pointer build-2.6/temp.linux-x86_64-2.6/numpy/fft/fftpack_litemodule.o build-2.6/temp.linux-x86_64-2.6/numpy/fft/fftpack.o -L/usr/lib64 -Lbuild-2.6/temp.linux-x86_64-2.6 -lpython2.6 -o build-2.6/lib.linux-x86_64-2.6/numpy/fft/
building 'numpy.linalg.lapack_lite' extension
compiling C sources
C compiler: x86_64-pc-linux-gnu-gcc -pthread -march=native -O2 -pipe -fomit-frame-pointer -fPIC

creating build-2.6/temp.linux-x86_64-2.6/numpy/linalg
compile options: '-DATLAS_INFO="\"3.9.23\"" -Inumpy/core/include -Ibuild-2.6/src.linux-x86_64-2.6/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.6 -Ibuild-2.6/src.linux-x86_64-2.6/numpy/core/src/multiarray -Ibuild-2.6/src.linux-x86_64-2.6/numpy/core/src/umath -c'
x86_64-pc-linux-gnu-gcc: numpy/linalg/lapack_litemodule.c
x86_64-pc-linux-gnu-gcc: numpy/linalg/python_xerbla.c
/opt/intel/Compiler/11.1/072/bin/intel64/ifort -shared -Wl,-O1 -Wl,--as-needed -shared build-2.6/temp.linux-x86_64-2.6/numpy/linalg/lapack_litemodule.o build-2.6/temp.linux-x86_64-2.6/numpy/linalg/python_xerbla.o -L/usr/lib64 -L/usr/lib64 -Lbuild-2.6/temp.linux-x86_64-2.6 -llapack -lblas -lcblas -latlas -lcblas -lblas -latlas -lpython2.6 -o build-2.6/lib.linux-x86_64-2.6/numpy/linalg/
ld: cannot find -limf
ld: cannot find -limf
error: Command "/opt/intel/Compiler/11.1/072/bin/intel64/ifort -shared -Wl,-O1 -Wl,--as-needed -shared build-2.6/temp.linux-x86_64-2.6/numpy/linalg/lapack_litemodule.o build-2.6/temp.linux-x86_64-2.6/numpy/linalg/python_xerbla.o -L/usr/lib64 -L/usr/lib64 -Lbuild-2.6/temp.linux-x86_64-2.6 -llapack -lblas -lcblas -latlas -lcblas -lblas -latlas -lpython2.6 -o build-2.6/lib.linux-x86_64-2.6/numpy/linalg/" failed with exit status 1
 * ERROR: dev-python/numpy-1.5.0 failed:
 *   Building failed with CPython 2.6 in distutils_building() function

