On Sun, Mar 1, 2009 at 9:28 PM, Martin Morgan wrote: > Hi Jacek -- > > Jacek Nowak writes: > > > 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 > > your 'preprocessCore' package looks out of date for the version of R > you are using. Have you tried following the directions at > > http://bioconductor.org/docs/install/ > > and in particular > > source("http://bioconductor.org/biocLite.R") > update.packages(repos=biocinstallRepos(), ask=FALSE) > > ? Martin > Hello Martin! preprocessCore 1.4 solved the problem. Thank You! Jacek > > > 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_Australia.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_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=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/CEL_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 > > *>>* > >> 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 > > *>>* > > 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 > > *>>* > 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 > > *>>* 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 > > > > *>* > > *>* _______________________________________________ > > *>* 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* > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M2 B169 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]