Hello Laurent,
Could you clarify what you suggested Laurent do? I am having the same
problem. I am running 10.5.8 not snow leopard with version 2.10 of R
(precompiled binary). I had to tweak the rpy_tools.py to recognize a 2 digit
version number by changing
version = re.search(" +([0-9]\.[0-9]\.[0-9])", output)
to
version = re.search(" +([0-9]\.[0-9][0-9]\.[0-9])", output)
then I ran python setup.py install in the rpy directory and I got something
like (full output below):
...
lipo: can't figure out the architecture type of:
/var/folders/vP/vPQDhHcNGa0Y3eXI5irYBU+++TI/-Tmp-//cc0pcmsa.out
error: command 'gcc-4.0' failed with exit status 1
Can you explain how to search for the solution to this problem. In your
previous post, you said "You'll need to edit rpy's source for R to
compile; look for posts about that.", but I cannot figure out what you mean by
rpy's source for R.
Thanks,
-Pat
RHOMES= []
DEBUG= True
Setting RHOMES to ['/Library/Frameworks/R.framework/Resources']
### Using R verion 2.10.0 installed at
/Library/Frameworks/R.framework/Resources ###
RHOME= /Library/Frameworks/R.framework/Resources
copying src/rpymodule.c -> src/rpymodule2100.c
copying src/R_eval.c -> src/R_eval2100.c
copying src/io.c -> src/io2100.c
running install
running build
running build_py
copying rpy_tools.py -> build/lib.macosx-10.3-fat-2.6
running build_ext
building '_rpy2100' extension
gcc-4.0 -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -DRPY_SHNAME=_rpy2100
-DINIT_RPY=init_rpy2100 -UPRE_2_2 -UWITH_NUMERIC
-I/Library/Frameworks/R.framework/Resources/include -Isrc
-I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c
src/rpymodule2100.c -o build/temp.macosx-10.3-fat-2.6/src/rpymodule2100.o
In file included from src/rpymodule2100.c:51:
src/RPy.h:77:51: error: Rdevices.h: No such file or directory
In file included from src/rpymodule2100.c:51:
src/RPy.h:77:51: error: Rdevices.h: No such file or directory
src/rpymodule2100.c:1565: warning: initialization from incompatible pointer
typesrc/rpymodule2100.c:1565: warning: initialization from incompatible pointer
type
src/rpymodule2100.c:1568: warning: ‘intargfunc’ is deprecated
src/rpymodule2100.c:1568: warning: initialization from incompatible pointer type
src/rpymodule2100.c:1569: warning: ‘intintargfunc’ is deprecated
src/rpymodule2100.c:1568: warning: ‘intargfunc’ is deprecated
src/rpymodule2100.c:1568: warning: initialization from incompatible pointer type
src/rpymodule2100.c:1569: warning: ‘intintargfunc’ is deprecated
src/rpymodule2100.c:1569: warning: initialization from incompatible pointer type
src/rpymodule2100.c:1570: warning: initialization from incompatible pointer type
src/rpymodule2100.c:1569: warning: initialization from incompatible pointer type
src/rpymodule2100.c:1570: warning: initialization from incompatible pointer type
lipo: can't figure out the architecture type of:
/var/folders/vP/vPQDhHcNGa0Y3eXI5irYBU+++TI/-Tmp-//cc0pcmsa.out
error: command 'gcc-4.0' failed with exit status 1
Patrick Lorch
Biological Sciences Dept.
Kent State University
256 Cunningham Hall
Kent, OH 44242-0001 USA
O: 330-672-7888 Lab: 330-672-2514
http://bioweb.biology.kent.edu/facultypages/lorch/lorch.html
Date: Fri, 06 Nov 2009 18:56:16 +0100
From: Laurent Gautier <lgaut...@gmail.com>
Subject: Re: [Rpy] Problem Installing RPy on OSX
To: joran.el...@gmail.com
Cc: "RPy help, support and design discussion list"
<rpy-list@lists.sourceforge.net>
Message-ID: <4af46340.7030...@gmail.com>
Content-Type: text/plain; charset=windows-1252; format=flowed
Wrong, wrong, wrong... I answered without reading the full details, and
your problem has _nothing_ to do with Rajarshi's issue.
You are using rpy (not rpy2), and there were changes in the R source
(circa version 2.8, I think). You'll need to edit rpy's source for R to
compile; look for posts about that.
L.
Laurent Gautier wrote:
> Rajarshi reported a similar situation
> but the thread is likely interrupted until more is known about the
> Python version used.
>
> http://sourceforge.net/mailarchive/forum.php?thread_name=4AB5CBEC.8070409%40gmail.com&forum_name=rpy-list
>
>
> I currently do not have a Snow Leopard install to play with.
>
>
> L.
>
>
>
>
> Joran Elias wrote:
>> I'm not entirely comfortable in a unix shell, so when I have problems
>> installing stuff like this, it's usually fairly simple. But I've
>> poked around a bit and haven't solved it yet, so I thought I'd ask...
>>
>> I am trying to install RPy on a Mac running 10.6 (Snow Leopard). I
>> have Xcode installed and am using the os x pre installed version of
>> python (2.6 I believe). I have the precompiled binary of R 2.9.1,
>> which I understand should have been compiled with enable-R-shlib.