Reproducible: Always
Comment 1 Benjamin Schulz 2010-09-04 03:59:38 UTC
 emerge --info
Portage (default/linux/amd64/10.0, gcc-4.4.4, glibc-2.12.1-r1, 2.6.35-gentoo-r4 x86_64)
System uname: Linux-2.6.35-gentoo-r4-x86_64-Intel-R-_Core-TM-2_Duo_CPU_T9300_@_2.50GHz-with-gentoo-2.0.1
Timestamp of tree: Sat, 04 Sep 2010 00:30:01 +0000
app-shells/bash:     4.1_p7
dev-java/java-config: 2.1.11
dev-lang/python:     2.6.5-r3, 3.1.2-r4
dev-util/cmake:      2.8.1-r2
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.6.3
sys-apps/sandbox:    2.3-r1
sys-devel/autoconf:  2.13, 2.65-r1
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1-r1
sys-devel/gcc:       4.3.4, 4.4.4-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.10
sys-devel/make:      3.81-r2
virtual/os-headers:  2.6.35
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA dlj-1.1 ut2003 sun-bcla-java-vm googleearth AdobeFlash-10"
CFLAGS="-march=native -O2 -pipe -fomit-frame-pointer"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/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"
CXXFLAGS="-march=native -O2 -pipe -fomit-frame-pointer"
FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTDIR_OVERLAY="/usr/layman/layman/xwing /usr/layman/layman/roslin /usr/layman/layman/dottout /usr/layman/layman/kde /usr/layman/layman/science /usr/layman/layman/anarchy /usr/layman/layman/sunrise /usr/layman/ownebuilds"
USE="64bit X Xaw3d a52 aac abiword abyss ace acl acpi activefilter addns addressbook admin adns adplug aften afterimage aim aio akonadi alsa amd64 amr amrnb analogtv animgif archive aspell assistant audacious audio audiofile audioscrobbler auth auto-completion automount autoreplace autotrace bash-completion battery bcmath berkdb binary-drivers binfilter bittorrent blender blender-game bluetooth bonjour boost browser bugzilla bzip2 cairo calendar caps cardbus ccache cdb cddax cddb cdio cdparanoia cdr cdrom cg cgi chroot cli clipboard clucene cluster cmake compat compress connection-sharing consolekit context contrast contrast-control contrib corefonts cpudetection cpulimit cracklib crypt ctype ctypes-python cuda cue cups cvs cxx cyrillic dbus dc1394 dcc dchroot deflate detex devfs-compat device-mapper dga dia dirac disk-partition diskio djvu dmraid dmx docbook dolby-record-switch dolbyinrec dot dpms drawing dri dts dv dvb dvbplayer dvbsetup dvd dvdarchive dvdchapjump dvdnav dvdr dvi dvi2tty dvipdfm dx dxr3 dynamicplugin ebook eclipse emacs emf emovix enca enchant encode ethernet ewf excel exif extensions extra extra-algorithms extras faad facebook fam fame fasttrack fat ffmpeg fftw filter firefox firefox3 fits flac flash flatfile fluidsynth flv fontconfig foomaticdb fortran fortran95 fpx freemail ftp fts3 fuse gadu gallium games gcj gcrypt gd gdbm gfortran ggi gif git github glib glibc-compat20 glibc-omitfp glsl glut glviewer gmm gmp gmtfull gmthigh gmtsuppl gnome-print gnomecanvas gnuplot gnutella gnutls google google-gadgets gphoto2 gpm grace grammar graph graphics graphite graphviz grass groupwise grub gs gsf gsl gsm gstreamer gtk gtk2-perl gtkhotkey gtkspell gzip gzip-el h224 h281 h323 hal hash hdaps hddtemp hdf hdri hepmc hfs highlight highvolume history hotpixels hpn html http httpd httppower humanities hunspell hyperestraier hyphenation i18n ibmvio icc iconv icq icu id3 id3tag idb ieee1394 ifc ilbc image image-cache imagemagick imaging imap imlib indi infowidget inherit-graph inifile inkjar inotify int64 ioctl ipp iproute2 ipsec iptc iptv ipv6 irda iso14755 jabber jack jadetex java java5 java6 javacomm javamail javascript jbig jce jfs joystick jpeg jpeg2k json kate kdcraw kde kde-qt kdevplatform kerberos keyboard kino kipi kmail kolab konqueror kontact kpathsea krb4 l7filter ladspa lame lapack laptop largefile lastfm lastfmradio latex latex3 lcms ldb lensfun libcaca libgig libmms libnl libnotify libproxy libssh2 libsysfs libv4l libv4l2 libwww lightning live lm_sensors logitech-mouse logrotate logviewer lqr lyx lzma lzo m17n-lib mad mail mailbox maildir maildrop maps math mathml matplotlib matroska max-idx-128 mcve md5sum mdb meanwhile mfd-rewrites mjpeg mkl mmx mmxext mng modplug modules mono motif mp2 mp3 mp3tunes mp4 mpeg mpi mplayer mppe-mppc mpqc msn mssql mtp mudflap multilib multimedia musepack music mysql nas nautilus ncurses neXt network networkmanager nfs nfsv3 nfsv4 nis nls nova nptl nptlonly nsplugin ntfs ntp numeric numpy nut nuv nvidia nvram nvtv octave odbc odk ogg ogg123 ogm omega openal opencore-amr openct openexr opengl openmp openssl optimization optimized-qmake oscar otr pam parse-clocks pcmcia pcntl pcre pcsc-lite pdf pdo perl pg-intdatetime phonon php pkcs11 plasma player plotutils pm-utils pmu png pnm policykit portaudio posix postgres postproc postscript ppds pppd preview-latex print ps pstoedit pstricks publishers pulseaudio pvr python qmake qt3support qt4 quicktime quota quotas radio ramfs rar raw rcs readline recording redeyes reflection reiserfs remote remoteosd replytolist resolvconf rle rpc rpm rss rtf rtsp ruby run-as-root samba sasl scanner schroedinger science sdl sdl-image secure-delete semantic-desktop sendmail sensord session sha1 shaders sharedext shine shout simplexml skey skins skype smartcard smbsharemodes smp sms smtp smux sndfile snmp sockets socks socks5 sound soundex sourceview spamassassin spamfilter speex spell spl sql sqlite sqlite3 sse sse2 sse3 sse4 sse4a sse5 ssh ssl ssse3 stream subversion suhosin suid svg swat sysfs syslog sysvipc szip t1lib taglib tcl tcpd templates tex tex4ht texmacs theora thinkpad threads thumbnail thumbnails thunderbird tidy tiff timezone tk tokenizer toolbar toolkit-scroll-bars totem transcode truetype tta tts tv tv_check tv_combiner tv_pick_cgi tvflash tvtime type3 udev udev-acl umfpack unicode unzip upnp usb utils v4l v4l2 vcd vcdinfo vcdx vdpau vga video vlm vorbis wav wavpack wcwidth wddx webcam webdav webdav-neon webdav-serf webinterface webkit webpresence websockets wicd wifi winbind winpopup wma wma-fixed wmf wordperfect wpd wpg wps wv2 wxwidgets x264 x264-static xattr xcomposite xemacs xetex xext xfs xft xhtml xim xine xinerama xinetd xml xmlpatterns xmlreader xmlrpc xmlwriter xmp xorg xpm xrender xsl xterm xterm-color xulrunner xv xvid xvmc yaz youtube yv12 zip zippy zlib zvbi" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse joystick synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia svga vesa v4l fbdev vmware virtualbox" 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" 

