I would suggest installing from scratch, making sure that you install from source and that your toolchain is set properly to compile from scratch on the Mac. Most likely there is some mismatch between compiler versions. If you want more information, tell us 1) Are you using Leopard? 2) Exactly what compiler you are using (include the build number please) and how did you install it. The answer to 2) might be simple like "I never installed a compiler" or "I installed Xcode 3 from the leopard disc" or ... A good idea would be to read http://r.research.att.com/tools/ carefully Kasper On Feb 13, 2008, at 7:42 AM, Diego Diez wrote: > Hi Helen, > > (sorry for the double message I forgot to cc bioc) > > I found the same problem when installing BioC development packages > with R-devel in a PPC Mac. The reason might be that the binary > packages are not compiled for PPC in the devel branch although I am > not sure about it. Anyway, to solve it you should use source packages, > i.e. either: > > source('http://bioconductor.org/bioLite.R') > biocLite(type="source") > > or if you want to update your installation: > > library(Biobase) > update.packages(repos=biocReposList(), type="source") > > unfortunately, after realizing my problem I was unable to fix the > installation and I had to reinstall R-devel and BioC again. Maybe I > didn't too hard. > > Hope this helps. > > Diego. > > On Feb 13, 2008 8:06 PM, Helen Zhou <zhou.helen at="" yahoo.com=""> wrote: >> Dear Ben, >> >> thanks your for your fast reply. I actually thought I >> installed everything with biocLite() when I changed to >> R-devel a couple of weeks ago, but I guess I must have >> messed up somewhere. >> >> Unfortunately, I suspect that I have some issues with >> my installation. I updated the packages by running >> >>> repos <- biocReposList() >>> update.packages(repos=repos, ask=FALSE) >> >> but now, what ever I try I run into a problem with >> Biobase. My previous version was 1.17.8, but after the >> update it's 1.17.12, but I can't actually load it. In >> a new R-session with nothing else loaded: >> >>> library(Biobase) >> Loading required package: tools >> Error in dyn.load(file, ...) : >> unable to load shared library >> '/Library/Frameworks/R.framework/Versions/2.7/Resources/library/ >> Biobase/libs/i386/Biobase.so': >> >> dlopen(/Library/Frameworks/R.framework/Versions/2.7/Resources/ >> library/Biobase/libs/i386/Biobase.so, >> 6): Library not loaded: /usr/lib/libiconv.2.dylib >> Referenced from: >> /Library/Frameworks/R.framework/Versions/2.7/Resources/library/ >> Biobase/libs/i386/Biobase.so >> Reason: Incompatible library version: Biobase.so >> requires version 7.0.0 or later, but libiconv.2.dylib >> provides version 5.0.0 >> Error: package/namespace load failed for 'Biobase' >> >> Regards >> - Helen >> >> >> --- Ben Bolstad <bmb at="" bmbolstad.com=""> wrote: >> >>> Looking at your sessionInfo() almost certainly your >>> affyio is out of >>> date (both for R-2.6.1 and R-2.7.0), >>> >>> Current Release version: 1.6.1 >>> Current Devel version: 1.7.11 >>> >>> Your error is likely due to mismatched versions of >>> the packages. >>> >>> Best, >>> >>> Ben >>> >>> >>> >>> >>> >>> On Wed, 2008-02-13 at 02:07 -0800, Helen Zhou wrote: >>>> Dear list, >>>> >>>> oddly enough, whenever I try to read in affymetrix >>>> files my R-session crashes. This includes when I >>> try >>>> to re-run old scripts. I've never had this issue >>>> before, but updated from 2.6.1 to 2.7.0 recently. >>>> >>>> Any help/comments would be much appreciated! The >>> full >>>> list of commands + sessionInfo is shown below. >>> I've >>>> tried with other cel files as well (affy mouse >>>> arrays), but the result is always the same. >>>> >>>>> setwd("~/Desktop") >>>>> library(affy) >>>> Loading required package: Biobase >>>> Loading required package: tools >>>> >>>> Welcome to Bioconductor >>>> >>>> Vignettes contain introductory material. To >>> view, >>>> type >>>> 'openVignette()'. To cite Bioconductor, see >>>> 'citation("Biobase")' and for packages >>>> 'citation(pkgname)'. >>>> >>>> Loading required package: affyio >>>> Loading required package: preprocessCore >>>>> sessionInfo() >>>> R version 2.7.0 Under development (unstable) >>>> (2007-12-22 r43762) >>>> i386-apple-darwin8.10.1 >>>> >>>> locale: >>>> >>> >> en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 >>>> >>>> attached base packages: >>>> [1] tools stats graphics grDevices utils >>> >>>> datasets methods base >>>> >>>> other attached packages: >>>> [1] affy_1.17.3 preprocessCore_1.1.5 >>>> affyio_1.5.11 Biobase_1.17.8 >>>>> raw <- ReadAffy("GSM172068.CEL") >>>> >>>> *** caught bus error *** >>>> address 0xc, cause 'non-existent physical address' >>>> >>>> Traceback: >>>> 1: .Call("ReadHeader", >>> as.character(filenames[[1]]), >>>> PACKAGE = "affyio") >>>> 2: read.affybatch(filenames = l$filenames, >>> phenoData >>>> = l$phenoData, description = l$description, >>> notes >>>> = notes, compress = compress, rm.mask = >>> rm.mask, >>>> rm.outliers = rm.outliers, rm.extra = rm.extra, >>> >>>> verbose = verbose, sd = sd, cdfname = cdfname) >>>> 3: ReadAffy("GSM172068.CEL") >>>> >>>> Possible actions: >>>> 1: abort (with core dump, if enabled) >>>> 2: normal R exit >>>> 3: exit R without saving workspace >>>> 4: exit R saving workspace >>>> Selection: >>>> >>>> Regards >>>> - Helen >>>> >>>> >>>> >>> >> _____________________________________________________________________ >> _______________ >>>> Be a better friend, newshound, and >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> >> >> >> _____________________________________________________________________ >> _______________ >> Looking for last minute shopping deals? >> >> >> _______________________________________________ >> 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 >> > > > > -- > Dr. Diego Diez > Bioinformatics center, > Institute for Chemical Research, > Kyoto University. > Gokasho, Uji, Kyoto 611-0011 JAPAN > diez at kuicr.kyoto-u.ac.jp > > _______________________________________________ > 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

--- Diego Diez <diez at="" kuicr.kyoto-u.ac.jp=""> wrote: > Hi Helen, > > (sorry for the double message I forgot to cc bioc) > > I found the same problem when installing BioC > development packages > with R-devel in a PPC Mac. The reason might be that > the binary > packages are not compiled for PPC in the devel > branch although I am > not sure about it. Anyway, to solve it you should > use source packages, > i.e. either: > > source('http://bioconductor.org/bioLite.R') > biocLite(type="source") > > or if you want to update your installation: > > library(Biobase) > update.packages(repos=biocReposList(), > type="source") > > unfortunately, after realizing my problem I was > unable to fix the > installation and I had to reinstall R-devel and BioC > again. Maybe I > didn't too hard. > Dear Diego Thanks for your advice, I will definitely keep that in mind!! However, I'm afraid it doesn't solve my problem - although it does slightly shift it. After reinstalling R-devel, fiddling around with a lot of things, updating/installing packages from source, I finally got Biobase working :). Only to get the problem with affyio instead :( > library(Biobase) Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > sessionInfo() R version 2.7.0 Under development (unstable) (2008-02-12 r44439) i386-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] Biobase_1.17.13 > library(affyio) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Library/Frameworks/R.framework/Versions/2.7/Resources/library/affyio /libs/i386/affyio.so': dlopen(/Library/Frameworks/R.framework/Versions/2.7/Resources/library/ affyio/libs/i386/affyio.so, 6): Library not loaded: /usr/lib/libiconv.2.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.7/Resources/library/affyio/ libs/i386/affyio.so Reason: Incompatible library version: affyio.so requires version 7.0.0 or later, but libiconv.2.dylib provides version 5.0.0 Error: package/namespace load failed for 'affyio' Will continue trying though; am still hopeful. Best - Helen > Hope this helps. > > Diego. > > On Feb 13, 2008 8:06 PM, Helen Zhou > <zhou.helen at="" yahoo.com=""> wrote: > > Dear Ben, > > > > thanks your for your fast reply. I actually > thought I > > installed everything with biocLite() when I > changed to > > R-devel a couple of weeks ago, but I guess I must > have > > messed up somewhere. > > > > Unfortunately, I suspect that I have some issues > with > > my installation. I updated