Yes, the issue is the same if I use
devtools::install_github("vladpetyuk/toypack", build_vignettes=TRUE,
dependencies=TRUE)I posted on Bioc-devel list because all the problematic packages are suspiciously similar - all related to Bioconductor and deal with some sort of databases (GO/KEGG/Reactome). On Thu, Jun 25, 2015 at 1:08 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote: > > > ----- Original Message ----- > > From: "Vladislav Petyuk" <pet...@gmail.com> > > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > > Cc: Bioc-devel@r-project.org > > Sent: Thursday, June 25, 2015 12:55:56 PM > > Subject: Re: [Bioc-devel] Challenges with package installation on fresh R > > > > > > Just added the full output to the README.md file > > https://github.com/vladpetyuk/toypack/blob/master/README.md > > > > > > Do you get the same results if you do: > > devtools::install_github("vladpetyuk/toypack", build_vignettes=TRUE, > dependencies=TRUE) > > ? > > When you pass biocLite() a username/repos argument as you've done, it just > delegates all the work to devtools::install_github(). > > If you get the same issue with install_github(), then the issue has > nothing to do with Bioconductor and you need to discuss it with the > maintainer of devtools. > If not, then maybe there is an issue with the way we delegate to that > command. > > Dan > > > > > > > > > > On Thu, Jun 25, 2015 at 12:28 PM, Dan Tenenbaum < > > dtene...@fredhutch.org > wrote: > > > > > > > > > > > > > > ----- Original Message ----- > > > From: "Vladislav Petyuk" < pet...@gmail.com > > > > To: Bioc-devel@r-project.org > > > Sent: Thursday, June 25, 2015 12:16:50 PM > > > Subject: [Bioc-devel] Challenges with package installation on fresh > > > R > > > > > > Hi all, > > > I ran into a problem with dependencies during package installation. > > > Here is an example that intends to reproduce the problem > > > > > > https://github.com/vladpetyuk/toypack > > > > > > Majority of the packages (in Imports/Depends/Suggests and their > > > Imports/Depends/Suggests) install just fine. > > > However there is a handful of packages ("DO.db", "GO.db", > > > "org.Ce.eg.db", > > > "org.Hs.eg.db" and "reactome.db") that are being skipped for not an > > > obvious > > > to me reason. > > > In this toy example there is no use of those skipped packages. So > > > it > > > won't > > > results in any kind of error. But in the real package their lack > > > results > > > in errors. > > > > > > > You need to provide the complete output of R when you try and install > > the package. > > The error is in that output somewhere. > > > > Dan > > > > > > > Thank you, > > > Vlad > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioc-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
