Dear Bioc users, I tried to install some bioconductor packages on our cluster run by OS X 10.4 with R 2.1.0 and failed as bellow. I issued the command as an admistrator and the root user: > source("http://www.bioconductor.org/biocLite.R") got Warning message: unable to load shared library '/common/Frameworks/R.framework/Resources/modules/R_X11.so': dlopen(/common/Frameworks/R.framework/Resources/modules/R_X11.so, 6): Library not loaded: /usr/X11R6/lib/libSM.6.dylib Referenced from: /common/Frameworks/R.framework/Resources/modules/R_X11.so Reason: image not foundQuoting dag via RT <inquiry-support at="" bioteam.net="">: thus after issuing > biocLite() got errors for compilation of several packages for instances: make: *** [Biobase.so] Error 1 ERROR: compilation failed for package 'Biobase' make: *** [Biostrings.so] Error 1 ERROR: compilation failed for package 'Biostrings' Loading required package: tools collect2: ld returned 1 exit status make: *** [affyPLM.so] Error 1 ERROR: compilation failed for package 'affyPLM'Error in library.dynam(lib, package, package.lib) : shared library 'Biobase' not found In addition: Warning messages: 1: package 'Biobase' contains no R code in: loadNamespace(package, c(which.lib.loc, lib.loc)) 2: S3 method 'as.data.frame.exprSet' was declared in NAMESPACE but not found Error: package 'Biobase' could not be loaded Execution halted ERROR: execution of package source for 'annaffy' failed . . . etc. Would you please help me out? Thank you in advance! Joshua

Hi Joshua, Before to go any further, do you have any particular reason to use R 2.1.0? Last R release is 2.3.0 and all R users are highly encouraged to use it. On the Bioconductor side, we follow the R development cycle by releasing a new version of our software a few days after a new R x.y version has been released (approx. every 6 months) and our release is aimed to work with this version of R _only_. Our previous release (BioC 1.7) was aimed to work with R 2.2.0 and our last release (BioC 1.8, released one month ago) is aimed to work with R 2.3.0. If you want to use R 2.1.0 then you will only be able to use BioC 1.6 which we don't support anymore. Best regards, H. szhan at uoguelph.ca wrote: > Dear Bioc users, > I tried to install some bioconductor packages on our cluster run by OS X 10.4 > with R 2.1.0 and failed as bellow. > I issued the command as an admistrator and the root user: > >> source("http://www.bioconductor.org/biocLite.R") >> > got Warning message: > unable to load shared library > '/common/Frameworks/R.framework/Resources/modules/R_X11.so': > dlopen(/common/Frameworks/R.framework/Resources/modules/R_X11.so, 6): Library > not loaded: /usr/X11R6/lib/libSM.6.dylib > Referenced from: /common/Frameworks/R.framework/Resources/modules/R_X11.so > Reason: image not foundQuoting dag via RT <inquiry-support at="" bioteam.net="">: > thus after issuing > >> biocLite() >> > got errors for compilation of several packages for instances: > make: *** [Biobase.so] Error 1 > ERROR: compilation failed for package 'Biobase' > make: *** [Biostrings.so] Error 1 > ERROR: compilation failed for package 'Biostrings' > Loading required package: tools > collect2: ld returned 1 exit status > make: *** [affyPLM.so] Error 1 > ERROR: compilation failed for package 'affyPLM'Error in library.dynam(lib, > package, package.lib) : > shared library 'Biobase' not found > In addition: Warning messages: > 1: package 'Biobase' contains no R code in: loadNamespace(package, > c(which.lib.loc, lib.loc)) > 2: S3 method 'as.data.frame.exprSet' was declared in NAMESPACE but not found > Error: package 'Biobase' could not be loaded > Execution halted > ERROR: execution of package source for 'annaffy' failed > . . . etc. > Would you please help me out? > Thank you in advance! > Joshua > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- ------------------------ Hervé Pagès E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319