Support Requests item #2721281, was opened at 2009-03-29 18:21 Message generated for change (Comment added) made by monipol You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=453022&aid=2721281&group_id=48422
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. 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: 2009-04-22 08:06 Message: Hello Laurent. I’d just like to let you know that RPy2 2.0.3 has been accepted by Fink. ---------------------------------------------------------------------- Comment By: lgautier (lgautier) Date: 2009-04-04 06:41 Message: Thanks for looking into this. I'd think that the empty output from running 'R CMD config LAPACK_LIBS' is an oddity on the R CMD config side, but I'll patch setup.py so it works properly. ---------------------------------------------------------------------- Comment By: Monic Polynomial (monipol) Date: 2009-04-03 15:28 Message: Laurent, I’d like to let you know that I’ve submitted a new RPy2 package to Fink. With regard to the problem with those link parameters, I forced RPy2 to use -framework vecLib because this is what is actually used during the linking process of R in Fink. ---------------------------------------------------------------------- Comment By: Monic Polynomial (monipol) Date: 2009-04-01 20:15 Message: I've been reading more about R and Mac OS X. From http://cran.r-project.org/doc/manuals/R-admin.html#Mac-OS-X : The vecLib library can be used via the (default) configuration options --with-blas="-framework vecLib" --with-lapack With this configure parameters, R dumps the following (I customised Fink's configuration params to match the previous line): $ R CMD config --ldflags -F/sw/Library/Frameworks/R.framework/.. -framework R $ R CMD config LAPACK_LIBS $ R CMD config BLAS_LIBS -framework vecLib With this setting, RPy2's setup.py fails because LAPACK_LIBS is empty and BLAS_LIBS doesn't start with -F (and it doesn't need to because vecLib is a standard framework, i.e., it's located under /System/Library/Frameworks). I guess I could modify the configure options to --with-blas="-F /System/Library/Frameworks -framework vecLib" --with-lapack="-F /System/Library/Frameworks -framework vecLib" so that it matches RPy2's setup.py regexps but this seems a tad fragile. What do you think? ---------------------------------------------------------------------- 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. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=453022&aid=2721281&group_id=48422 ------------------------------------------------------------------------------ Stay on top of everything new and different, both inside and around Java (TM) technology - register by April 22, and save $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. 300 plus technical and hands-on sessions. Register today. Use priority code J9JMT32. http://p.sf.net/sfu/p _______________________________________________ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
