Hi! I'm still getting an error after running justGCRMA: Computing affinities.Done. Adjusting for optical effect.........................Done. Adjusting for non-specific binding........................Done. Error in just.gcrma(filenames = l$filenames, phenoData = l$phenoData, : INTEGER() can only be applied to a 'integer', not a 'language' > sessionInfo() R version 2.8.1 (2008-12-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=pl_PL.UTF-8;LC_NUMERIC=C;LC_TIME=pl_PL.UTF-8;LC_COLLATE=pl_PL .UTF-8;LC_ MONETARY=C;LC_MESSAGES=pl_PL.UTF-8;LC_PAPER=pl_PL.UTF-8; LC_NAME=C;LC_ADDRESS=C;L C_TELEPHONE=C;LC_MEASUREMENT=pl_PL.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] hgu133plus2probe_2.0.0 hgu133plus2cdf_2.3.0 gcrma_2.15.3 [4] matchprobes_1.10.0 affy_1.16.0 preprocessCore_1.0.0 [7] affyio_1.11.3 Biobase_1.16.3 loaded via a namespace (and not attached): [1] splines_2.8.1 The problem is the same with affyio 1.10.1 and gcrma 2.14.1. Everything was fine till I decided to upgrade from previous gcrma version (2.8 I guess) Any ideas? Jacek Nowak >Jenny, >Given this bug was making it difficult to use the gcrma package in BioC >2.3 (release), I back-ported the fix Ben put in place for affyio and >gcrma for BioC 2.4 (devel). It will take roughly a day for these >packages to make it through the build and release process, but look for >affyio 1.10.1 and gcrma 2.14.1 to correct this justGCRMA issue in BioC 2.3. > > > >Patrick Jenny Drnevich wrote: >* Hi Ben, *>* *>* Thanks for making the fix - I was having the same error as the *>* original poster on my PC (non-reproducible example below, although it *>* probably doesn't matter now). Just to clarify - the fix will only be *>* in the developmental version of gcrma, 2.15.1, which will take a day *>* to become available (only 2.15.0 is available as of 9 am CDS: *>* http://bioconductor.org/packages/devel/bioc/html/gcrma.html)? *>* *>* Thanks, *>* Jenny *>* *>* *>* > gcrma.all <- *>* justGCRMA(filenames=targets$FileName[1:2],celfile.path="K:/clough/ Stacey/affy/CELfiles") *>* *>* Computing affinities.Done. *>* Adjusting for optical effect...Done. *>* Adjusting for non-specific binding..Done. *>* Error in just.gcrma(filenames = l$filenames, phenoData = l$phenoData, : *>* INTEGER() can only be applied to a 'integer', not a 'environment' *>* > *>* > sessionInfo() *>* R version 2.8.0 (2008-10-20) *>* i386-pc-mingw32 *>* *>* locale: *>* LC_COLLATE=English_United States.1252;LC_CTYPE=English_United *>* States.1252;LC_MONETARY=English_United *>* States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 *>* *>* attached base packages: *>* [1] splines tools stats graphics grDevices utils datasets *>* [8] methods base *>* *>* other attached packages: *>* [1] soybeanprobe_2.3.0 soybeancdf_2.3.0 affyQCReport_1.20.0 *>* [4] geneplotter_1.20.0 lattice_0.17-15 RColorBrewer_1.0-2 *>* [7] simpleaffy_2.18.0 made4_1.16.0 ade4_1.4-9 *>* [10] affyPLM_1.18.0 preprocessCore_1.4.0 affycoretools_1.14.0 *>* [13] annaffy_1.14.0 KEGG.db_2.2.5 gcrma_2.14.0 *>* [16] matchprobes_1.14.0 biomaRt_1.16.0 GOstats_2.8.0 *>* [19] Category_2.8.0 genefilter_1.22.0 survival_2.34-1 *>* [22] RBGL_1.18.0 annotate_1.20.0 xtable_1.5-4 *>* [25] GO.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 *>* [28] AnnotationDbi_1.4.0 graph_1.20.0 limma_2.16.2 *>* [31] affy_1.20.0 Biobase_2.2.0 RWinEdt_1.8-0 *>* *>* loaded via a namespace (and not attached): *>* [1] affyio_1.10.0 cluster_1.11.11 grid_2.8.0 *>* GSEABase_1.4.0 *>* [5] KernSmooth_2.22-22 RCurl_0.91-0 XML_1.94-0.1 *>* *>* At 11:02 PM 10/28/2008, Ben Bolstad wrote: *>>* The crash that Patrick identifies below is an issue with pthreads *>>* enabled builds of affyio, which is why it manifests on Linux builds but *>>* not windows build. Basically, the stack allocated to the thread was *>>* being exhausted. I have fixed that issue in affyio 1.11.1. Also, since *>>* the two CEL files in matchprobes are of different types