Question: Question regarding Installation of annotation package which was built using SQLforge (Suyog Pol)
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gravatar for Suyog Pol
9.9 years ago by
Suyog Pol40
Suyog Pol40 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 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_ensemb le_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]]
ADD COMMENTlink modified 9.9 years ago by Martin Morgan ♦♦ 24k • written 9.9 years ago by Suyog Pol40
Answer: Question regarding Installation of annotation package which was built using SQLf
0
gravatar for Martin Morgan
9.9 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k 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") 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 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
ADD COMMENTlink written 9.9 years ago by Martin Morgan ♦♦ 24k
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
ADD REPLYlink written 9.9 years ago by Martin Morgan ♦♦ 24k
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