org.*.eg.db packages other than mouse/human are not in namespace
bpolacco opened this issue · comments
Hi David,
I came across these today, the first time I tried something other than human/mouse. These aren't insurmountable problems for the experienced R/Bioconductor users, but still are at least an annoyance.
Setting a species to one other than MOUSE or HUMAN, for example FLY, will result in one error and one messaging issue:
-
the species database is not loaded in the namespace.
Error in eval(as.symbol(thePack)) : object 'org.Dm.eg.db' not found
The workaround is of course to library(org.Dm.eg.db) before the artMS call, so not a critical problem, but should be easy enough for you to#' @importthem I'm guessing. -
the suggested method of install for a not-installed species databse should probably be changed to the bioconductor version. Sample output:
>> ANNOTATING THE RESULTS (adding gene symbols and protein names)
---(-) The package <org.Ce.eg.db> is not installed in your system.
Just run: install.packages('org.Ce.eg.db') and try again
---(-) The package <org.Ce.eg.db> is not installed in your system.
Just run: install.packages('org.Ce.eg.db') and try again
And when attempting to install as artMS suggests:
> install.packages('org.Ce.eg.db')
Warning in install.packages :
package ‘org.Ce.eg.db’ is not available (for R version 3.6.1)
But works from Bioconductor:
> BiocManager::install('org.Ce.eg.db')
Bioconductor version 3.9 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installing package(s) 'org.Ce.eg.db'
...
