justGCRMA problem :(
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@cecile-laurent-2766
Last seen 9.6 years ago
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_Lig nees/") > 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?
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Patrick Aboyoun ★ 1.6k
@patrick-aboyoun-6734
Last seen 9.6 years ago
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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_TELEPHON E=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_L ignees/") > > > 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
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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_M ONETARY=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_MONETA RY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPH ONE=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
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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_Australi a.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_MONE TARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=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 > >> 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
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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$FileName[1:2],celfile.path="K:/clough/Stac ey/affy/CELfiles") Computing affinities.Done. Adjusting for optical effect...Done. Adjusting for non-specific binding..Done. Error in just.gcrma(filenames = l$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_Australi a.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_MONETA RY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPH ONE=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_L ignees/") > > >> > > >> > 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
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Entering edit mode
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/St acey/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;L C_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Austral ia.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_MONET ARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEP HONE=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
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