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_ens emble_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 at 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