[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") :
âorg.Tguttata.eg.dbâ 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
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