Support Requests item #2903284, was opened at 2009-11-24 19:51
Message generated for change (Comment added) made by lgautier
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Category: Install Problem (example)
Group: rpy2-2.0.x
Status: Open
Priority: 5
Private: No
Submitted By: Christopher Maxwell (chrisimaxwell)
Assigned to: Nobody/Anonymous (nobody)
Summary: rpy2 not installing in OS X 10.6.2
Initial Comment:
I'm getting the following error when trying to install rpy2 on my Mac.
$ python setup.py install
Traceback (most recent call last):
File "setup.py", line 153, in <module>
ri_ext = getRinterface_ext(RHOME, r_packversion)
File "setup.py", line 139, in getRinterface_ext
get_rconfig(RHOME, 'BLAS_LIBS'),
File "setup.py", line 85, in get_rconfig
raise Exception(cmd + '\nreturned\n' + rconfig)
Exception: "/opt/local/lib/R/bin/R" CMD config BLAS_LIBS
returned
This happens whether I use easy_install or the command-line install.
I'm trying to install the latest rpy2 (rpy2-2.0.8).
I'm using Python 2.5.4 |EPD 5.1.1| (r254:67916, Jul 20 2009, 15:41:21),
though the problem also occurs when I use Python 2.6.4 (r264:75706, Nov 6
2009, 10:44:01) [GCC 4.2.1 (Apple Inc. build 5646)] on darwin.
I have tried to do my homework and solve this myself, but have had no luck.
A similar problem has been addressed here:
https://sourceforge.net/tracker/?func=detail&atid=453022&aid=2721281&group_id=48422
but that involved Fink (which I'm not using) and the problem was apparently
since fixed.
Any help would be much appreciated - I dearly miss this package.
(it used to work, before I started over from scratch with Snow Leopard a few
months ago)
----------------------------------------------------------------------
>Comment By: lgautier (lgautier)
Date: 2009-11-25 23:05
Message:
I'd suggest you try one of the following:
a- desinstall macports R and install the R binary from CRAN, then install
rpy2 again
(note: the CRAN binary should be at /usr/bin/R)
b- download rpy2 from macports (since they package rpy2)
----------------------------------------------------------------------
Comment By: Christopher Maxwell (chrisimaxwell)
Date: 2009-11-25 22:16
Message:
Well, changing to R 2.10.0 (installed by MacPorts) did not fix the
problem.
I confirmed that "/opt/local/lib/R/bin/R" points to 2.10.0
but
"/opt/local/lib/R/bin/R" CMD config BLAS_LIBS
still returns nothing
----------------------------------------------------------------------
Comment By: Christopher Maxwell (chrisimaxwell)
Date: 2009-11-25 22:11
Message:
I have R installed from MacPorts
http://trac.macports.org/browser/trunk/dports/math/R/Portfile
(that was version 2.9.2, currently upgrading to 2.10.0 but not done yet)
I also have R 2.10.0 installed from CRAN binary:
http://cran.fhcrc.org/bin/macosx/ (or more specifically
http://cran.fhcrc.org/bin/macosx/R-2.10.0.pkg)
2.10.0 is what runs from the GUI. 2.9.2 runs from the command line.
I downloaded 2.10.0 and tried to ./configure and make it myself, but it it
crashes in ./configure here:
checking for dummy main to link with Fortran 77 libraries... rm:
conftest.dSYM: is a directory
none
checking for Fortran 77 name-mangling scheme... rm: conftest.dSYM: is a
directory
unknown
configure: WARNING: unknown Fortran name-mangling scheme
checking whether gfortran appends underscores to external names...
unknown
configure: error: cannot use Fortran
Argh.
----------------------------------------------------------------------
Comment By: lgautier (lgautier)
Date: 2009-11-25 21:29
Message:
Where is your R coming from ?
Did you compile it yourself or installed pre-built binaries (and if yes,
from where) ?
----------------------------------------------------------------------
Comment By: Christopher Maxwell (chrisimaxwell)
Date: 2009-11-25 21:23
Message:
Thank you (thank you!) for helping - it would help me very greatly to have
this working again.
I agree that R is not returning information regarding it's BLAS_LIBS
config, although I cannot figure out why. I tried some associated queries
below - hopefully it will help.
R is version 2.9.2 (2009-08-24)
$ "/opt/local/lib/R/bin/R" CMD config BLAS_LIBS
$ "/opt/local/lib/R/bin/R" CMD config LAPACK_LIBS
-L/opt/local/lib/R/lib -lRlapack
$ "/opt/local/lib/R/bin/R" CMD config LDFLAGS
-L/opt/local/lib
Is there a way I can set the BLAS_LIBS in R? I looked and looked, but was
unsuccessful - not surprising in the setting of my lack of understanding...
----------------------------------------------------------------------
Comment By: lgautier (lgautier)
Date: 2009-11-25 21:07
Message:
The problem occurs when the setup script tries to obtain informations from
R
(the exception says that a call to R CMD config returned an empty string)
Can you open a terminal and investigate why the following does not return
anything ?
"/opt/local/lib/R/bin/R" CMD config BLAS_LIBS
----------------------------------------------------------------------
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