[R] Previously compilation procedure on Mac OS X no longer works

[Rob J Goedman]

Isaac,

On Mac OS 10. 4.4 with Xcode 2.2 installed, after setting:

sudo gcc_select 3.3, I get:

Robs-Laptop:~ rob$ gcc_select
Current default compiler:
gcc version 3.3 20030304 (Apple Computer, Inc. build 1819)

Robs-Laptop:~ rob$ cd Downloads/
Robs-Laptop:~/Downloads rob$ R CMD INSTALL sigPathway_1.1-0.tar.gz

gzip: sigPathway_1.1-0.tar.gz: decompression OK, trailing garbage  
ignored
* Installing *source* package 'sigPathway' ...
** libs
gcc-3.3 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include  -I/usr/local/include   -fno-common  -g -O2 -c sigPathway.c - 
o sigPathway.o
gcc-3.3 -bundle -flat_namespace -undefined suppress -L/usr/local/lib - 
o sigPathway.so sigPathway.o  -framework vecLib -lcc_dynamic -F/ 
Library/Frameworks/R.framework/.. -framework R
ld: warning multiple definitions of symbol _xerbla_
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/ 
vecLib.framework/Versions/A/libBLAS.dylib(single module) definition  
of _xerbla_
/Library/Frameworks/R.framework/../R.framework/R(print.lo) definition  
of _xerbla_
ld: warning multiple definitions of symbol _signgam
/Library/Frameworks/R.framework/../R.framework/R(lgamma.lo)  
definition of _signgam
/usr/lib/libSystem.dylib(gamma9.o) definition of _signgam
** R
** data
** help
 >>> Building/Updating help pages for package 'sigPathway'
      Formats: text html latex example
   GenesetsU133a                     text    html    latex
   MuscleData                        text    html    latex
   calcTNullFast                     text    html    latex
   calcTStatFast                     text    html    latex   example
   calculate.GSEA                    text    html    latex
   calculatePathwayStatistics        text    html    latex   example
   getPathwayStatistics              text    html    latex
   rankPathways                      text    html    latex
   runSigPathway                     text    html    latex   example
   selectGeneSets                    text    html    latex
** building package indices ...
* DONE (sigPathway)

and

 > library(sigPathway)
 > example(runSigPathway)

rnSgPt> data(MuscleData)

rnSgPt> sf <- apply(MuscleData, 2, mean, tr = 0.025)

... lots more output, seems to work.

R-Sig-Mac might be a better list to ask specific Mac questions.

Rob


> On Fri, 27 Jan 2006, Isaac Kohane wrote:
>
>> Hi,
>>
>> 	I was a happy user of Peter Parks' package (see http://www.chip.org/
>> ~ppark/Supplements/PNAS05/) and could compile it without error under
>> Mac OS X 10.4. I then had a disk crash and had to re-install the
>> developer tools and now I get hideous messages such as  the one
>> below. I have tried installing an earlier version of Mac OS X
>> developer tools. No joy, Could anyone put me out of my misery and
>> compile  this code and post the binaries for mac os X so that I can
>> just get back to work? Please? Or is there a surefire way to get the
>> compilation process working again?
>
> One source of information is:
>
> http://wiki.urbanek.info/index.cgi?HomePage
>
> and the R-sig-Mac list
>
>>
>> Thanks in advance.
>>
>>
>> -Zak
>>
>>
>>
>> ld: warning -L: directory name (/usr/local/lib) does not exist
>> ld: can't locate file for: -lcc_dynamic
>> make: *** [sigPathway.so] Error 1
>> ERROR: compilation failed for package 'sigPathway'
>> ** Removing '/Library/Frameworks/R.framework/Versions/2.2/Resources/
>> library/sigPathway'
>>
>> ______________________________________________
>> R-help at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! http://www.R-project.org/posting- 
>> guide.html
>>
>
> -- 
> Roger Bivand
> Economic Geography Section, Department of Economics, Norwegian  
> School of
> Economics and Business Administration, Helleveien 30, N-5045 Bergen,
> Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
> e-mail: Roger.Bivand at nhh.no
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting- 
> guide.html