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Bug 263514 - dev-python/rpy-2.0.2 setup.py fails
Summary: dev-python/rpy-2.0.2 setup.py fails
Status: RESOLVED LATER
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Development (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Python Gentoo Team
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2009-03-23 16:44 UTC by Helmut Jarausch
Modified: 2009-03-25 11:47 UTC (History)
0 users

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


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Description Helmut Jarausch 2009-03-23 16:44:37 UTC
>>> Compiling source in /var/tmp/portage/dev-python/rpy-2.0.2/work/rpy2-2.0.2 ...
Traceback (most recent call last):
  File "setup.py", line 144, in <module>
    ri_ext = getRinterface_ext(RHOME, r_packversion)
  File "setup.py", line 129, in getRinterface_ext
    tuple(get_rconfig(RHOME, 'LAPACK_LIBS')[0].split()) +\
  File "setup.py", line 78, in get_rconfig
    raise Exception(cmd + '\nreturned\n' + rconfig)
Exception: "/usr/lib64/R/bin/R" CMD config LAPACK_LIBS
returned
-Wl,--no-as-needed -L/opt/acml4.2.0/gfortran64_mp/lib -lacml_mp -lacml_mv -lgfortran -lpthread


Reproducible: Always




8 % emerge --info
Portage 2.2_rc26 (default/linux/amd64/2008.0/desktop, gcc-4.3.3, glibc-2.9_p20081201-r2, 2.6.28-gentoo-r4 x86_64)
=================================================================
System uname: Linux-2.6.28-gentoo-r4-x86_64-AMD_Phenom-tm-_II_X4_940_Processor-with-glibc2.2.5
Timestamp of tree: Mon, 23 Mar 2009 06:45:01 +0000
ccache version 2.4 [disabled]
app-shells/bash:     3.2_p48
dev-java/java-config: 1.3.7-r1, 2.1.7
dev-lang/python:     2.5.4-r2
dev-python/pycrypto: 2.0.1-r8
dev-util/ccache:     2.4-r8
dev-util/cmake:      2.6.3
sys-apps/baselayout: 2.0.0
sys-apps/openrc:     0.4.3-r1
sys-apps/sandbox:    1.6
sys-devel/autoconf:  2.13, 2.63
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2
sys-devel/binutils:  2.19.1-r1
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6a
virtual/os-headers:  2.6.28-r1
ACCEPT_KEYWORDS="amd64 ~amd64"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-mtune=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"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /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 /etc/udev/rules.d"
CXXFLAGS="-mtune=native -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="buildpkg distlocks fixpackages parallel-fetch preserve-libs protect-owned sandbox sfperms strict unmerge-orphans userfetch"
GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo "
LDFLAGS="-Wl,-O1"
LINGUAS="en de"
MAKEOPTS="-j4"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage /usr/local/portage/layman/java-overlay"
SYNC="rsync://rsync.informatik.RWTH-Aachen.de/gentoo-portage"
USE="3dnow 3dnowext 3dnowprefetch X acl acpi alsa amd64 atm avahi berkdb bluetooth branding bzip2 cairo cdr cli cracklib crypt cups dbus dri dvd dvdr dvdread eds emboss encode esd evo fam ffmpeg fftw firefox fortran gdbm gfortran gif gimp gnome gpm gstreamer gtk gtk2 hal iconv ipv6 isdnlog jpeg kde lapack lcms libnotify mad midi mikmod mmx mmxext mp3 mpeg mudflap multilib ncurses nls nptl nptlonly ogg opengl openmp pam pcre pdf perl png ppds pppd python qt qt3 qt3support qt4 quicktime readline reflection sdl session smp spell spl sqlite sqlite3 sse sse2 sse3 sse4a ssl startup-notification svg sysfs tcl tcpd threads tiff tk truetype unicode usb vorbis xml xorg xulrunner xv zlib" 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 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="keyboard mouse evdev wacom" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en de" USERLAND="GNU" VIDEO_CARDS="radeonhd"
Unset:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Jesus Rivero (RETIRED) gentoo-dev 2009-03-24 04:26:56 UTC
Hello, 
   I cannot reproduce this on on x86 with python-2.5.4..

   Can somebody check this out on amd64 please?

    Best regards,
Comment 2 Sébastien Fabbro (RETIRED) gentoo-dev 2009-03-24 11:46:59 UTC
This is probably due to the fact you are using acml as a blas/lapack implementation.

Could you show the output for "eselect lapack list"?

Note if you are using acml-4.1.0 with gfortran, you need gcc-4.2.4, which you don't seem to have selected given your emerge --info.
No matter what, I would recommand using another lapack implementation, re-emerging R and rpy.


