Organism annotation package created with makeOrgPackage doesn't install properly
"Lasse Nielsen [guest]" <[email protected]> Wed, 10 Sep 2014 07:12:37 -0700 (PDT)
| Newsgroups | gmane.science.biology.informatics.conductor |
|---|---|
| Message-ID | <[email protected]> |
I work with the plant Sorghum bicolor and want to make my own organism anno=
tation package. I created package with makeOrgPackage and also tried the ex=
ample in: http://www.bioconductor.org/packages/release/bioc/vignettes/Annot=
ationForge/inst/doc/MakingNewOrganismPackages.html
They both were created without any errors. Following the example i try to i=
nstall the package by typing in:
install.packages("./org.Tguttata.eg.db", repos=3DNULL)
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 =3D 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 re=
ason 'No such file or directory'
If i zip the file i'm able to install it, but then and error occurs when lo=
ading the library:
Error in library("org.Tguttata.eg.db") : =
=E2=80=98org.Tguttata.eg.db=E2=80=99 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=3DDanish_Denmark.1252 LC_CTYPE=3DDanish_Denmark.1252 LC_=
MONETARY=3DDanish_Denmark.1252 LC_NUMERIC=3DC LC_TIME=3D=
Danish_Denmark.1252 =
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods b=
ase =
other attached packages:
[1] GO.db_2.14.0 AnnotationForge_1.6.1 org.Hs.eg.db_2.14.0 RSQLi=
te_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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