Fwd: [R] osx/fink: cannot do "R INSTALL" (library mixup)

[Dan Kelley]

Begin forwarded message:

> From: Dan Kelley <Dan.Kelley at Dal.Ca>
> Date: March 19, 2004 12:00:01 PM AST
> To: Don MacQueen <macq at llnl.gov>
> Subject: Re: [R] osx/fink: cannot do "R INSTALL" (library mixup)
>
> That works perfectly!  THanks.  I did
>   524  export PKG_LIBS="-L/usr/local/lib -L/sw/lib"
>   525  R INSTALL pspline
> and all is fine.  Cheers!
>
>
> On Mar 19, 2004, at 11:51 AM, Don MacQueen wrote:
>
>> Did you install the so-called "Developer Tools"? Or perhaps it's more 
>> correctly called "XTools" in 10.3 (Panther).
>>
>> You may have learned about this already, but perhaps not since you 
>> just switched. A default OS X installation does not include all of 
>> the resources needed for code development. I've kind of lost track of 
>> the exact details of what's included in a default installation and 
>> what's not; I find it easier just to install everything.
>>
>> Note that on my system (which is still 10.2.8):
>>    [161]% locate frtbegin
>>    /usr/local/lib/libfrtbegin.a
>> As I understand it, the folks who maintain RAqua binaries for OS X 
>> tend to not want to use fink, so they suggest getting additional 
>> resources from other sources. Evidently I did that.
>>
>>
>> The R documentation is pretty good about installation options. Here 
>> are a few pointers.
>>
>> R INSTALL --help
>>
>> You can set env vars before running R INSTALL, for example:
>>      setenv PKG_CPPFLAGS "-I/usr/local/mysql/include"
>>      setenv PKG_LIBS "-L/usr/local/mysql/lib -lmysqlclient"
>> (csh syntax)
>>
>> -Don
>>
>>> Hello friends.  I've just switched from linux to osx, and I'm liking 
>>> it, except now that I'm getting down to brass tacks, and needing to 
>>> install some R packages, I'm at a roadblock.  I'm hoping someone can 
>>> help.
>>>
>>> My R is installed from a .dmg, and resides as follows:
>>> 	$ which R
>>> 	/usr/local/bin/R
>>> The problem is that I cannot build packages.  For example, see the 
>>> below (which also indicates that libfrtbegin.a is in the
>>> 	/sw
>>> directory, i.e. that it was installed by the FINK setup).  Does 
>>> anybody know how I can solve this problem, e.g. how to alter the
>>> 	-L(directory)
>>>  commands that are employed?
>>>
>>> (Aside: I looked for a solution on the R archives.  Also, I've tried 
>>> to make my subject-line clear enough that an answer will benefit 
>>> other osx/fink users.  Thanks!!)
>>>
>>> 	$ R INSTALL pspline
>>> 	* Installing *source* package 'pspline' ...
>>> 	** libs
>>> 	gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o 
>>> pspline.so Pspline.o  -L/usr/local/lib 
>>> -L/usr/local/lib/gcc/powerpc-	apple-darwin6.6/3.4 
>>> -L/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/../../.. -lfrtbegin 
>>> -lg2c -lSystem -lcc_dynamic
>>> 	ld: warning -L: directory name 
>>> (/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4) does not exist
>>> 	ld: warning -L: directory name 
>>> (/usr/local/lib/gcc/powerpc-apple-darwin6.6/3.4/../../..) does not 
>>> exist
>>> 	ld: can't locate file for: -lfrtbegin
>>> 	make: *** [pspline.so] Error 1
>>> 	ERROR: compilation failed for package 'pspline'
>>> 	** Removing '/Applications/StartR.app/RAqua.app/Contents/pspline'
>>>
>>> 	$ locate frtbegin
>>> 	/sw/lib/libfrtbegin.a
>>>
>>> Dan E. Kelley, Associate Professor                phone:(902)494-1694
>>> Oceanography Department, Dalhousie University       fax:(902)494-2885
>>> Halifax, Nova Scotia                         mailto:Dan.Kelley at Dal.CA
>>> Canada B3H 4J1   http://www.phys.ocean.dal.ca/~kelley/Kelley_Dan.html
>>>
>>> ______________________________________________
>>> R-help at stat.math.ethz.ch mailing list
>>> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide! 
>>> http://www.R-project.org/posting-guide.html
>>
>>
>> -- 
>> --------------------------------------
>> Don MacQueen
>> Environmental Protection Department
>> Lawrence Livermore National Laboratory
>> Livermore, CA, USA
>> --------------------------------------
>>
> Dan E. Kelley, Associate Professor                phone:(902)494-1694
> Oceanography Department, Dalhousie University       fax:(902)494-2885
> Halifax, Nova Scotia                         mailto:Dan.Kelley at Dal.CA
> Canada B3H 4J1   http://www.phys.ocean.dal.ca/~kelley/Kelley_Dan.html
>
Dan E. Kelley, Associate Professor                phone:(902)494-1694
Oceanography Department, Dalhousie University       fax:(902)494-2885
Halifax, Nova Scotia                         mailto:Dan.Kelley at Dal.CA
Canada B3H 4J1   http://www.phys.ocean.dal.ca/~kelley/Kelley_Dan.html