Hi

Thanks a lot Martin for pointing out the mistake. I rebuilt the package
from
scratch with the "_" replaced with "." now it is working fine. I was able to
install
, load  and use the package successfully.

Suyog P

On Sun, Jan 31, 2010 at 5:50 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi Suyong --
>
> I'm replying on-list, in case this is helpful to others.
>
> On 01/31/2010 11:05 AM, Martin Morgan wrote:
> > Hi Suyong --
> >
> > On 01/30/2010 03:49 PM, Suyog Pol wrote:
> >> HI
> >>
> >> Thank You Seth for your suggestion. I was able to install the Package
> >> using the following command.
> >>
> >> install.packages("illuminaHumanv3_ensemble_beta.db",
> >> repos = NULL, type = "source")
> >> However I am still unable to use the installed package. Although
> >> this time I am facing a different error
> >>
> >> I was applying the nsFilter from the genefilter library to filter my
> >> Expression set object eset. The eset was generated and used as follows:-
> >>
> >> dataMatrix <- exprs(eset.generated_using_lumi_package)
> >>
> >> #setting the rownames to the values which can be used by standard
> >> #package illuminaHumanv3
> >>
> >> rownames(dataMatrix) <- corrected.Probe_ID[1:48795]
> >>
> >> annotation <- 'illuminaHumanv3.ensemble.beta.db'
> >>
> >> eset <- new("ExpressionSet", exprs = dataMatrix ,
> >>             annotation = 'illuminaHumanv3.ensemble.beta.db'
> >>
> >> library(genefilter)
> >> library("illuminaHumanv3.ensemble.beta.db") #The code for making and
> >> installing this package was discussed in my previous mail
> >> nsF <- nsFilter(eset, var.filter = FALSE)$eset
> >>
> >> I am getting the following error:-
> >>
> >>> nsF <- nsFilter(eset, var.filter = FALSE)$eset
> >> Error in get(mapName, envir = pkgEnv, inherits = FALSE) :
> >>   object 'illuminaHumanv3.ensemble.beta_dbconn' not found
> >
> > Are your names consistent, for instance below you use an underscore '_'
> > rather than a '.' to separate 'illuminaHumanv3' and 'ensemble'. It would
> > help to see, after loading your database, the output of
> >
> >> search()
> >
> > and
> >
> >> ls("package:illuminaHumanv3.ensemble.beta.db")
>
>
> Here the package name is '.' separated
>
> > search()
>  [1] ".GlobalEnv"
>  [2] "package:illuminaHumanv3.db"
>  [3] "package:illuminaHumanv3.ensemble.beta.db"
>  [4] "package:org.Hs.eg.db"
>
>
> but here the package has variables with '_' separation
>
> > ls("package:illuminaHumanv3.ensemble.beta.db")
>  [1] "illuminaHumanv3_ensemble_beta"
>  [2] "illuminaHumanv3_ensemble_beta_dbconn"
>  [3] "illuminaHumanv3_ensemble_beta_dbfile"
>  [4] "illuminaHumanv3_ensemble_beta_dbInfo"
>  [5] "illuminaHumanv3_ensemble_beta_dbschema"
>  [6] "illuminaHumanv3_ensemble_betaACCNUM"
>  [7] "illuminaHumanv3_ensemble_betaALIAS2PROBE"
>
> You mentioned in an off-list email that you changed the DESCRIPTION file
> when you were trying to install the package (because R did not allow _
> in a package name). Unfortunately, you need to start with the correct
> name earlier in the package build process, I think when you say
>
> >>>> makeDBPackage("HUMANCHIP_DB",
> >>> + affy=FALSE,
> >>> + prefix="illuminaHumanv3_ensemble_beta",
> >>> + fileName=filename,
> >>> + baseMapType="eg",
> >>> + outputDir = tmpout,
> >>> + version="1.0.0",
> >>> + manufacturer = "Illumina",
> >>> + chipName = "HT-12",
> g>>> + manufacturerUrl = "http://www.illumina.com")
>
> it should be with
>
>   prefix="illuminaHumanv3.ensemble.beta"
>
> Martin
>
>
> >
> > Martin
> >
> >>
> >> I was unable to figure out if this issue is related to procedure used
> for
> >> making the object or code for its installation.
> >>
> >> Your help will be much appreciated
> >>
> >> Suyog P
> >>
> >>
> >>> sessionInfo()
> >> R version 2.10.1 (2009-12-14)
> >> i386-pc-mingw32
> >>
> >> locale:
> >> [1] LC_COLLATE=English_United States.1252
> >> [2] LC_CTYPE=English_United States.1252
> >> [3] LC_MONETARY=English_United States.1252
> >> [4] LC_NUMERIC=C
> >> [5] LC_TIME=English_United States.1252
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> other attached packages:
> >>  [1] illuminaHumanv3.db_1.4.1
> >>  [2] illuminaHumanv3.ensemble.beta.db_1.0.0
> >>  [3] org.Hs.eg.db_2.3.6
> >>  [4] genefilter_1.28.2
> >>  [5] lumi_1.12.2
> >>  [6] MASS_7.3-4
> >>  [7] RSQLite_0.8-1
> >>  [8] DBI_0.2-5
> >>  [9] preprocessCore_1.8.0
> >> [10] mgcv_1.6-1
> >> [11] affy_1.24.2
> >> [12] annotate_1.24.1
> >> [13] AnnotationDbi_1.8.1
> >> [14] Biobase_2.6.1
> >>
> >> loaded via a namespace (and not attached):
> >> [1] affyio_1.14.0      grid_2.10.1        lattice_0.17-26
> >> Matrix_0.999375-33
> >> [5] nlme_3.1-96        splines_2.10.1     survival_2.35-7
> >> tools_2.10.1
> >> [9] xtable_1.5-6
> >>
> >>
> >>
> >>> Hi
> >>>
> >>> I have built an annotation package with the help of guidlines set in
> the
> >>> vignette/document
> >>> "SQLforge by Marc Carlson et al." I am having problem installing it.
> >>> The following code was used for building the  package:-
> >>>
> >>> if(interactive()){
> >>> mart<- useMart("ensembl")
> >>> datasets<- listDatasets(mart)
> >>> mart<-useDataset("hsapiens_
> >>> gene_ensembl",mart)
> >>> ensemble.illumina<-
> >>> getBM(attributes=c("illumina_
> >> humanwg_6_v3","entrezgene"),filters="illumina_humanwg_6_v3",
> >>> values=illumina.humanv3.probeset, mart=mart,na.value = NA)
> >>>
> >>> }
> >>>
> >>> ##ensemble.Illumina was written into a file and modified to satisfy the
> >>> requisites of the input vector
> >>> ##required for the function makeDBPackage.  The following code was used
> >> for
> >>> making the final
> >>> ##package:-
> >>>
> >>>> tmpout<- "Y:/path/to/annotation/package"
> >>>> library("human.db0")
> >>> Loading required package: AnnotationDbi
> >>> Loading .......
> >>>
> >>>> library("AnnotationDbi")
> >>>> makeDBPackage("HUMANCHIP_DB",
> >>> + affy=FALSE,
> >>> + prefix="illuminaHumanv3_ensemble_beta",
> >>> + fileName=filename,
> >>> + baseMapType="eg",
> >>> + outputDir = tmpout,
> >>> + version="1.0.0",
> >>> + manufacturer = "Illumina",
> >>> + chipName = "HT-12",
> >>> + manufacturerUrl = "http://www.illumina.com")
> >>> Loading required package: RSQLite
> >>> Loading required package: DBI
> >>> baseMapType is eg
> >>> Prepending Metadata
> >>> Creating Genes table
> >>> Appending Probes
> >>> Found 0 Probe Accessions
> >>> Appending Gene Info
> >>> Found 24758 Gene Names
> >>> Found 24758 Gene Symbols
> >>> Appending Chromosomes
> >>> Appending Cytogenetic Locations
> >>> Appending Omim
> >>> Appending RefSeq
> >>> Appending Pubmed
> >>> Appending Unigene
> >>> Appending ChrLengths
> >>> Appending 3 GO tables
> >>> Appending 3 GO ALL tables
> >>> Appending KEGG
> >>> Appending EC
> >>> Appending Chromosome Locations
> >>> Appending Pfam
> >>> Appending Prosite
> >>> Appending Alias
> >>> Appending Ensembl
> >>> Appending Uniprot
> >>> Appending Metadata
> >>>
> >>>
> >>> simplifying probes table
> >>> dropping redundant data
> >>> Creating package in
> >>> Y:/path/to/annotation/package/illuminaHumanv3_ensemble_beta.db
> >>>
> >>> #To install the above package : -
> >>>
> >>>>
> >>>
> >>
> install.packages("Y:/path/to/annotation/package/illuminaHumanv3_ensemble_beta.db",
> >>> +                  repos = NULL)
> >>> *Warning in install.packages("Y:/Genomics/ArrayData/Jan 2010 - CD140aO4
> >>> sorts/annotation/anno2/illuminaHumanv3_ensemble_beta.db",  :
> >>>    argument 'lib' is missing: using
> >>> 'C:\Users\suyogpol\Documents/R/win-library/2.10'
> >>> Error in gzfile(file, "r") : cannot open the connection
> >>> In addition: Warning messages:
> >>> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
> file
> >>> 2: In gzfile(file, "r") :
> >>>    cannot open compressed file
> >>> 'illuminaHumanv3_ensemble_beta.db/DESCRIPTION', probable reason 'No
> such
> >>> file or directory*
> >>>
> >>> # I assumed that install.packages by default attempts to unzip the
> >> requested
> >>> package file
> >>> #To fix this I zipped the package directory and re used the
> >> install.packages
> >>> function:-
> >>>
> >>>
> >>>> setwd("Y:/path/to/annotation/package" )
> >>>> install.packages("illuminaHumanv3_ensemble_beta.db",
> >>> +                  repos = NULL)
> >>
> >> Can you please try again with:
> >>
> >>
> >> install.packages("illuminaHumanv3_ensemble_beta.db",
> >> repos = NULL, type = "source")
> >>
> >> I think that adding the type = "source" argument will get things going
> >> for you.  If you want to be able to build package archives (.tar.gz as
> >> well as Windows binary packages .zip) you need to install Rtools (see R
> >> admin manual).
> >>
> >> + seth
> >>
> >>
> >> --
> >> Seth Falcon
> >> Bioconductor Core Team | FHCRC
> >>
> >>      [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> 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
> >
> >
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
Masters Student
Department of Chemical and Biological Eng,
University at Buffalo,
Buffalo, NY .
Ph: 801 814 3893

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