Comment 2 Markos Chandras (RETIRED) gentoo-dev 2010-09-06 14:39:51 UTC
full build.log please
Comment 3 Benjamin Schulz 2010-09-07 00:28:30 UTC
Created attachment 246328 [details]
build log
Comment 4 Benjamin Schulz 2010-09-07 00:32:51 UTC
Perhaps this here says something:
It is the beginning of the emerge, the configure part:

(Because apparently, numpy stops during compilation after mentioning my intel compiler)

Usage of get_output is deprecated: please do not 
use it anymore, and avoid configuration checks 
involving running executable on the target machine.

customize GnuFCompiler
Could not locate executable g77
Could not locate executable f77
customize IntelFCompiler
Found executable /opt/intel/Compiler/11.1/072/bin/intel64/ifort
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgf90
Could not locate executable pgf77
customize AbsoftFCompiler
Could not locate executable f90
customize NAGFCompiler
Could not locate executable f95
customize VastFCompiler
customize CompaqFCompiler
Could not locate executable fort
customize IntelItaniumFCompiler
customize IntelEM64TFCompiler
customize IntelEM64TFCompiler
customize IntelEM64TFCompiler using config
compiling '_configtest.c':

Comment 5 Benjamin Schulz 2010-09-07 00:37:58 UTC
What is strange:

I have built gcc with fortran useflat:
sys-devel/gcc-4.4.4-r1  USE="fortran gcj graphite gtk mudflap (multilib) nls nptl openmp (-altivec) -bootstrap -build -doc (-fixed-point) (-hardened) (-libffi) -multislot (-n32) (-n64) -nocxx -nopie -nossp -objc -objc++ -objc-gc -test -vanilla" 62,926 kB

Sp, numpy should find a gnu fortran compiler if it needs it.
Comment 6 Jaroslav Hron 2010-09-07 21:44:17 UTC
same problem here

if I unmerge intel ifort/icc then numpy finds gfortran and compiles fine

maybe numpy could use USE flag ifort/icc to ignore/use intel compilers? 
Comment 7 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2010-09-08 09:48:52 UTC
Created attachment 246435 [details, diff]
enforce gnu compiler

Could try if this fixes the problem for you?
Comment 8 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2010-09-08 09:59:35 UTC
*** Bug 336077 has been marked as a duplicate of this bug. ***
Comment 9 Jaroslav Hron 2010-09-08 10:52:49 UTC
(In reply to comment #7)
> Created an attachment (id=246435) [details]
> enforce gnu compiler
> Could try if this fixes the problem for you?

yes - compilation works using this patch 
the detection phase still claim only ifort compiler

customize GnuFCompiler
Could not locate executable g77
Could not locate executable f77
customize IntelFCompiler
Found executable /opt/intel/Compiler/11.1/072/bin/intel64/ifort
customize LaheyFCompiler
Could not locate executable lf95
customize PGroupFCompiler
Could not locate executable pgf90
Could not locate executable pgf77
customize AbsoftFCompiler
Could not locate executable f90
customize NAGFCompiler
Could not locate executable f95
customize VastFCompiler
customize CompaqFCompiler
Could not locate executable fort
customize IntelItaniumFCompiler
customize IntelEM64TFCompiler
customize IntelEM64TFCompiler
customize IntelEM64TFCompiler using config

Comment 10 Jaroslav Hron 2010-09-08 10:54:13 UTC
why is numpy not using this package?

*  dev-python/numscons
      Latest version available: 0.10.1
      Latest version installed: [ Not Installed ]
      Size of files: 579 kB
      Description:   Support library for building numpy with scons
      License:       BSD
Comment 11 Benjamin Schulz 2010-09-08 20:19:39 UTC
numpy got installed now. Thank you
Comment 12 Kacper Kowalik (Xarthisius) (RETIRED) gentoo-dev 2010-09-09 09:45:11 UTC
Thanks, one thing fixed:
+*numpy-1.5.0-r1 (09 Sep 2010)
+  09 Sep 2010; Kacper Kowalik <> -numpy-1.2.1.ebuild,
+  -numpy-1.5.0.ebuild, +numpy-1.5.0-r1.ebuild:
+  Force numpy to use GNU compilers for linking when FC is set to gfortran,
+  wrt bug 335908. Drop old.

Remaining part to do is check how other compilers behave
Comment 13 Sébastien Fabbro (RETIRED) gentoo-dev 2010-09-16 04:37:14 UTC
> ld: cannot find -limf

This was actually caused by bug #297542. I propose closing this bug since I don't think this is reasonable to check every single fortran compiler, and we can not also track which compiler was used to build lapack which needs to be consistent. The extra building flag that Kapcer included should be enough for now.