Comment 3 Helmut Jarausch 2009-03-24 19:32:35 UTC
(In reply to comment #2)
> This is probably due to the fact you are using acml as a blas/lapack
> implementation.
> 
> Could you show the output for "eselect lapack list"?
> 
> Note if you are using acml-4.1.0 with gfortran, you need gcc-4.2.4, which you
> don't seem to have selected given your emerge --info.
> No matter what, I would recommand using another lapack implementation,
> re-emerging R and rpy.
> 
eselect lapack list shows acml-gfortran-openmp, indeed.

But after
eselect lapack <atlas>, reemering R and rpy it still fails - see below.
setup.py executes:
/usr/lib64/R/bin/R CMD config LAPACK_LIBS   
which still shows
-Wl,--no-as-needed -L/usr/lib64/lapack/atlas -L/opt/acml4.2.0/gfortran64_mp/lib -llapack -latlas -lacml_mp -lacml_mv -lgfortran -lpthread -lcblas


Failed to emerge dev-python/rpy-2.0.2, Log file:
>>>  '/var/tmp/portage/dev-python/rpy-2.0.2/temp/build.log'
>>> Jobs: 1 of 2 complete, 1 failed                 Load avg: 1.37, 1.26, 0.58
>>> Unpacking source...
>>> Unpacking rpy2-2.0.2.tar.gz to /var/tmp/portage/dev-python/rpy-2.0.2/work
>>> Source unpacked in /var/tmp/portage/dev-python/rpy-2.0.2/work
>>> Preparing source in /var/tmp/portage/dev-python/rpy-2.0.2/work/rpy2-2.0.2 ...
 * Applying rpy-2.0.1-setup.patch ...                                     [ ok ]
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/dev-python/rpy-2.0.2/work/rpy2-2.0.2 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/dev-python/rpy-2.0.2/work/rpy2-2.0.2 ...
Traceback (most recent call last):
  File "setup.py", line 144, in <module>
    ri_ext = getRinterface_ext(RHOME, r_packversion)
  File "setup.py", line 129, in getRinterface_ext
    tuple(get_rconfig(RHOME, 'LAPACK_LIBS')[0].split()) +\
  File "setup.py", line 78, in get_rconfig
    raise Exception(cmd + '\nreturned\n' + rconfig)
Exception: "/usr/lib64/R/bin/R" CMD config LAPACK_LIBS
returned
-Wl,--no-as-needed -L/usr/lib64/lapack/atlas -L/opt/acml4.2.0/gfortran64_mp/lib -llapack -latlas -lacml_mp -lacml_mv -lgfortran -lpthread -lcblas
 * 
 * ERROR: dev-python/rpy-2.0.2 failed.
Comment 4 Sébastien Fabbro (RETIRED) gentoo-dev 2009-03-24 19:46:36 UTC
You need also to reselect blas (and cblas if you don't want to ask for trouble).
If you go for atlas, make sure you eselect blas/cblas to atlas(-threads) and lapack to atlas. You also want to make sure you did install lapack-atlas with atlas(-threads) selected as blas and cblas.
Check the result of "pkg-config --libs blas cblas lapack" which should be free of any acml stuff.
Then re-emerge R and rpy.

I know this is a bit messy, hopefully I will find the time to regularize all the lapack libs.
Thanks
Comment 5 Helmut Jarausch 2009-03-24 20:48:44 UTC
(In reply to comment #4)
> You need also to reselect blas (and cblas if you don't want to ask for
> trouble).
> If you go for atlas, make sure you eselect blas/cblas to atlas(-threads) and
> lapack to atlas. You also want to make sure you did install lapack-atlas with
> atlas(-threads) selected as blas and cblas.
> Check the result of "pkg-config --libs blas cblas lapack" which should be free
> of any acml stuff.
> Then re-emerge R and rpy.
> 
> I know this is a bit messy, hopefully I will find the time to regularize all
> the lapack libs.
> Thanks

Thanks, now it installed without problems.
But atlas provides less performance than libgoto or libacml which provides
more functions.
What's the problem with libacml and gfortran-4.3.3 ?
Thanks,
Helmut.

Comment 6 Sébastien Fabbro (RETIRED) gentoo-dev 2009-03-25 11:47:20 UTC
(In reply to comment #5)

> Thanks, now it installed without problems.
> But atlas provides less performance than libgoto or libacml which provides
> more functions.

You can also eselect blas goto, cblas reference, and lapack reference.
I doubt that for rpy you will see a difference in speed though.

> What's the problem with libacml and gfortran-4.3.3 ?

AMD devs compiled acml-4.1 with gfortran 4.2. And before 4.3, the libgfortran abi were not compatible among versions.

Closing this bug to be resolved when acml package and ebuilds are more stable.