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Question: AnnotationDbi
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gravatar for John Lande
8.9 years ago by
John Lande280
John Lande280 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]]
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