[BioC] Organism annotation package created with makeOrgPackage doesn't install properly

[James W. MacDonald]

Hi Lasse,

On Windows you have to include the 'type' argument:

install.packages("org.Tguttata.eg.db", repos = NULL, type = "source")

Best,

Jim



On Wed, Sep 10, 2014 at 7:12 AM, Lasse Nielsen [guest] <
guest at bioconductor.org> wrote:

> I work with the plant Sorghum bicolor and want to make my own organism
> annotation package. I created package with makeOrgPackage and also tried
> the example in:
> http://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationForge/inst/doc/MakingNewOrganismPackages.html
>
> They both were created without any errors. Following the example i try to
> install the package by typing in:
>
> install.packages("./org.Tguttata.eg.db", repos=NULL)
>
> after which i get the error:
>
> Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type"))
> :
>   cannot open the connection
> In addition: Warning messages:
> 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
> 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
>   cannot open compressed file 'org.Tguttata.eg.db/DESCRIPTION', probable
> reason 'No such file or directory'
>
> If i zip the file i'm able to install it, but then and error occurs when
> loading the library:
>
> Error in library("org.Tguttata.eg.db") :
>   ‘org.Tguttata.eg.db’ is not a valid installed package
>
>  -- output of sessionInfo():
>
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252
> LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C
> LC_TIME=Danish_Denmark.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>  base
>
> other attached packages:
> [1] GO.db_2.14.0          AnnotationForge_1.6.1 org.Hs.eg.db_2.14.0
>  RSQLite_0.11.4        DBI_0.3.0             AnnotationDbi_1.26.0
> GenomeInfoDb_1.0.2
> [8] Biobase_2.24.0        BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.22.10 stats4_3.1.1    tools_3.1.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

	[[alternative HTML version deleted]]