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Question: Organism annotation package created with makeOrgPackage doesn't install properly
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3.2 years ago by
Guest User12k
Guest User12k 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: [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.
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ADD COMMENTlink modified 3.2 years ago by James W. MacDonald45k • written 3.2 years ago by Guest User12k
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3.2 years ago by
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James W. MacDonald45k wrote:
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/Annotati onForge/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]]
ADD COMMENTlink written 3.2 years ago by James W. MacDonald45k
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