Dear all,
I encountered a problem with running oneChannelGUI under Windows 7 OS. First I installed Tcl 8.6 / Tk 8.6. Then I installed R. Finally I installed packages using:
source("http://bioconductor.org/biocLite.R")
biocLite(c("Biobase", "limma", "affylmGUI", "tkWidgets", "GOstats", "AnnotationDbi", "preprocessCore", "IRanges", "baySeq", "Rsamtools", "R.utils", "annotate", "genefilter", "maSigPro", "pamr", "pdmclass", "ChIPpeakAnno", "chipseq", "BSgenome", "Rgraphviz", "affy" ,"annaffy", "affyPLM", "multtest", "ssize", "sizepower", "siggenes", "RankProd", "org.Hs.eg.db", "org.Mm.eg.db", "org.Rn.eg.db", "edgeR", "metaArray", "MergeMaid", "biomaRt", "GenomeGraphs","AffyCompatible", "Biostrings", "rtracklayer", "Genominator", "hugene10sttranscriptcluster.db", "mogene10sttranscriptcluster.db", "ragene10sttranscriptcluster.db", "HuExExonProbesetLocation", "MoExExonProbesetLocation", "RaExExonProbesetLocation", "snow", "RmiR", "RmiR.Hs.miRNA", "R.utils", "EDASeq","DESeq", "DEXSeq","goseq", "BSgenome.Hsapiens.UCSC.hg19", "TxDb.Hsapiens.UCSC.hg19.knownGene", "oneChannelGUI","chimera", "cummeRbund"))
I could open a graphical interface of oneChannelGUI, but when I started a run, I got the following errors:
*error in file(file,"rt"):can not open the connection
*error in grep (target array names [i], names [i], names(my.exons)):object 'my.exons' not found
*error in try(exp,TRUE):object 'my.exons' not found
*error in names(my.exons)<-tmp1.pd$FileName:object 'my.exons' not found
*Error in annotatedDataFrameFrom(expr,byrow=TRUE), error in evaluating the argument 'object' in selecting a method for function....
*Error in validObject(NormalizedArrayData): NormalizedArrayData not found.
I installed an older version of R (3.1.2 from October 2014) and re-installed libraries. I get the same errors. My actual setup is:
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] splines stats4 tools tcltk parallel stats graphics grDevices utils datasets
[11] methods base
other attached packages:
[1] oneChannelGUI_1.32.0 chimera_1.8.5
[3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.18.7
[5] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.34.1
[7] rtracklayer_1.26.3 org.Hs.eg.db_3.0.0
[9] RSQLite_1.0.0 DBI_0.3.1
[11] AnnotationDbi_1.28.2 GenomicAlignments_1.2.2
[13] siggenes_1.40.0 multtest_2.22.0
[15] Rsamtools_1.18.3 Biostrings_2.34.1
[17] XVector_0.6.0 GenomicRanges_1.18.4
[19] GenomeInfoDb_1.2.5 IRanges_2.0.1
[21] S4Vectors_0.4.0 tkWidgets_1.44.0
[23] DynDoc_1.44.0 widgetTools_1.44.0
[25] affylmGUI_1.40.2 tkrplot_0.0-23
[27] affyPLM_1.42.0 preprocessCore_1.28.0
[29] gcrma_2.38.0 affy_1.44.0
[31] Biobase_2.26.0 BiocGenerics_0.12.1
loaded via a namespace (and not attached):
[1] affyio_1.34.0 base64enc_0.1-3 BatchJobs_1.6 BBmisc_1.9 BiocInstaller_1.16.5
[6] BiocParallel_1.0.3 biomaRt_2.22.0 bitops_1.0-6 brew_1.0-6 checkmate_1.6.2
[11] codetools_0.2-14 digest_0.6.8 fail_1.3 foreach_1.4.3 iterators_1.0.8
[16] limma_3.22.7 magrittr_1.5 MASS_7.3-44 R2HTML_2.3.1 RCurl_1.95-4.7
[21] sendmailR_1.2-1 stringi_0.5-5 stringr_1.0.0 survival_2.38-3 XML_3.98-1.3
[26] xtable_1.7-4 zlibbioc_1.12.0
> affylmGUIenvironment$aptDir
[1] "C:/DATA/Affymetrix/Affymetrix Power Tools/APT-1.18.0"
> affylmGUIenvironment$libDirLocation
[1] "C:/Program Files/R/R-3.1.2/library/oneChannelGUI/affylibs"
I get the following warning messages:
Warning messages:
1: package ‘tkrplot’ was built under R version 3.1.3
2: package ‘GenomeInfoDb’ was built under R version 3.1.3
3: package ‘AnnotationDbi’ was built under R version 3.1.3
4: package ‘RSQLite’ was built under R version 3.1.3
5: package ‘DBI’ was built under R version 3.1.3
6: package ‘rtracklayer’ was built under R version 3.1.3
7: package ‘GenomicFeatures’ was built under R version 3.1.3
Gene level probe sets summary started
Gene level probe sets summary ended
Warning messages:
1: running command 'C:/DATA/Affymetrix/Affymetrix Power Tools/APT-1.18.0/bin/apt-probeset-summarize -a rma-sketch -p C:/Program Files/R/R-3.1.2/library/oneChannelGUI/affylibs/HuEx-1_0-st-v2.r2.pgf -c C:/Program Files/R/R-3.1.2/library/oneChannelGUI/affylibs/HuEx-1_0-st-v2.r2.clf -m C:/Program Files/R/R-3.1.2/library/oneChannelGUI/affylibs/HuEx-1_0-st-v2.r2.dt1.hg18.extended.mps -o C:/DATA/ExonArraySet/CELfiles/out1bc0622846de --cel-files C:/DATA/ExonArraySet/CELfiles/target1bc029952282' had status 127
2: In file(file, "rt") :
cannot open file 'C:/DATA/ExonArraySet/CELfiles/out1bc0622846de/': No such file or directory
A file target1bc029952282 is generated, but not a directory out1bc0622846de containing output files.
I double checked target file. It is tab-delimited .txt.
I am really greatful for any suggestions. Thank you very much for your help and input!
Kind Regards,
Anna
