On Mac OS X 10.4.1, using a freshly installed R-2.1.0.dmg (with patch R-2.1.0a.dmg), I ran > source ("http://www.bioconductor.org/getBioC.R") > getBioC ("affy") and then got the error message: /usr/bin/ld: can't locate file for: -lcc_dynamic installation of package 'affy' had non-zero exit status in:n install.packages(pkgs = "affy", repos = c("http://www.bioconductor.org/packages/bioc/stable", while linking gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o \ affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o \ read_abatch.o rma2.o rma_background2.o rma_common.o -lz -lcc_dynamic \ -framework R The full session is included below. Can anyone help? Thanks! - Paul R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. > source ("http://www.bioconductor.org/getBioC.r") Error in file(file, "r", encoding = encoding) : unable to open connection In addition: Warning message: cannot open: HTTP status was '404 Not Found' > source ("http://www.bioconductor.org/getBioC.R") > getBioC ("affy") Running getBioC version 0.2 with R version 2.1.0 http://www.bioconductor.org/scripts/2.1/biocinstall.R Running biocinstall version 0.9 with R version 2.1.0 trying URL 'http://www.bioconductor.org/packages/bioc/stable/src/contr ib/affy_1.6.7.tar.gz' Content type 'application/x-gzip' length 1164993 bytes opened URL ================================================== downloaded 1137Kb * Installing *source* package 'affy' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c chipbackground.c -o chipbackground.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c getall_locations.c -o getall_locations.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c mas5calls.c -o mas5calls.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c qnorm.c -o qnorm.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c read_abatch.c -o read_abatch.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c rma2.c -o rma2.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c rma_background2.c -o rma_background2.o gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 -I/usr/local/include -fno-common -g -O2 -c rma_common.c -o rma_common.o gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o read_abatch.o rma2.o rma_background2.o rma_common.o -lz -lcc_dynamic -framework R ** Removing '/Users/paulshannon/Library/R/library/affy' ** Restoring previous '/Users/paulshannon/Library/R/library/affy' /usr/bin/ld: can't locate file for: -lcc_dynamic collect2: ld returned 1 exit status make: *** [affy.so] Error 1 ERROR: compilation failed for package 'affy' The downloaded packages are in /private/tmp/Rtmp5sLDRX/downloaded_packages Warning message: installation of package 'affy' had non-zero exit status in: install.packages(pkgs = "affy", repos = c("http://www.bioconductor.org/packages/bioc/stable",

Hi Paul, Paul Shannon <pshannon@systemsbiology.org> writes: > On Mac OS X 10.4.1, using a freshly installed R-2.1.0.dmg (with > patch R-2.1.0a.dmg), I ran > > > source ("http://www.bioconductor.org/getBioC.R") > > getBioC ("affy") > > and then got the error message: > > /usr/bin/ld: can't locate file for: -lcc_dynamic > > installation of package 'affy' had non-zero exit status in:n > install.packages(pkgs = "affy", repos = c("http://www.bioconductor.org/packages/bioc/stable", > > while linking > > gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o \ > affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o \ > read_abatch.o rma2.o rma_background2.o rma_common.o -lz -lcc_dynamic \ > -framework R We don't yet have OS X 10.4 installed on any of our systems, but we will soon. Building R packages from source, as your system is attempting, requires a number of tools and libraries. Have you configured your system for building source packages? If so, then I'm afraid I don't have any suggestions at the moment. If not, then you should take a look at the R for OSX FAQ. Best, + seth

