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_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>
*>>* > >> 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*

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