cannot open file './', reason 'Permission denied' in: file(file, "r")
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@meteseasupennedu-2318
Last seen 10.3 years ago
Dear All, I get an error message after executing the following commands on RGUI > library(arrayQuality) > library(marray) > TargetInfo<-read.marrayInfo("TargetMSS.txt") > mraw<-read.Agilent(targets=TargetInfo) I get the following: Reading ... ./RCP6NEW.txt Reading ... ./RCP7NEW.txt Reading ... ./RCP8NEW.txt Reading ... ./ Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file './', reason 'Permission denied' in: file(file, "r") The working directory is correct and I do have an active internet connection. I am not sure why I am getting this warning message. Any comments will be appreciated. Best, Mete Civelek
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Mete, what is the value of your Variable "TargetInfo"? Does it contain empty strings? Also, what is the output of sessionInfo()? Best wishes Wolfgang @seas.upenn.edu ha scritto: > Dear All, > > I get an error message after executing the following commands on RGUI > >> library(arrayQuality) >> library(marray) >> TargetInfo<-read.marrayInfo("TargetMSS.txt") >> mraw<-read.Agilent(targets=TargetInfo) > > > I get the following: > > Reading ... ./RCP6NEW.txt > Reading ... ./RCP7NEW.txt > Reading ... ./RCP8NEW.txt > Reading ... ./ > Error in file(file, "r") : unable to open connection > In addition: Warning message: > cannot open file './', reason 'Permission denied' in: file(file, "r") > > The working directory is correct and I do have an active internet > connection. I am not sure why I am getting this warning message. Any > comments will be appreciated. > > Best, > > Mete Civelek >
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Hi Wolfgang, Thanks for your quick reply. To answer your questions. TargetInfo is > TargetInfo An object of class "marrayInfo" @maLabels [1] "AbA1NEW.txt" "AbA2NEW.txt" "AbA3NEW.txt" "AbA4NEW.txt" "AbA5NEW.txt" 111 more elements ... @maInfo FileName SampleID HybridizationSeq Cy3 Cy5 HybDate 1 AbA1NEW.txt 113 61 RefRNA AbA1 9/28/2006 2 AbA2NEW.txt 114 77 RefRNA AbA2 10/6/2006 3 AbA3NEW.txt 115 59 RefRNA AbA3 9/29/2006 4 AbA4NEW.txt 116 57 RefRNA AbA4 9/28/2006 5 AbA5NEW.txt 117 55 RefRNA AbA5 9/23/2006 111 more rows ... @maNotes [1] "TargetMSS.txt" and sessionInfo is: > sessionInfo() R version 2.5.1 (2007-06-27) 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] "grid" "tools" "tcltk" "stats" "graphics" "grDevices" [7] "utils" "datasets" "methods" "base" other attached packages: arrayQuality RColorBrewer gridBase hexbin lattice convert "1.12.0" "1.0-1" "0.4-3" "1.10.0" "0.16-2" "1.10.0" marray tkWidgets DynDoc Biobase widgetTools limma "1.14.0" "1.14.0" "1.14.0" "1.14.1" "1.12.0" "2.9.17" Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: > Dear Mete, > > what is the value of your Variable "TargetInfo"? Does it contain empty > strings? Also, what is the output of sessionInfo()? > > Best wishes > Wolfgang > > @seas.upenn.edu ha scritto: >> Dear All, >> >> I get an error message after executing the following commands on RGUI >> >>> library(arrayQuality) >>> library(marray) >>> TargetInfo<-read.marrayInfo("TargetMSS.txt") >>> mraw<-read.Agilent(targets=TargetInfo) >> >> >> I get the following: >> >> Reading ... ./RCP6NEW.txt >> Reading ... ./RCP7NEW.txt >> Reading ... ./RCP8NEW.txt >> Reading ... ./ >> Error in file(file, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './', reason 'Permission denied' in: file(file, "r") >> >> The working directory is correct and I do have an active internet >> connection. I am not sure why I am getting this warning message. >> Any comments will be appreciated. >> >> Best, >> >> Mete Civelek >>
