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 texthtmllatex
MuscleDatatexthtmllatex
calcTNullFast texthtmllatex
calcTStatFast texthtmllatex example
calculate.GSEAtexthtmllatex
calculatePathwayStatisticstexthtmllatex example
getPathwayStatistics texthtmllatex
rankPathways texthtmllatex
runSigPathway texthtmllatex example
selectGeneSetstexthtmllatex
** 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'
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