On Tue, Nov 4, 2008 at 9:15 PM, Mary Putt <mputt@mail.med.upenn.edu>
wrote:
> Yes you're right but I'm stumped about how to do this for a self-
made
> package? There is install.packge() and install from a local zip but
> otherwise I'm stumped?
Are you on Windows? If so, you will need the RTools--see the R-for-
Windows
FAQ. If not, then you can, at the command line, type:
R CMD INSTALL directory
where directory is the directory of the package.
Sean
>
>
> Sean Davis wrote:
>
>>
>>
>> On Tue, Nov 4, 2008 at 5:10 PM, Mary Putt
<mputt@mail.med.upenn.edu<mailto:>> 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
>> <http: 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
>> <mailto: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 <http: is.na="">(x) : is.na <http: is.na="">() applied
to
>> non-(list or vector) of type 'NULL'
>> 2: In is.na <http: is.na="">(x) : is.na <http: 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
>> <http: 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
>> <mailto: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 <http: is.na="">(x) : is.na <http: is.na="">()
>> applied to non-(list or vector) of type 'NULL'
>> Execution halted
>>
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