Dear list, I have a problem when I try to use the IlluminaHumanMethylation27k.db (in marticular the method IlluminaHumanMethylation27kCHR) package from a package I am writing. In a previous post I asked how to integrate the information about the chromosomes in a MethyLumiM object. Tim (thanks for your help) suggested me this solution: /fData(AML)$chrom<- as.factor(unlist(mget(featureNames(AML), IlluminaHumanMethylation27kCHR)))/ It works perfectly if I use it from command line. But when I launch the same command from my package I have the following error: */Error in mget(featureNames(lumiMethy), IlluminaHumanMethylation27kCHR) : second argument must be an environment/* / /Inside the namespace of my package, I import the entire package IlluminaHumanMethylation27k.db. To solve the problem, I have already tried to use "as.environment()" and to require() the IlluminaHumanMethylation27k.db package inside mine. I tried also to use the function "getAnnMap" specifying as type "env". Nothing worked. Any new suggestion is welcomed!!! Many thanks! Francesco > sessionInfo() R version 2.12.2 (2011-02-25) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tcltk grid splines stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation27k.db_1.4.0 org.Hs.eg.db_2.4.6 AnnotationDbi_1.12.0 [4] HumMeth27QCReport_1.2.0 RSQLite_0.9-4 DBI_0.2-5 [7] WriteXLS_2.1.0 plotrix_3.0-9 gplots_2.8.0 [10] caTools_1.11 bitops_1.0-4.1 gdata_2.8.1 [13] gtools_2.6.2 Hmisc_3.8-3 survival_2.36-5 [16] amap_0.8-5 lumi_2.2.1 methylumi_1.6.1 [19] Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0 cluster_1.13.3 hdrcde_2.15 KernSmooth_2.23-4 [7] lattice_0.19-17 MASS_7.3-11 Matrix_0.999375-46 mgcv_1.7-3 nlme_3.1-98 preprocessCore_1.12.0 [13] xtable_1.5-6 -- *Francesco Mattia Mancuso* - Bioinformatician at Bioinformatics Core Facility - Bioinformatician at Proteomics Core Facility CRG-Centre for Genomic Regulation C/ Dr. Aiguader, 88 Edif. PRBB 08003 Barcelona, Spain Telephone: +34 933160202 francesco.mancuso@crg.es <mailto:francesco.mancuso@crg.es> www.crg.es <http: pasteur.crg.es="" portal="" page="" portal="" internet=""/> [[alternative HTML version deleted]]

Thanks to Martin Morgan and Tim Triche I solved the problem. The mget generic function is defined in AnnotationDbi. Simply, I was not importing this function into my package getting base::mget, which doesn't know anything about the AnnotationDbi packages. So adding in the DESCRIPTION file * Imports: AnnotationDbi* and in the NAMESPACE file * importMethodsFrom(AnnotationDbi, mget)* the package works fine. Best, Francesco On 02/03/2011 11:03, Francesco Mancuso wrote: > Dear list, > I have a problem when I try to use the IlluminaHumanMethylation27k.db > (in marticular the method IlluminaHumanMethylation27kCHR) package from > a package I am writing. > > In a previous post I asked how to integrate the information about the > chromosomes in a MethyLumiM object. Tim (thanks for your help) > suggested me this solution: > > /fData(AML)$chrom<- as.factor(unlist(mget(featureNames(AML), > IlluminaHumanMethylation27kCHR)))/ > > It works perfectly if I use it from command line. But when I launch > the same command from my package I have the following error: > > */Error in mget(featureNames(lumiMethy), > IlluminaHumanMethylation27kCHR) : > second argument must be an environment/* > / > /Inside the namespace of my package, I import the entire package > IlluminaHumanMethylation27k.db. > To solve the problem, I have already tried to use "as.environment()" > and to require() the IlluminaHumanMethylation27k.db package inside > mine. I tried also to use the function "getAnnMap" specifying as type > "env". Nothing worked. > > Any new suggestion is welcomed!!! > > Many thanks! > Francesco > > > > sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] tcltk grid splines stats graphics grDevices > utils datasets methods base > > other attached packages: > [1] IlluminaHumanMethylation27k.db_1.4.0 > org.Hs.eg.db_2.4.6 AnnotationDbi_1.12.0 > [4] HumMeth27QCReport_1.2.0 > RSQLite_0.9-4 DBI_0.2-5 > [7] WriteXLS_2.1.0 > plotrix_3.0-9 gplots_2.8.0 > [10] caTools_1.11 > bitops_1.0-4.1 gdata_2.8.1 > [13] gtools_2.6.2 > Hmisc_3.8-3 survival_2.36-5 > [16] amap_0.8-5 > lumi_2.2.1 methylumi_1.6.1 > [19] Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.0 > cluster_1.13.3 hdrcde_2.15 KernSmooth_2.23-4 > [7] lattice_0.19-17 MASS_7.3-11 Matrix_0.999375-46 > mgcv_1.7-3 nlme_3.1-98 preprocessCore_1.12.0 > [13] xtable_1.5-6 > > > > -- > > *Francesco Mattia Mancuso* > - Bioinformatician at Bioinformatics Core Facility > - Bioinformatician at Proteomics Core Facility > > CRG-Centre for Genomic Regulation > C/ Dr. Aiguader, 88 > Edif. PRBB > 08003 Barcelona, Spain > > Telephone: +34 933160202 > francesco.mancuso@crg.es <mailto:francesco.mancuso@crg.es> > www.crg.es <http: pasteur.crg.es="" portal="" page="" portal="" internet=""/> -- *Francesco Mattia Mancuso* - Bioinformatician at Bioinformatics Core Facility - Bioinformatician at Proteomics Core Facility CRG-Centre for Genomic Regulation C/ Dr. Aiguader, 88 Edif. PRBB 08003 Barcelona, Spain Telephone: +34 933160202 francesco.mancuso@crg.es <mailto:francesco.mancuso@crg.es> www.crg.es <http: pasteur.crg.es="" portal="" page="" portal="" internet=""/> [[alternative HTML version deleted]]