Benilton, Thanks for your reply. It occurred to me as well that this might be a version problem. The original error message was based on a run on a linux server running R 2.6. Then I updated my PC to R 2.8 and to the most recent bioconductor. This time it appeared as if the package was created. However when I tried to attach the library it failed and gave me the following error. >library("pd.hugene.1.0.st.v1") Error in library("pd.hugene.1.0.st.v1") : 'pd.hugene.1.0.st.v1' is not a valid package -- installed < 2.0.0? Thank you, Mary R version 2.8.0 (2008-10-20) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] > getwd() [1] "L:/Affy/Hugene" > setwd("L:/Affy/Hugene") > > library("pdInfoBuilder") 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: RSQLite Loading required package: DBI Loading required package: affxparser Loading required package: oligo Loading required package: splines Loading required package: preprocessCore Loading required package: AnnotationDbi Loading required package: oligoClasses oligo Package - Series 1.5.x > library("makePlatformDesign") Loading required package: affyio > > list.files() [1] "HuGene-1_0-st-v1.AFFX_README.Sequence-Files.txt" [2] "HuGene-1_0-st-v1.exon_analysis_configuration" [3] "HuGene-1_0-st-v1.na26.AFFX_README.NetAffx-CSV-Files.txt" [4] "HuGene-1_0-st-v1.na26.hg18.transcript.csv" [5] "HuGene-1_0-st-v1.probe.tab" [6] "HuGene-1_0-st-v1.r3.bgp" [7] "HuGene-1_0-st-v1.r3.clf" [8] "HuGene-1_0-st-v1.r3.mps" [9] "HuGene-1_0-st-v1.r3.pgf" [10] "HuGene-1_0-st-v1.r3.qcc" [11] "HuGene-1_0-st-v1.r3.README.txt" [12] "HuGene-1_0-st-v1.r3.transcript-probesets.ps" [13] "Hugene.mps" [14] "mk.hugene.pdf.r" [15] "mk.hugene.pdf.win.R" > tmp<-list.files() > #downloaded files from Affy website for hugene array > > pgfFile<-tmp[9] > clfFile<-tmp[7] > probeFile<-tmp[5] > transFile<-tmp[4] > > pgfFile [1] "HuGene-1_0-st-v1.r3.pgf" > clfFile [1] "HuGene-1_0-st-v1.r3.clf" > probeFile [1] "HuGene-1_0-st-v1.probe.tab" > transFile [1] "HuGene-1_0-st-v1.na26.hg18.transcript.csv" > > pkg<-new("AffyGenePDInfoPkgSeed", version="0.1.0", author="Mary Putt", email="mputt at mail.med.upenn.edu", biocViews="AnnotationData", genomebuild="UPenn Nov 2008", clfFile=clfFile, pgfFile=pgfFile, probeFile=probeFile, transFile=transFile) > > > makePdInfoPackage(pkg, destDir=".") Creating package in ./pd.hugene.1.0.st.v1 loadUnitsByBatch took 119.71 sec loadAffyCsv took 398.77 sec loadAffySeqCsv took 221.52 sec DB sort, index creation took 554.41 sec [1] TRUE Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' >library("pd.hugene.1.0.st.v1") Error in library("pd.hugene.1.0.st.v1") : 'pd.hugene.1.0.st.v1' is not a valid package -- installed < 2.0.0? Benilton Carvalho wrote: > Hello Mary, > > can you also provide your sessionInfo()? > > I also wonder if it is reproducible on the latest R. > > Thank you, > b > > On Nov 4, 2008, at 1:01 PM, Mary Putt wrote: > >> Hi, >> >> I have been trying to follow earlier posts as to how to make a package >> that I could use in oligo to read in an Affy expression dataset from the >> HuGene platform. I downloaded what appear to be the correct files from >> the Affy website and tried to run the makePdInfoPackage(pkg, >> destDir=".") function but received an error as shown below. >> >> Also I was not able to find much documentation on how to build this >> specific package in pdInfoBuilder--are there other sources of >> documentation that I've missed? >> >> Thank you, >> >> Mary >> >> >> R version 2.6.0 (2007-10-03) >> >>> >>> >>> library("pdInfoBuilder") >> 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: RSQLite >> Loading required package: DBI >> Loading required package: affxparser >> Loading required package: oligo >> Loading required package: splines >> Loading required package: preprocessCore >> Loading required package: AnnotationDbi >> Loading required package: oligoClasses >> oligo Package - Series 1.5.x >>> library("makePlatformDesign") >> Loading required package: affyio >>> >>> list.files() >> [1] "HuGene-1_0-st-v1.AFFX_README.Sequence-Files.txt" >> [2] "HuGene-1_0-st-v1.exon_analysis_configuration" >> [3] "HuGene-1_0-st-v1.na26.AFFX_README.NetAffx-CSV-Files.txt" >> [4] "HuGene-1_0-st-v1.na26.hg18.transcript.csv" >> [5] "HuGene-1_0-st-v1.probe.tab" >> [6] "HuGene-1_0-st-v1.r3.bgp" >> [7] "HuGene-1_0-st-v1.r3.clf" >> [8] "HuGene-1_0-st-v1.r3.mps" >> [9] "HuGene-1_0-st-v1.r3.pgf" >> [10] "HuGene-1_0-st-v1.r3.qcc" >> [11] "HuGene-1_0-st-v1.r3.README.txt" >> [12] "HuGene-1_0-st-v1.r3.transcript-probesets.ps" >> [13] "Hugene.mps" >> [14] "mk.hugene.pdf.r" >>> tmp<-list.files() >>> #downloaded files from Affy website for hugene array >>> >>> pgfFile<-tmp[9] >>> clfFile<-tmp[7] >>> probeFile<-tmp[5] >>> transFile<-tmp[4] >>> >>> pgfFile >> [1] "HuGene-1_0-st-v1.r3.pgf" >>> clfFile >> [1] "HuGene-1_0-st-v1.r3.clf" >>> probeFile >> [1] "HuGene-1_0-st-v1.probe.tab" >>> transFile >> [1] "HuGene-1_0-st-v1.na26.hg18.transcript.csv" >>> >>> pkg<-new("AffyGenePDInfoPkgSeed", version="0.1.0", author="Mary >> Putt", email="mputt at mail.med.upenn.edu", biocViews="AnnotationData", >> genomebuild="UPenn Nov 2008", clfFile=clfFile, pgfFile=pgfFile, >> probeFile=probeFile, transFile=transFile) >>> >>> >>> makePdInfoPackage(pkg, destDir=".") >> Creating package in ./pd.hugene.1.0.st.v1 >> Error in if (isdir[k]) { : missing value where TRUE/FALSE needed >> Calls: makePdInfoPackage ... makePdInfoPackage -> createPackage -> >> copySubstitute -> cpSubs >> In addition: Warning message: >> In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' >> Execution halted >> >> _______________________________________________ >> 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 >

On Tue, Nov 4, 2008 at 5:10 PM, Mary Putt <mputt@mail.med.upenn.edu> wrote: > Benilton, > > Thanks for your reply. It occurred to me as well that this might be a > version problem. The original error message was based on a run on a linux > server running R 2.6. Then I updated my PC to R 2.8 and to the most recent > bioconductor. > > This time it appeared as if the package was created. However when I tried > to attach the library it failed and gave me the following error. > > >library("pd.hugene.1.0.st.v1") > Error in library("pd.hugene.1.0.st.v1") : > 'pd.hugene.1.0.st.v1' is not a valid package -- installed < 2.0.0? > This error typically arises from copying a library into a library directory without actually installing it. You need to install the package before calling library(). Sean > > R version 2.8.0 (2008-10-20) > Copyright (C) 2008 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > [Previously saved workspace restored] > > getwd() > [1] "L:/Affy/Hugene" > > setwd("L:/Affy/Hugene") > > > > library("pdInfoBuilder") > 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: RSQLite > Loading required package: DBI > Loading required package: affxparser > Loading required package: oligo > Loading required package: splines > Loading required package: preprocessCore > Loading required package: AnnotationDbi > Loading required package: oligoClasses > oligo Package - Series 1.5.x > > library("makePlatformDesign") > Loading required package: affyio > > > > list.files() > [1] "HuGene-1_0-st-v1.AFFX_README.Sequence-Files.txt" [2] > "HuGene-1_0-st-v1.exon_analysis_configuration" [3] > "HuGene-1_0-st-v1.na26.AFFX_README.NetAffx-CSV-Files.txt" > [4] "HuGene-1_0-st-v1.na26.hg18.transcript.csv" [5] > "HuGene-1_0-st-v1.probe.tab" [6] > "HuGene-1_0-st-v1.r3.bgp" [7] > "HuGene-1_0-st-v1.r3.clf" [8] > "HuGene-1_0-st-v1.r3.mps" [9] > "HuGene-1_0-st-v1.r3.pgf" [10] > "HuGene-1_0-st-v1.r3.qcc" [11] > "HuGene-1_0-st-v1.r3.README.txt" [12] " > HuGene-1_0-st-v1.r3.transcript-probesets.ps" [13] "Hugene.mps" > [14] "mk.hugene.pdf.r" > [15] "mk.hugene.pdf.win.R" > > tmp<-list.files() > > #downloaded files from Affy website for hugene array > > > > pgfFile<-tmp[9] > > clfFile<-tmp[7] > > probeFile<-tmp[5] > > transFile<-tmp[4] > > > > pgfFile > [1] "HuGene-1_0-st-v1.r3.pgf" > > clfFile > [1] "HuGene-1_0-st-v1.r3.clf" > > probeFile > [1] "HuGene-1_0-st-v1.probe.tab" > > transFile > [1] "HuGene-1_0-st-v1.na26.hg18.transcript.csv" > > > > pkg<-new("AffyGenePDInfoPkgSeed", version="0.1.0", author="Mary Putt", > email="mputt@mail.med.upenn.edu", biocViews="AnnotationData", > genomebuild="UPenn Nov 2008", clfFile=clfFile, pgfFile=pgfFile, > probeFile=probeFile, transFile=transFile) > > > > > makePdInfoPackage(pkg, destDir=".") > Creating package in ./pd.hugene.1.0.st.v1 > loadUnitsByBatch took 119.71 sec > loadAffyCsv took 398.77 sec > loadAffySeqCsv took 221.52 sec > DB sort, index creation took 554.41 sec > [1] TRUE > Warning messages: > 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' > > > >library("pd.hugene.1.0.st.v1") > Error in library("pd.hugene.1.0.st.v1") : > 'pd.hugene.1.0.st.v1' is not a valid package -- installed < 2.0.0? > > > > > > > Benilton Carvalho wrote: > >> Hello Mary, >> >> can you also provide your sessionInfo()? >> >> I also wonder if it is reproducible on the latest R. >> >> Thank you, >> b >> >> On Nov 4, 2008, at 1:01 PM, Mary Putt wrote: >> >> Hi, >>> >>> I have been trying to follow earlier posts as to how to make a package >>> that I could use in oligo to read in an Affy expression dataset from the >>> HuGene platform. I downloaded what appear to be the correct files from >>> the Affy website and tried to run the makePdInfoPackage(pkg, >>> destDir=".") function but received an error as shown below. >>> >>> Also I was not able to find much documentation on how to build this >>> specific package in pdInfoBuilder--are there other sources of >>> documentation that I've missed? >>> >>> Thank you, >>> >>> Mary >>> >>> >>> R version 2.6.0 (2007-10-03) >>> >>> >>>> >>>> library("pdInfoBuilder") >>>> >>> 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: RSQLite >>> Loading required package: DBI >>> Loading required package: affxparser >>> Loading required package: oligo >>> Loading required package: splines >>> Loading required package: preprocessCore >>> Loading required package: AnnotationDbi >>> Loading required package: oligoClasses >>> oligo Package - Series 1.5.x >>> >>>> library("makePlatformDesign") >>>> >>> Loading required package: affyio >>> >>>> >>>> list.files() >>>> >>> [1] "HuGene-1_0-st-v1.AFFX_README.Sequence-Files.txt" >>> [2] "HuGene-1_0-st-v1.exon_analysis_configuration" >>> [3] "HuGene-1_0-st-v1.na26.AFFX_README.NetAffx-CSV-Files.txt" >>> [4] "HuGene-1_0-st-v1.na26.hg18.transcript.csv" >>> [5] "HuGene-1_0-st-v1.probe.tab" >>> [6] "HuGene-1_0-st-v1.r3.bgp" >>> [7] "HuGene-1_0-st-v1.r3.clf" >>> [8] "HuGene-1_0-st-v1.r3.mps" >>> [9] "HuGene-1_0-st-v1.r3.pgf" >>> [10] "HuGene-1_0-st-v1.r3.qcc" >>> [11] "HuGene-1_0-st-v1.r3.README.txt" >>> [12] "HuGene-1_0-st-v1.r3.transcript-probesets.ps" >>> [13] "Hugene.mps" >>> [14] "mk.hugene.pdf.r" >>> >>>> tmp<-list.files() >>>> #downloaded files from Affy website for hugene array >>>> >>>> pgfFile<-tmp[9] >>>> clfFile<-tmp[7] >>>> probeFile<-tmp[5] >>>> transFile<-tmp[4] >>>> >>>> pgfFile >>>> >>> [1] "HuGene-1_0-st-v1.r3.pgf" >>> >>>> clfFile >>>> >>> [1] "HuGene-1_0-st-v1.r3.clf" >>> >>>> probeFile >>>> >>> [1] "HuGene-1_0-st-v1.probe.tab" >>> >>>> transFile >>>> >>> [1] "HuGene-1_0-st-v1.na26.hg18.transcript.csv" >>> >>>> >>>> pkg<-new("AffyGenePDInfoPkgSeed", version="0.1.0", author="Mary >>>> >>> Putt", email="mputt@mail.med.upenn.edu", biocViews="AnnotationData", >>> genomebuild="UPenn Nov 2008", clfFile=clfFile, pgfFile=pgfFile, >>> probeFile=probeFile, transFile=transFile) >>> >>>> >>>> >>>> makePdInfoPackage(pkg, destDir=".") >>>> >>> Creating package in ./pd.hugene.1.0.st.v1 >>> Error in if (isdir[k]) { : missing value where TRUE/FALSE needed >>> Calls: makePdInfoPackage ... makePdInfoPackage -> createPackage -> >>> copySubstitute -> cpSubs >>> In addition: Warning message: >>> In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' >>> Execution halted >>> >>> _______________________________________________ >>> 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 >>> >> >> > _______________________________________________ > 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 > [[alternative HTML version deleted]]