Dear Henrik, I followed your code and installed affxparser from aroma. And it works!!! Thanks a lot for that. Yours sincerely, Jianhong Ou jianhong.ou at umassmed.edu On Sep 26, 2012, at 3:50 PM, Henrik Bengtsson wrote: > I'm rather sure this is related to the 'affxparser' package. More > specifically, this problem occurs only for OSX users who have > installed the OSX binary distribution of affxparser available from > Bioconductor. As far as I understand it, it appears to be a > Bioconductor server farm configuration. BioC (Dan Tenenbaum) has > helped us (maintainers of affxparser) trying to figure out what's > causing this, but still to date it remains a "mystery" why the BioC > OSX binaries for affxparser causes core dumps. It appears to only > happen on the BioC farm. As a workaround, we've built a separate OSX > binary for affxparser that can be installed via: > > source("http://aroma-project.org/affxparser.R"); > installAffxparser(); > > That script will check your current setup decide whether the > workaround or the default BioC built will be installed, i.e. anyone > who wish to install affxparser can use that script. The script will > also run validation tests to assert that the installed version of > affxparser works properly. (Those tests are only available for > affxparser >= 1.29.2 (BioC devel)). The tests can be ran separately > too by > > source("http://aroma-project.org/affxparser.R"); > testAffxparser(); > > Jianhong, please report back and let us know if this solved your > original problem. > > /Henrik > (affxparser) > > > > > On Tue, Sep 25, 2012 at 3:51 PM, Benilton Carvalho > <benilton.carvalho at="" cancer.org.uk=""> wrote: >> Most likely a damaged file. Check all the file sizes (I'd go to the terminal and run "du -hsc *.CEL" (without quotes). My guess is that most of them will be about the size size and one will show a strange (usual smaller) value, and this one is a strong candidate for being the problematic file. >> >> >> Sent from a mobile device. Please apologise for brevity, spelling and punctuation. >> >> Robert Scharpf <rscharpf at="" jhsph.edu=""> wrote: >> Jianhong, >> >> This could be a corrupt file. try reading the cel headers directly: >> >> library(affxparser) >> file.exists(celfiles) >> for(i in seq_along(celfiles)) readCelHeader(celfiles[i]) >> >> Rob >> >> >> On Sep 25, 2012, at 4:21 PM, "Ou, Jianhong" <jianhong.ou at="" umassmed.edu=""> wrote: >> >>> Hi all, >>> >>> When I run oligo to analysis the data of http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7822 at Mac OS X (10.6.8), the R always crash. How could I figure out this? Here is my codes and sessionInfo. >>> >>>> library(oligo) >>> Loading required package: oligoClasses >>> Loading package bit 1.1-8 >>> package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2) >>> creators: bit bitwhich >>> coercion: as.logical as.integer as.bit as.bitwhich which >>> operator: ! & | xor != == >>> querying: print length any all min max range sum summary >>> bit access: length<- [ [<- [[ [[<- >>> for more help type ?bit >>> Loading package ff2.2-7 >>> - getOption("fftempdir")=="/var/folders/Dj/Dj+bWjS7HxiNJ0kYFeKdTE+ ++TI/-Tmp-//RtmpPa6Fh5" >>> >>> - getOption("ffextension")=="ff" >>> >>> - getOption("ffdrop")==TRUE >>> >>> - getOption("fffinonexit")==TRUE >>> >>> - getOption("ffpagesize")==65536 >>> >>> - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes >>> >>> - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system >>> >>> - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system >>> >>> Welcome to oligoClasses version 1.18.0 >>> ================================================================== ====================================================================== =================================== >>> Welcome to oligo version 1.20.4 >>> ================================================================== ====================================================================== =================================== >>>> celfiles <- c(paste("GSM1879", 38:49, ".CEL", sep=""), paste("GSM1881", 16:22, ".CEL", sep="")) >>>> library("pd.mapping50k.hind240") >>> Loading required package: RSQLite >>> Loading required package: DBI >>>> crlmm(celfiles, "hindIIout") >>> >>> *** caught segfault *** >>> address 0xfffffffc, cause 'memory not mapped' >>> >>> Traceback: >>> 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser") >>> 2: readCelHeader(filenames[1]) >>> 3: tolower(x) >>> 4: paste("pd.", tolower(x), sep = "") >>> 5: gsub("[_-]", ".", paste("pd.", tolower(x), sep = "")) >>> 6: cleanPlatformName(readCelHeader(filenames[1])$chiptype) >>> 7: crlmm(celfiles, "hindIIout") >>> >>> Possible actions: >>> 1: abort (with core dump, if enabled) >>> 2: normal R exit >>> 3: exit R without saving workspace >>> 4: exit R saving workspace >>> >>>> sessionInfo() >>> R version 2.15.1 (2012-06-22) >>> Platform: i386-apple-darwin9.8.0/i386 (32-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] pd.mapping50k.hind240_1.6.0 RSQLite_0.11.2 DBI_0.2-5 oligo_1.20.4 oligoClasses_1.18.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.28.1 affyio_1.24.0 Biobase_2.16.0 BiocGenerics_0.2.0 BiocInstaller_1.4.7 Biostrings_2.25.8 bit_1.1-8 >>> [8] codetools_0.2-8 ff_2.2-7 foreach_1.4.0 IRanges_1.15.24 iterators_1.0.6 preprocessCore_1.18.0 splines_2.15.1 >>> [15] stats4_2.15.1 zlibbioc_1.2.0 >>> >>> >>> Yours sincerely, >>> >>> Jianhong Ou >>> >>> jianhong.ou at umassmed.edu<mailto:jianhong.ou at="" umassmed.edu=""> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >> >> NOTICE AND DISCLAIMER >> This e-mail (including any attachments) is intended for the above- named person(s). 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