>>
>> When I run python setup.py install, I get the following:
>>
>> RHOMES= []
>> DEBUG= True
>> Setting RHOMES to ['/Library/Frameworks/R.framework/Resources']
>> ### Using R verion 2.9.1 installed at
>> /Library/Frameworks/R.framework/Resources ###
>> RHOME= /Library/Frameworks/R.framework/Resources
>> copying src/rpymodule.c -> src/rpymodule2091.c
>> copying src/R_eval.c -> src/R_eval2091.c
>> copying src/io.c -> src/io2091.c
>> running install
>> running build
>> running build_py
>> running build_ext
>> building '_rpy2091' extension
>> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv
>> -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch ppc
>> -arch x86_64 -pipe -DWITH_NUMERIC=3 -DPY_ARRAY_TYPES_PREFIX=PyArray_
>> -DRPY_SHNAME=_rpy2091 -DINIT_RPY=init_rpy2091 -UPRE_2_2
>> -I/Library/Frameworks/R.framework/Resources/include -Isrc
>> -I/Library/Python/2.6/site-packages/numpy-1.4.0.dev7542-py2.6-macosx-10.6-universal.egg/numpy/core/include
>> -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6
>> -c src/rpymodule2091.c -o
>> build/temp.macosx-10.6-universal-2.6/src/rpymodule2091.o
>> In file included from src/RPy.h:57,
>> from src/rpymodule2091.c:51:
>> /Library/Frameworks/R.framework/Resources/include/R_ext/Rdynload.h:26:
>> warning: function declaration isn?t a prototype
>> In file included from src/rpymodule2091.c:51:
>> src/RPy.h:77:51: error: Rdevices.h: No such file or directory
>> src/rpymodule2091.c:1565: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1568: warning: ?intargfunc? is deprecated
>> src/rpymodule2091.c:1568: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1569: warning: ?intintargfunc? is deprecated
>> src/rpymodule2091.c:1569: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1570: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c: In function ?r_finalize?:
>> src/rpymodule2091.c:1782: warning: implicit declaration of function
>> ?Rf_KillAllDevices?
>> src/rpymodule2091.c:1788: warning: implicit declaration of function
>> ?R_CleanTempDir?
>> src/rpymodule2091.c:1776: warning: unused variable ?tmpdir?
>> src/rpymodule2091.c:1775: warning: unused variable ?buf?
>> In file included from src/RPy.h:57,
>> from src/rpymodule2091.c:51:
>> /Library/Frameworks/R.framework/Resources/include/R_ext/Rdynload.h:26:
>> warning: function declaration isn?t a prototype
>> In file included from src/rpymodule2091.c:51:
>> src/RPy.h:77:51: error: Rdevices.h: No such file or directory
>> src/rpymodule2091.c:1565: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1568: warning: ?intargfunc? is deprecated
>> src/rpymodule2091.c:1568: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1569: warning: ?intintargfunc? is deprecated
>> src/rpymodule2091.c:1569: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1570: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c: In function ?r_finalize?:
>> src/rpymodule2091.c:1782: warning: implicit declaration of function
>> ?Rf_KillAllDevices?
>> src/rpymodule2091.c:1788: warning: implicit declaration of function
>> ?R_CleanTempDir?
>> src/rpymodule2091.c:1776: warning: unused variable ?tmpdir?
>> src/rpymodule2091.c:1775: warning: unused variable ?buf?
>> In file included from src/rpymodule2091.c:42:
>> /Library/Frameworks/R.framework/Resources/include/Rversion.h:9:29:
>> error: x86_64/Rversion.h: No such file or directory
>> src/rpymodule2091.c:43:28: error: missing binary operator before token
>> "("
>> In file included from
>> /Library/Frameworks/R.framework/Resources/include/R.h:40,
>> from src/RPy.h:51,
>> from src/rpymodule2091.c:51:
>> /Library/Frameworks/R.framework/Resources/include/Rconfig.h:9:28:
>> error: x86_64/Rconfig.h: No such file or directory
>> In file included from src/RPy.h:57,
>> from src/rpymodule2091.c:51:
>> /Library/Frameworks/R.framework/Resources/include/R_ext/Rdynload.h:26:
>> warning: function declaration isn?t a prototype
>> In file included from src/RPy.h:71,
>> from src/rpymodule2091.c:51:
>> src/rpy_Rinterface.h:85: warning: function declaration isn?t a prototype
>> src/rpy_Rinterface.h:96: warning: function declaration isn?t a prototype
>> src/rpy_Rinterface.h:101: warning: function declaration isn?t a prototype
>> src/rpy_Rinterface.h:102: warning: function declaration isn?t a prototype
>> src/rpy_Rinterface.h:103: warning: function declaration isn?t a prototype
>> In file included from src/rpymodule2091.c:51:
>> src/RPy.h:77:51: error: Rdevices.h: No such file or directory
>> src/rpymodule2091.c:1565: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1568: warning: ?intargfunc? is deprecated
>> src/rpymodule2091.c:1568: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1569: warning: ?intintargfunc? is deprecated
>> src/rpymodule2091.c:1569: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1570: warning: initialization from incompatible
>> pointer type
>> src/rpymodule2091.c:1781:28: error: missing binary operator before
>> token "("
>> src/rpymodule2091.c: In function ?r_finalize?:
>> src/rpymodule2091.c:1784: warning: implicit declaration of function
>> ?KillAllDevices?
>> src/rpymodule2091.c:1787:28: error: missing binary operator before
>> token "("
>> lipo: can't open input file:
>> /var/folders/WA/WAQSKhXYF9eYDiqVddaOd++++TI/-Tmp-//ccoTLLAg.out (No
>> such file or directory)
>> error: command 'gcc-4.2' failed with exit status 1
>>
>> Any ideas?
>>
>> Thanks!
>>
>>
>> Joran
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