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

Lasse Nielsen [guest] guest at bioconductor.org
Wed Sep 10 16:12:37 CEST 2014

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)

[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.

More information about the Bioconductor mailing list