On Thu, Apr 14, 2011 at 4:13 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > Thank you for the report, Vince and Janet. > > We have identified the problem and it will be fixed in tomorrow's > builds (around noon Seattle time). Just a clarification -- all Mac binary packages are affected by this problem, not just Biobase. They will all be fixed in tomorrow's build, and Vince's suggestion is a workaround if you need them before that. Thanks Dan > > Dan > > > On Thu, Apr 14, 2011 at 4:08 PM, Vincent Carey > <stvjc at="" channing.harvard.edu=""> wrote: >> I reproduced this error with a fresh install of the R for MacOSX >> binary. ?I do not know the specific solution for the binary >> installation of Biobase at this time. ?However, I do routinely install >> and update Xcode tools for mac osx. ?And biocLite("Biobase", >> type="source") created a properly loadable installation. ?I would >> recommend installation of Xcode tools to allow you greater versatility >> in such situations. >> >> On Thu, Apr 14, 2011 at 6:29 PM, Janet Young <jayoung at="" fhcrc.org=""> wrote: >>> Hi, >>> >>> Thanks for the new version - I'm looking forward to using it. ?I've installed it fine on the >>> linux machine I use, but not on Mac - I'm not sure if it's a problem with R, or with >>> Biobase, or with my setup (do I need to to try harder to get rid of R-2.12?). ?I think >>> I've given all the relevant information below. >>> >>> all the best, >>> >>> Janet >>> >>> >>> >>> >>>> source("http://www.bioconductor.org/biocLite.R") >>> BioC_mirror = http://bioconductor.org >>> Change using chooseBioCmirror(). >>>> biocLite("Biobase") >>> Using R version 2.13.0, biocinstall version 2.8.3. >>> Installing Bioconductor version 2.8 packages: >>> [1] "Biobase" >>> Please wait... >>> >>> trying URL >>> 'http://bioconductor.org/packages/2.8/bioc/bin/macosx/leopard/cont rib/2.13/Biobase_2.12.0.tgz' >>> Content type 'application/x-gzip' length 2427717 bytes (2.3 Mb) >>> opened URL >>> ================================================== >>> downloaded 2.3 Mb >>> >>> >>> The downloaded packages are in >>> ? ? ? ?/var/folders/z5/z5O6DCxcG60UeeZiA7+v1E+++Tc/-Tmp-//RtmpP6YQ AN/downloaded_packages >>>> library(Biobase) >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> ?unable to load shared object >>> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/B iobase/libs/i386/Biobase.so': >>> >>> dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/lib rary/Biobase/libs/i386/Biobase. >>> so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib >>> ?Referenced from: >>> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/Bi obase/libs/i386/Biobase.so >>> ?Reason: image not found >>> Error: package/namespace load failed for 'Biobase' >>> >>> >>> >>>> sessionInfo() >>> R version 2.13.0 (2011-04-13) >>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.13.0 >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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 >> >

On Thu, Apr 14, 2011 at 4:13 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > Thank you for the report, Vince and Janet. > > We have identified the problem and it will be fixed in tomorrow's > builds (around noon Seattle time). > > Dan > Hello, All Mac binary packages in the new Bioconductor release are working now. Please install the packages with source("http://bioconductor.org/biocLite.R") biocLite("packagename") Don't use update.packages(). You should be using the version of R available from CRAN: http://cran.r-project.org/bin/macosx/ To be extra thorough, you may want to uninstall/reinstall R before reinstalling Biobase or other packages. Please let us know if you still run into any issues. Thanks Dan > > On Thu, Apr 14, 2011 at 4:08 PM, Vincent Carey > <stvjc at="" channing.harvard.edu=""> wrote: >> I reproduced this error with a fresh install of the R for MacOSX >> binary. ?I do not know the specific solution for the binary >> installation of Biobase at this time. ?However, I do routinely install >> and update Xcode tools for mac osx. ?And biocLite("Biobase", >> type="source") created a properly loadable installation. ?I would >> recommend installation of Xcode tools to allow you greater versatility >> in such situations. >> >> On Thu, Apr 14, 2011 at 6:29 PM, Janet Young <jayoung at="" fhcrc.org=""> wrote: >>> Hi, >>> >>> Thanks for the new version - I'm looking forward to using it. ?I've installed it fine on the >>> linux machine I use, but not on Mac - I'm not sure if it's a problem with R, or with >>> Biobase, or with my setup (do I need to to try harder to get rid of R-2.12?). ?I think >>> I've given all the relevant information below. >>> >>> all the best, >>> >>> Janet >>> >>> >>> >>> >>>> source("http://www.bioconductor.org/biocLite.R") >>> BioC_mirror = http://bioconductor.org >>> Change using chooseBioCmirror(). >>>> biocLite("Biobase") >>> Using R version 2.13.0, biocinstall version 2.8.3. >>> Installing Bioconductor version 2.8 packages: >>> [1] "Biobase" >>> Please wait... >>> >>> trying URL >>> 'http://bioconductor.org/packages/2.8/bioc/bin/macosx/leopard/cont rib/2.13/Biobase_2.12.0.tgz' >>> Content type 'application/x-gzip' length 2427717 bytes (2.3 Mb) >>> opened URL >>> ================================================== >>> downloaded 2.3 Mb >>> >>> >>> The downloaded packages are in >>> ? ? ? ?/var/folders/z5/z5O6DCxcG60UeeZiA7+v1E+++Tc/-Tmp-//RtmpP6YQ AN/downloaded_packages >>>> library(Biobase) >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> ?unable to load shared object >>> '/Library/Frameworks/R.framework/Versions/2.13/Resources/library/B iobase/libs/i386/Biobase.so': >>> >>> dlopen(/Library/Frameworks/R.framework/Versions/2.13/Resources/lib rary/Biobase/libs/i386/Biobase. >>> so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib >>> ?Referenced from: >>> /Library/Frameworks/R.framework/Versions/2.13/Resources/library/Bi obase/libs/i386/Biobase.so >>> ?Reason: image not found >>> Error: package/namespace load failed for 'Biobase' >>> >>> >>> >>>> sessionInfo() >>> R version 2.13.0 (2011-04-13) >>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> loaded via a namespace (and not attached): >>> [1] tools_2.13.0 >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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 >> >