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Mete, what is the complete set of 111 values of TargetInfo at maInfo$Filename? Best wishes Wolfgang mete at seas.upenn.edu ha scritto: > Hi Wolfgang, > > Thanks for your quick reply. To answer your questions. TargetInfo is > >> TargetInfo > An object of class "marrayInfo" > @maLabels > [1] "AbA1NEW.txt" "AbA2NEW.txt" "AbA3NEW.txt" "AbA4NEW.txt" "AbA5NEW.txt" > 111 more elements ... > > @maInfo > FileName SampleID HybridizationSeq Cy3 Cy5 HybDate > 1 AbA1NEW.txt 113 61 RefRNA AbA1 9/28/2006 > 2 AbA2NEW.txt 114 77 RefRNA AbA2 10/6/2006 > 3 AbA3NEW.txt 115 59 RefRNA AbA3 9/29/2006 > 4 AbA4NEW.txt 116 57 RefRNA AbA4 9/28/2006 > 5 AbA5NEW.txt 117 55 RefRNA AbA5 9/23/2006 > 111 more rows ... > > @maNotes > [1] "TargetMSS.txt" > > and sessionInfo is: > >> sessionInfo() > R version 2.5.1 (2007-06-27) > 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] "grid" "tools" "tcltk" "stats" "graphics" > "grDevices" > [7] "utils" "datasets" "methods" "base" > > other attached packages: > arrayQuality RColorBrewer gridBase hexbin lattice > convert > "1.12.0" "1.0-1" "0.4-3" "1.10.0" "0.16-2" > "1.10.0" > marray tkWidgets DynDoc Biobase widgetTools > limma > "1.14.0" "1.14.0" "1.14.0" "1.14.1" "1.12.0" > "2.9.17" > > > > Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: > >> Dear Mete, >> >> what is the value of your Variable "TargetInfo"? Does it contain empty >> strings? Also, what is the output of sessionInfo()? >> >> Best wishes >> Wolfgang >> >> @seas.upenn.edu ha scritto: >>> Dear All, >>> >>> I get an error message after executing the following commands on RGUI >>> >>>> library(arrayQuality) >>>> library(marray) >>>> TargetInfo<-read.marrayInfo("TargetMSS.txt") >>>> mraw<-read.Agilent(targets=TargetInfo) >>> >>> >>> I get the following: >>> >>> Reading ... ./RCP6NEW.txt >>> Reading ... ./RCP7NEW.txt >>> Reading ... ./RCP8NEW.txt >>> Reading ... ./ >>> Error in file(file, "r") : unable to open connection >>> In addition: Warning message: >>> cannot open file './', reason 'Permission denied' in: file(file, "r") >>> >>> The working directory is correct and I do have an active internet >>> connection. I am not sure why I am getting this warning message. >>> Any comments will be appreciated. >>> >>> Best, >>> >>> Mete Civelek >>> > > -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
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Hi Wolfgang, Here is the answer: > target.info at maInfo$Filename NULL Thanks so much for your help. Mete Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: > > Mete, > > what is the complete set of 111 values of TargetInfo at maInfo$Filename? > > Best wishes > Wolfgang > > mete at seas.upenn.edu ha scritto: >> Hi Wolfgang, >> >> Thanks for your quick reply. To answer your questions. TargetInfo is >> >>> TargetInfo >> An object of class "marrayInfo" >> @maLabels >> [1] "AbA1NEW.txt" "AbA2NEW.txt" "AbA3NEW.txt" "AbA4NEW.txt" "AbA5NEW.txt" >> 111 more elements ... >> >> @maInfo >> FileName SampleID HybridizationSeq Cy3 Cy5 HybDate >> 1 AbA1NEW.txt 113 61 RefRNA AbA1 9/28/2006 >> 2 AbA2NEW.txt 114 77 RefRNA AbA2 10/6/2006 >> 3 AbA3NEW.txt 115 59 RefRNA AbA3 9/29/2006 >> 4 AbA4NEW.txt 116 57 RefRNA AbA4 9/28/2006 >> 5 AbA5NEW.txt 117 55 RefRNA AbA5 9/23/2006 >> 111 more rows ... >> >> @maNotes >> [1] "TargetMSS.txt" >> >> and sessionInfo is: >> >>> sessionInfo() >> R version 2.5.1 (2007-06-27) >> 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] "grid" "tools" "tcltk" "stats" "graphics" "grDevices" >> [7] "utils" "datasets" "methods" "base" >> >> other attached packages: >> arrayQuality RColorBrewer gridBase hexbin lattice >> convert >> "1.12.0" "1.0-1" "0.4-3" "1.10.0" "0.16-2" "1.10.0" >> marray tkWidgets DynDoc Biobase widgetTools limma >> "1.14.0" "1.14.0" "1.14.0" "1.14.1" "1.12.0" "2.9.17" >> >> >> >> Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: >> >>> Dear Mete, >>> >>> what is the value of your Variable "TargetInfo"? Does it contain empty >>> strings? Also, what is the output of sessionInfo()? >>> >>> Best wishes >>> Wolfgang >>> >>> @seas.upenn.edu ha scritto: >>>> Dear All, >>>> >>>> I get an error message after executing the following commands on RGUI >>>> >>>>> library(arrayQuality) >>>>> library(marray) >>>>> TargetInfo<-read.marrayInfo("TargetMSS.txt") >>>>> mraw<-read.Agilent(targets=TargetInfo) >>>> >>>> >>>> I get the following: >>>> >>>> Reading ... ./RCP6NEW.txt >>>> Reading ... ./RCP7NEW.txt >>>> Reading ... ./RCP8NEW.txt >>>> Reading ... ./ >>>> Error in file(file, "r") : unable to open connection >>>> In addition: Warning message: >>>> cannot open file './', reason 'Permission denied' in: file(file, "r") >>>> >>>> The working directory is correct and I do have an active internet >>>> connection. I am not sure why I am getting this warning >>>> message. Any comments will be appreciated. >>>> >>>> Best, >>>> >>>> Mete Civelek >>>> >> >> > > > -- > > Best wishes > Wolfgang > > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
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Hi Wolfgang, Thanks for pointing me out to the right direction. After looking at TargetInfo at maInfo, I realized that there were three extra lines in the TargetMSS.txt file. That is why I was getting an error message. Thanks again, Best, Mete Quoting mete at seas.upenn.edu: > Hi Wolfgang, > > Here is the answer: > >> target.info at maInfo$Filename > NULL > > Thanks so much for your help. > > Mete > > Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: > >> >> Mete, >> >> what is the complete set of 111 values of TargetInfo at maInfo$Filename? >> >> Best wishes >> Wolfgang >> >> mete at seas.upenn.edu ha scritto: >>> Hi Wolfgang, >>> >>> Thanks for your quick reply. To answer your questions. TargetInfo is >>> >>>> TargetInfo >>> An object of class "marrayInfo" >>> @maLabels >>> [1] "AbA1NEW.txt" "AbA2NEW.txt" "AbA3NEW.txt" "AbA4NEW.txt" "AbA5NEW.txt" >>> 111 more elements ... >>> >>> @maInfo >>> FileName SampleID HybridizationSeq Cy3 Cy5 HybDate >>> 1 AbA1NEW.txt 113 61 RefRNA AbA1 9/28/2006 >>> 2 AbA2NEW.txt 114 77 RefRNA AbA2 10/6/2006 >>> 3 AbA3NEW.txt 115 59 RefRNA AbA3 9/29/2006 >>> 4 AbA4NEW.txt 116 57 RefRNA AbA4 9/28/2006 >>> 5 AbA5NEW.txt 117 55 RefRNA AbA5 9/23/2006 >>> 111 more rows ... >>> >>> @maNotes >>> [1] "TargetMSS.txt" >>> >>> and sessionInfo is: >>> >>>> sessionInfo() >>> R version 2.5.1 (2007-06-27) >>> 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] "grid" "tools" "tcltk" "stats" "graphics" "grDevices" >>> [7] "utils" "datasets" "methods" "base" >>> >>> other attached packages: >>> arrayQuality RColorBrewer gridBase hexbin lattice >>> convert >>> "1.12.0" "1.0-1" "0.4-3" "1.10.0" "0.16-2" >>> "1.10.0" >>> marray tkWidgets DynDoc Biobase widgetTools >>> limma >>> "1.14.0" "1.14.0" "1.14.0" "1.14.1" "1.12.0" >>> "2.9.17" >>> >>> >>> >>> Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: >>> >>>> Dear Mete, >>>> >>>> what is the value of your Variable "TargetInfo"? Does it contain empty >>>> strings? Also, what is the output of sessionInfo()? >>>> >>>> Best wishes >>>> Wolfgang >>>> >>>> @seas.upenn.edu ha scritto: >>>>> Dear All, >>>>> >>>>> I get an error message after executing the following commands on RGUI >>>>> >>>>>> library(arrayQuality) >>>>>> library(marray) >>>>>> TargetInfo<-read.marrayInfo("TargetMSS.txt") >>>>>> mraw<-read.Agilent(targets=TargetInfo) >>>>> >>>>> >>>>> I get the following: >>>>> >>>>> Reading ... ./RCP6NEW.txt >>>>> Reading ... ./RCP7NEW.txt >>>>> Reading ... ./RCP8NEW.txt >>>>> Reading ... ./ >>>>> Error in file(file, "r") : unable to open connection >>>>> In addition: Warning message: >>>>> cannot open file './', reason 'Permission denied' in: file(file, "r") >>>>> >>>>> The working directory is correct and I do have an active internet >>>>> connection. I am not sure why I am getting this warning >>>>> message. Any comments will be appreciated. >>>>> >>>>> Best, >>>>> >>>>> Mete Civelek >>>>> >>> >>> >> >> >> -- >> >> Best wishes >> Wolfgang >> >> ------------------------------------------------------------------ >> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber > > _______________________________________________ > 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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