On 23/mag/05, at 02:20, Paul Shannon wrote: > On Mac OS X 10.4.1, using a freshly installed R-2.1.0.dmg (with patch > R-2.1.0a.dmg), > I ran > >> source ("http://www.bioconductor.org/getBioC.R") >> getBioC ("affy") > > and then got the error message: > > /usr/bin/ld: can't locate file for: -lcc_dynamic > > installation of package 'affy' had non-zero exit status in:n > install.packages(pkgs = "affy", repos = > c("http://www.bioconductor.org/packages/bioc/stable", > > while linking > > gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib > -o \ > affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o > \ > read_abatch.o rma2.o rma_background2.o rma_common.o -lz > -lcc_dynamic \ > -framework R > Hi Paul, the binary distribution of R (R.app) has been configured on Panther so, in principle, to build packages from source, you should have the same setup. Tiger has no cc_dynamic around and comes with gcc 4.0, but you can still build R from sources switching to gcc3.3 which is supported by panther as well. The same applies to the fortran compiler: you need g77 for panther and not gfortran. You should follow the instructions reported here http://wiki.urbanek.info/index.cgi?TigeR under the section "CRAN build and Tiger". stefano p.s. BTW, we currently build binary packages for Mac OS X and in a couple of days they'll be ready to be downloaded in binary form directly from inside R.app > The full session is included below. > > Can anyone help? Thanks! > > - Paul > > > > > > R : Copyright 2005, The R Foundation for Statistical Computing > Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for a HTML browser interface to help. > Type 'q()' to quit R. > >> source ("http://www.bioconductor.org/getBioC.r") > Error in file(file, "r", encoding = encoding) : > unable to open connection > In addition: Warning message: > cannot open: HTTP status was '404 Not Found' >> source ("http://www.bioconductor.org/getBioC.R") >> getBioC ("affy") > > Running getBioC version 0.2 with R version 2.1.0 > http://www.bioconductor.org/scripts/2.1/biocinstall.R > Running biocinstall version 0.9 with R version 2.1.0 > trying URL > 'http://www.bioconductor.org/packages/bioc/stable/src/contrib/ > affy_1.6.7.tar.gz' > Content type 'application/x-gzip' length 1164993 bytes > opened URL > ================================================== > downloaded 1137Kb > > * Installing *source* package 'affy' ... > creating cache ./config.cache > checking how to run the C preprocessor... cc -E > checking for main in -lz... yes > checking for zlib.h... yes > checking if zlib version >= 1.1.3... yes > updating cache ./config.cache > creating ./config.status > creating src/Makevars > ** libs > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 > -I/usr/local/include -fno-common -g -O2 -c chipbackground.c -o > chipbackground.o > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 > -I/usr/local/include -fno-common -g -O2 -c getall_locations.c -o > getall_locations.o > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 > -I/usr/local/include -fno-common -g -O2 -c mas5calls.c -o > mas5calls.o > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 > -I/usr/local/include -fno-common -g -O2 -c qnorm.c -o qnorm.o > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 > -I/usr/local/include -fno-common -g -O2 -c read_abatch.c -o > read_abatch.o > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 > -I/usr/local/include -fno-common -g -O2 -c rma2.c -o rma2.o > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 > -I/usr/local/include -fno-common -g -O2 -c rma_background2.c -o > rma_background2.o > gcc -no-cpp-precomp > -I/Library/Frameworks/R.framework/Resources/include -DHAVE_ZLIB=1 > -I/usr/local/include -fno-common -g -O2 -c rma_common.c -o > rma_common.o > gcc -bundle -flat_namespace -undefined suppress -L/usr/local/lib -o > affy.so chipbackground.o getall_locations.o mas5calls.o qnorm.o > read_abatch.o rma2.o rma_background2.o rma_common.o -lz -lcc_dynamic > -framework R > ** Removing '/Users/paulshannon/Library/R/library/affy' > ** Restoring previous '/Users/paulshannon/Library/R/library/affy' > /usr/bin/ld: can't locate file for: -lcc_dynamic > collect2: ld returned 1 exit status > make: *** [affy.so] Error 1 > ERROR: compilation failed for package 'affy' > > The downloaded packages are in > /private/tmp/Rtmp5sLDRX/downloaded_packages > Warning message: > installation of package 'affy' had non-zero exit status in: > install.packages(pkgs = "affy", repos = > c("http://www.bioconductor.org/packages/bioc/stable", > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >