Hi John, I am having trouble reproducing this. Can you please send me your "ilmn_cust_raw.txt" file along with the sessionInfo() when you built your package? Marc John Lande wrote: > dear All, > > I am trying to build an annotation package with annotationDbi. I followed > the instruction to build the package, with this script: > > #### > library(AnnotationDbi) > Illumina_8v <- 'ilmn_cust_raw.txt' > myMeta = c("DBSCHEMA"="illumina", "ORGANISM"="Homo sapiens", > "SPECIES"="Human", "MANUFACTURER"="Illumina", "CHIPNAME"="Illumina > pre-release", "MANUFACTURERURL"="http://www.illumina.com") > tmpout = tempdir() > populateDB("HUMANCHIP_DB", affy = FALSE, prefix = > "Illumina8vprerelease",fileName = Illumina_8v, metaDataSrc = > myMeta,baseMapType = "gb", outputDir = tmpout) > seed <- new("AnnDbPkgSeed", Package = "Illumina8vprerelease.db", Version = > "1.0.0", PkgTemplate = "HUMANCHIP.DB", AnnObjPrefix = > "Illumina8vprerelease") > makeAnnDbPkg(seed, file.path(tmpout, "Illumina8vprerelease.sqlite"), > dest_dir = tmpout) > > #### > > however I fail, when I check the package integrity. > > R CMD check Illumina8vprerelease.db/ > > * using log directory '/home/xxx/Illumina8vprerelease.db.Rcheck' > * using R version 2.10.1 (2009-12-14) > * using session charset: UTF-8 > * checking for file 'Illumina8vprerelease.db/DESCRIPTION' ... OK > * this is package 'Illumina8vprerelease.db' version '1.0.0' > * checking package name space information ... OK > * checking package dependencies ... OK > * checking if this is a source package ... OK > * checking for executable files ... OK > * checking whether package 'Illumina8vprerelease.db' can be installed ... OK > * checking package directory ... OK > * checking for portable file names ... OK > * checking for sufficient/correct file permissions ... OK > * checking DESCRIPTION meta-information ... OK > * checking top-level files ... OK > * checking index information ... OK > * checking package subdirectories ... OK > * checking R files for non-ASCII characters ... OK > * checking R files for syntax errors ... OK > * checking whether the package can be loaded ... ERROR > Loading required package: AnnotationDbi > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: org.Hs.eg.db > Loading required package: DBI > Error in as.environment(pos) : using 'as.environment(NULL)' is defunct > Error : .onLoad failed in 'loadNamespace' for 'Illumina8vprerelease.db' > Error: package/namespace load failed for 'Illumina8vprerelease.db' > Execution halted > > It looks like this package has a loading problem: see the messages for > details. > > > what am I doing wrong??? > > [[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 > >