you get the *>>* error about incorrect dimensions. *>>* *>>* However, the original posters error is unrelated to this crash. Instead, *>>* it is an issue with how justGCRMA() is calling some C code. In *>>* particular it looks like a .Call() was using a previous version of *>>* something that had been changed quite awhile ago. In any case I fixed *>>* this, at least for justGCRMA() in gcrma 2.15.1 *>>* *>>* Ben *>>* *>>* *>>* On Wed, 2008-10-29 at 11:46 +1100, Keith Satterley wrote: *>>* > Just thought I would test this on a Windows platform: *>>* > It reports: *>>* > Cel file *>>* C:/R/R-2.8.0/library/matchprobes/extdata/CL2001032020AA.cel does not *>>* > seem to have the correct dimensions. *>>* > *>>* > Details below: *>>* > *>>* > sessionInfo() *>>* > R version 2.8.0 (2008-10-20) *>>* > i386-pc-mingw32 *>>* > locale: *>>* > *>>* LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252 ;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Austr alia.1252 *>>* *>>* > attached base packages: *>>* > [1] splines tools stats graphics grDevices datasets utils *>>* > methods base *>>* > other attached packages: *>>* > [1] gcrma_2.14.0 matchprobes_1.14.0 affy_1.20.0 *>>* Biobase_2.2.0 *>>* > loaded via a namespace (and not attached): *>>* > [1] affyio_1.10.0 preprocessCore_1.4.0 *>>* > *>>* > > celfile.path <- *>>* file.path("C:/R/R-2.8.0/library/matchprobes/extdata") *>>* > > celfile.path *>>* > [1] "C:/R/R-2.8.0/library/matchprobes/extdata" *>>* > > filenames <- list.celfiles(path=celfile.path, full.names=FALSE) *>>* > > filenames *>>* > [1] "118T1.cel" "CL2001032020AA.cel" *>>* > > normData <- justGCRMA(filenames=filenames, *>>* celfile.path=celfile.path, *>>* > type="affinities", fast=TRUE) *>>* > Computing affinities.Done. *>>* > Error in read.probematrix(filenames = filenames, which = "pm", *>>* cdfname = *>>* > cdfname, : *>>* > Cel file *>>* C:/R/R-2.8.0/library/matchprobes/extdata/CL2001032020AA.cel does not *>>* > seem to have the correct dimensions *>>* > > *>>* > maybe that helps pinpoint a problem. *>>* > *>>* > cheers, *>>* > *>>* > Keith *>>* > *>>* > ======================== *>>* > Keith Satterley *>>* > Bioinformatics Division *>>* > The Walter and Eliza Hall Institute of Medical Research *>>* > Parkville, Melbourne, *>>* > Victoria, Australia *>>* > ======================= *>>* > *>>* > Patrick Aboyoun wrote: *>>* > > Cecile, *>>* > > I took a look at the gcrma package to see if this was a Mac OS *>>* > > X-specific issue and the best I can tell it is not. When I tried *>>* a naive *>>* > > application of the justGCRMA function to some cel files found in the *>>* > > matchprobes package when using a Linux machine, I got a segmentation *>>* > > fault that brought down R 2.8.0. I am cc'ing Jean(ZHIJIN) Wu, the *>>* gcrma *>>* > > package maintainer, to address this issue. *>>* > > *>>* > > *>>* > > > library(gcrma) *>>* > > 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: affy *>>* > > Loading required package: matchprobes *>>* > > Loading required package: splines *>>* > > > sessionInfo() *>>* > > R version 2.8.0 (2008-10-20) *>>* > > x86_64-unknown-linux-gnu *>>* > > *>>* > > locale: *>>* > > *>>* LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MON ETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TEL EPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C *>>* *>>* > > *>>* > > *>>* > > attached base packages: *>>* > > [1] splines tools stats graphics grDevices utils *>>* datasets *>>* > > [8] methods base *>>* > > other attached packages: *>>* > > [1] gcrma_2.14.0 matchprobes_1.14.0 affy_1.20.0 *>>* > > Biobase_2.2.0 *>>* > > loaded via a namespace (and not attached): *>>* > > [1] affyio_1.10.0 preprocessCore_1.4.0 *>>* > > > celfile.path <- file.path("matchprobes/inst/extdata") *>>* > > > filenames <- list.celfiles(path=celfile.path, full.names=FALSE) *>>* > > > filenames *>>* > > [1] "118T1.cel" "CL2001032020AA.cel" *>>* > > > normData <- justGCRMA(filenames=filenames, *>>* celfile.path=celfile.path, *>>* > > type="affinities", fast=TRUE) *>>* > > Computing affinities.Done. *>>* > > Segmentation fault *>>* > > *>>* > > *>>* > > *>>* > > Cecile Laurent wrote: *>>* > >> Dear BioC, *>>* > >> *>>* > >> I've just updated R (2.8) and bioconductor (2.3), and justGCRMA *>>* > >> function doesn't work : *>>* > >> *>>* > >> *>>* > >> > sessionInfo() *>>* > >> R version 2.8.0 (2008-10-20) *>>* > >> powerpc-apple-darwin8.11.1 *>>* > >> *>>* > >> locale: *>>* > >> C *>>* > >> *>>* > >> attached base packages: *>>* > >> [1] splines tools stats graphics grDevices utils *>>* datasets *>>* > >> [8] methods base other attached packages: *>>* > >> [1] gcrma_2.14.0 matchprobes_1.14.0 affy_1.20.0 *>>* > >> Biobase_2.2.0 loaded via a namespace (and not attached): *>>* > >> [1] affyio_1.10.0 preprocessCore_1.4.0 *>>* > >> *>>* > >> *>>* > >> *>>* > >> > require(gcrma) *>>* > >> > celfile.path <- *>>* > >> *>>* file.path("/Users/claurent/Documents/MU_Doc/Data/Transcriptome/CE L_Lignees/") *>>* *>>* > >> *>>* > >> > filenames <- list.celfiles(path=celfile.path, full.names=FALSE) *>>* > >> > normData <- justGCRMA(filenames=filenames, *>>* > >> celfile.path=celfile.path, type="affinities", fast=TRUE) *>>* > >> Computing affinities.Done. *>>* > >> Adjusting for optical effect..............Done. *>>* > >> Adjusting for non-specific binding.............Done. *>>* > >> Erreur dans just.gcrma(filenames = l$filenames, phenoData = *>>* > >> l$phenoData, : *>>* > >> INTEGER() can only be applied to a 'integer', not a 'environment' *>>* > >> *>>* > >> *>>* > >> *>>* > >> *>>* > >> Any idea of what is going wrong with the new version? *>>* > >> *>>* > >> _______________________________________________ *>>* > >> Bioconductor mailing list *>>* > >> Bioconductor at stat.math.ethz.ch <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> *>>* > >> https://stat.ethz.ch/mailman/listinfo/bioconductor *>>* > >> Search the archives: *>>* > >> http://news.gmane.org/gmane.science.biology.informatics.conductor *>>* > > *>>* > > _______________________________________________ *>>* > > Bioconductor mailing list *>>* > > Bioconductor at stat.math.ethz.ch <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> *>>* > > https://stat.ethz.ch/mailman/listinfo/bioconductor *>>* > > Search the archives: *>>* > > http://news.gmane.org/gmane.science.biology.informatics.conductor *>>* > *>>* > _______________________________________________ *>>* > Bioconductor mailing list *>>* > Bioconductor at stat.math.ethz.ch <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> *>>* > https://stat.ethz.ch/mailman/listinfo/bioconductor *>>* > Search the archives: *>>* http://news.gmane.org/gmane.science.biology.informatics.conductor *>>* *>>* _______________________________________________ *>>* Bioconductor mailing list *>>* Bioconductor at stat.math.ethz.ch <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> *>>* https://stat.ethz.ch/mailman/listinfo/bioconductor *>>* Search the archives: *>>* http://news.gmane.org/gmane.science.biology.informatics.conductor *>* *>* Jenny Drnevich, Ph.D. *>* *>* Functional Genomics Bioinformatics Specialist *>* W.M. Keck Center for Comparative and Functional Genomics *>* Roy J. Carver Biotechnology Center *>* University of Illinois, Urbana-Champaign *>* *>* 330 ERML *>* 1201 W. Gregory Dr. *>* Urbana, IL 61801 *>* USA *>* *>* ph: 217-244-7355 *>* fax: 217-265-5066 *>* e-mail: drnevich at illinois.edu <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> *>* *>* _______________________________________________ *>* Bioconductor mailing list *>* Bioconductor at stat.math.ethz.ch <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> *>* https://stat.ethz.ch/mailman/listinfo/bioconductor *>* Search the archives: *>* http://news.gmane.org/gmane.science.biology.informatics.conductor* [[alternative HTML version deleted]]