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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>>
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>>
>>
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