the packages by running > > > > > repos <- biocReposList() > > > update.packages(repos=repos, ask=FALSE) > > > > but now, what ever I try I run into a problem with > > Biobase. My previous version was 1.17.8, but after > the > > update it's 1.17.12, but I can't actually load it. > In > > a new R-session with nothing else loaded: > > > > > library(Biobase) > > Loading required package: tools > > Error in dyn.load(file, ...) : > > unable to load shared library > > > '/Library/Frameworks/R.framework/Versions/2.7/Resources/library/Biobas e/libs/i386/Biobase.so': > > > > > dlopen(/Library/Frameworks/R.framework/Versions/2.7/Resources/library/ Biobase/libs/i386/Biobase.so, > > 6): Library not loaded: /usr/lib/libiconv.2.dylib > > Referenced from: > > > /Library/Frameworks/R.framework/Versions/2.7/Resources/library/Biobase /libs/i386/Biobase.so > > Reason: Incompatible library version: Biobase.so > > requires version 7.0.0 or later, but > libiconv.2.dylib > > provides version 5.0.0 > > Error: package/namespace load failed for 'Biobase' > > > > Regards > > - Helen > > > > > > --- Ben Bolstad <bmb at="" bmbolstad.com=""> wrote: > > > > > Looking at your sessionInfo() almost certainly > your > > > affyio is out of > > > date (both for R-2.6.1 and R-2.7.0), > > > > > > Current Release version: 1.6.1 > > > Current Devel version: 1.7.11 > > > > > > Your error is likely due to mismatched versions > of > > > the packages. > > > > > > Best, > > > > > > Ben > > > > > > > > > > > > > > > > > > On Wed, 2008-02-13 at 02:07 -0800, Helen Zhou > wrote: > > > > Dear list, > > > > > > > > oddly enough, whenever I try to read in > affymetrix > > > > files my R-session crashes. This includes when > I > > > try > > > > to re-run old scripts. I've never had this > issue > > > > before, but updated from 2.6.1 to 2.7.0 > recently. > > > > > > > > Any help/comments would be much appreciated! > The > > > full > > > > list of commands + sessionInfo is shown below. > > > I've > > > > tried with other cel files as well (affy mouse > > > > arrays), but the result is always the same. > > > > > > > > > setwd("~/Desktop") > > > > > library(affy) > > > > Loading required package: Biobase > > > > Loading required package: tools > > > > > > > > Welcome to Bioconductor > > > > > > > > Vignettes contain introductory material. To > > > view, > > > > type > > > > 'openVignette()'. To cite Bioconductor, see > > > > 'citation("Biobase")' and for packages > > > > 'citation(pkgname)'. > > > > > > > > Loading required package: affyio > > > > Loading required package: preprocessCore > > > > > sessionInfo() > > > > R version 2.7.0 Under development (unstable) > > > > (2007-12-22 r43762) > > > > i386-apple-darwin8.10.1 > > > > > > > > locale: > > > > > > > > > > en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > > > > > > > attached base packages: > > > > [1] tools stats graphics grDevices > utils > > > > > > > datasets methods base > > > > > > > > other attached packages: > > > > [1] affy_1.17.3 preprocessCore_1.1.5 > > > > affyio_1.5.11 Biobase_1.17.8 > > > > > raw <- ReadAffy("GSM172068.CEL") > > > > > > > > *** caught bus error *** > > > > address 0xc, cause 'non-existent physical > address' > > > > > > > > Traceback: > > > > 1: .Call("ReadHeader", > > > as.character(filenames[[1]]), > > > > PACKAGE = "affyio") > > > > 2: read.affybatch(filenames = l$filenames, > > > phenoData > > > > = l$phenoData, description = > l$description, > > > notes > > > > = notes, compress = compress, rm.mask = > > > rm.mask, > > > > rm.outliers = rm.outliers, rm.extra = > rm.extra, > > > > > > > verbose = verbose, sd = sd, cdfname = cdfname) > > > > 3: ReadAffy("GSM172068.CEL") > > > > > > > > Possible actions: > > > > 1: abort (with core dump, if enabled) > > > > 2: normal R exit > > > > 3: exit R without saving workspace > > > > 4: exit R saving workspace > > > > Selection: > > > > > > > > Regards > > > > - Helen > > > > > > > > > > > > > > > > > > ______________________________________________________________________ ______________ > > > > Be a better friend, newshound, and > === message truncated === ________________________________________________________________ ____________________ Never miss a thing. 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