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@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: [EMAIL PROTECTED] > > ______________________________________________ > R-help@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 ______________________________________________ R-help@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