Support Requests item #2721281, was opened at 2009-03-29 18:21
Message generated for change (Comment added) made by monipol
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Category: Install Problem (example)
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Monic Polynomial (monipol)
Assigned to: lgautier (lgautier)
Summary: RPy2 with Fink's R: no LAPACK_LIBS; setup.py fails
Initial Comment:
I'm trying to install RPy2 on Mac OS X 10.5.6 using R supplied by Fink. R
(2.7.0) outputs the following link parameters:
$ R CMD config --ldflags
-F/sw/Library/Frameworks/R.framework/.. -framework R
$ R CMD config BLAS_LIBS
-framework vecLib -dylib_file
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib:/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
$ R CMD config LAPACK_LIBS
As you may see, BLAS_LIBS points to libLAPACK (vecLib) and LAPACK_LIBS is empty
(Apple's vecLib includes both BLAS and LAPACK). I was browsing the configure
(autoconf) file distributed with R 2.7.0 and it seems that LAPACK_LIBS is
intended to be blank:
## Note that (see R-admin) that our main intention is to allow a
## LAPACK-containing BLAS to be used, so this is rarely needed, and
## it is not used if the BLAS already contains LAPACK.
## LAPACK_LIBS=
However, RPy'2 setup.py fails if "R CMD config LAPACK_LIBS" doesn't output
something. Should LAPACK_LIBS really be mandatory?
For your information, these are the relevant configure parameters that Fink
uses when building R:
--with-blas="-framework vecLib -dylib_file
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib:/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib"
--with-lapack --enable-R-framework=/sw/Library/Frameworks
----------------------------------------------------------------------
>Comment By: Monic Polynomial (monipol)
Date: 2009-03-30 06:52
Message:
rpy2-2.0.3 (it’s not in Fink yet, I downloaded the tarball from
SourceForge)
$ python setup.py install
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
get_rconfig(RHOME, 'LAPACK_LIBS') +\
File "setup.py", line 78, in get_rconfig
raise Exception(cmd + '\nreturned\n' + rconfig)
Exception: "/sw/Library/Frameworks/R.framework/Resources/bin/R" CMD config
LAPACK_LIBS
returned
$
If I comment out the line in setup.py which calls get_rconfig(RHOME,
'LAPACK_LIBS') then I get another exception wrt BLAS_LIBS:
$ python setup.py install
Traceback (most recent call last):
File "setup.py", line 144, in <module>
ri_ext = getRinterface_ext(RHOME, r_packversion)
File "setup.py", line 130, in getRinterface_ext
get_rconfig(RHOME, 'BLAS_LIBS'),
File "setup.py", line 78, in get_rconfig
raise Exception(cmd + '\nreturned\n' + rconfig)
Exception: "/sw/Library/Frameworks/R.framework/Resources/bin/R" CMD config
BLAS_LIBS
returned
-framework vecLib -dylib_file
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib:/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
$
If I comment out both calls get_rconfig(RHOME, 'LAPACK_LIBS') and
get_rconfig(RHOME, 'BLAS_LIBS') then setup.py proceeds.
----------------------------------------------------------------------
Comment By: lgautier (lgautier)
Date: 2009-03-30 02:41
Message:
What is the exact error message returned ?
What is the version of rpy2 in Fink ?
Thanks,
L.
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