[BioC] AnnotationDbi

[Marc Carlson]

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???
>
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