Question: Organism annotation package created with makeOrgPackage doesn't install properly
4.1 years ago by
Guest User • 12k
Guest User • 12k 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/bio c/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:  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:  parallel stats graphics grDevices utils datasets methods base other attached packages:  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  Biobase_2.24.0 BiocGenerics_0.10.0 loaded via a namespace (and not attached):  IRanges_1.22.10 stats4_3.1.1 tools_3.1.1 -- Sent via the guest posting facility at bioconductor.org.
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