Question: Question regarding Installation of annotation package which was built using SQLforge (Suyog Pol)
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gravatar for Suyog Pol
9.8 years ago by
Suyog Pol40
Suyog Pol40 wrote:
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_ense mble_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 [[alternative HTML version deleted]]
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