Yes, I do build R from source. I use the macport package manager. It's strange I always had a problems with affxparser and rgl. For rgl I could download the binary version and install it with R CMD INSTALL but today I could not download the binary version of affxparser from bioconductor.org. Thanks for your help! David On Apr 9, 2012, at 12:37 PM, Dan Tenenbaum wrote: > On Mon, Apr 9, 2012 at 12:35 PM, David Ruau <druau at="" stanford.edu=""> wrote: >> Thanks, it worked. >> > > Great. I'm guessing you built R from source and that is why > getOption("pkgType") > returns "source". > So biocLite() will always try to install from source unless you pass > type="mac.binary.leopard" > > If you want, you can put > options("pkgType" = "mac.binary.leopard") > in your ~/.Rprofile > and biocLite will always do a binary install. > Or > options("pkgType" = "both") > will cause it to install binary unless a newer source package is available. > > Dan > > > >> David >> >> On Apr 9, 2012, at 12:25 PM, Dan Tenenbaum wrote: >> >>> On Mon, Apr 9, 2012 at 12:23 PM, David Ruau <druau at="" stanford.edu=""> wrote: >>>> Hi Dan, >>>> >>>> I pasted the output here http://pastebin.com/Lnt79kC5 >>>> biocLite() tries to install affxparser, fails and ask you if you want to update it (at the same time as other packages). And then fails again. >>>> >>> OK, what if you do this: >>> biocLite("affxparser", type="mac.binary.leopard") >>> >>> ? >>> Dan >>> >>> >>>> Thanks, >>>> David >>>> >>>> On Apr 9, 2012, at 11:47 AM, Dan Tenenbaum wrote: >>>> >>>>> Hi David, >>>>> >>>>> On Mon, Apr 9, 2012 at 11:33 AM, David Ruau <druau at="" stanford.edu=""> wrote: >>>>>> Hello, >>>>>> >>>>>> I am experiencing an error trying to install affxparser on my mac (Snow Leopard 10.6.8) >>>>>> I cannot install from source and the binary version that is not available from Mac OSX snow leopard. >>>>> >>>>> >>>>> Can you show the output of >>>>> biocLite("affxparser") >>>>> >>>>> without type="source"? >>>>> >>>>> It works on my lion system with R 2.15.0 and BiocInstaller 1.4.3. >>>>> >>>>> Dan >>>>> >>>>> >>>>>> Below are the relevant lines of the install process. >>>>>> >>>>>> --- >>>>>>> biocLite("affxparser", type='source') >>>>>> BioC_mirror: http://bioconductor.org >>>>>> Using R version 2.15, BiocInstaller version 1.4.3. >>>>>> Installing package(s) 'affxparser' >>>>>> trying URL 'http://www.bioconductor.org/packages/2.10/bioc/src/ contrib/affxparser_1.28.0.tar.gz' >>>>>> >>>>>> [snip...] >>>>>> >>>>>> /opt/local/bin/g++-mp-4.5 -I/opt/local/lib/R/include -I/opt/local/lib/R/include/x86_64 -DNDEBUG -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/file/TsvFile -Ifusion_sdk/portability -Ifusion_sdk/util -Ifusion_sdk -D_USE_MEM_MAPPING_ -I/opt/local/include -fPIC -pipe -O2 -m64 -O0 -c fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp -o fusion_sdk/calvin_files/fusion/src/FusionCELData.o >>>>>> In file included from fusion_sdk/calvin_files/fusion/src/GCOSAd apter/GCOSCELDataAdapter.h:30:0, >>>>>> from fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp:24: >>>>>> fusion_sdk/file/CELFileData.h:91:23: warning: malformed '#pragma options align={mac68k|power|reset}', ignoring >>>>>> fusion_sdk/file/CELFileData.h:127:23: error: too many #pragma options align=reset >>>>>> make: *** [fusion_sdk/calvin_files/fusion/src/FusionCELData.o] Error 1 >>>>>> ERROR: compilation failed for package ?affxparser? >>>>>> * removing ?/opt/local/lib/R/library/affxparser? >>>>>> * restoring previous ?/opt/local/lib/R/library/affxparser? >>>>>> >>>>>> The downloaded source packages are in >>>>>> ?/private/var/folders/e9/e9-5zLVqFgGBR2S8qU74+U+++TM/-Tm p-/Rtmpn4Zczi/downloaded_packages? >>>>>> Updating HTML index of packages in '.Library' >>>>>> Making packages.html ... done >>>>>> Old packages: 'affxparser', 'oligo', 'pd.mogene.1.0.st.v1' >>>>>> Update all/some/none? [a/s/n]: n >>>>>> Warning message: >>>>>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>>>>> installation of package ?affxparser? had non-zero exit status >>>>>> >>>>>>> sessionInfo() >>>>>> R version 2.15.0 (2012-03-30) >>>>>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>> >>>>>> other attached packages: >>>>>> [1] BiocInstaller_1.4.3 >>>>>> >>>>>> loaded via a namespace (and not attached): >>>>>> [1] inline_0.3.8 Rcpp_0.9.10 tools_2.15.0 >>>>>> >>>>>> >>>>>> Thanks, >>>>>> David >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>