Dan, Herve, thanks for taking a look. This gives some leads. On Thu, Jun 25, 2015 at 7:26 PM, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
> > > ----- Original Message ----- > > From: "Hervé Pagès" <hpa...@fredhutch.org> > > To: "Vladislav Petyuk" <pet...@gmail.com>, "Dan Tenenbaum" < > dtene...@fredhutch.org> > > Cc: Bioc-devel@r-project.org > > Sent: Thursday, June 25, 2015 6:56:56 PM > > Subject: Re: [Bioc-devel] Challenges with package installation on fresh R > > > > Hi Vladislav, > > > > On 06/25/2015 01:13 PM, Vladislav Petyuk wrote: > > > 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). > > > > What all these packages have in common is that we don't provide > > binaries > > for them anymore. That's because install.packages() (and thus > > biocLite(), which uses install.packages() internally) knows how to > > deal with this (via type="both", which is now the default on Windows > > and Mac). However, some core utilities like > > utils::download.packages() > > have not been properly adapted to handle the situation where a binary > > is missing. For example with R-3.2.1 on Windows: > > > > > library(BiocInstaller) > > > download.packages("GO.db", destdir=".", > > > repos=biocinstallRepos()) > > trying URL > > ' > http://bioconductor.org/packages/3.2/data/annotation/src/contrib/GO.db_3.1.2 > ' > > Error in download.file(url, destfile, method, mode = "wb", ...) : > > cannot open URL > > ' > http://bioconductor.org/packages/3.2/data/annotation/src/contrib/GO.db_3.1.2 > ' > > In addition: Warning message: > > In download.file(url, destfile, method, mode = "wb", ...) : > > cannot open: HTTP status was '404 Not Found' > > Warning in download.packages("GO.db", destdir = ".", repos = > > biocinstallRepos()): > > download of package 'GO.db' failed > > [,1] [,2] > > > > This could be what breaks install_github() (which doesn't seem to > > use install.packages() internally but to instead handle the > > downloading > > of the packages itself). > > install_github() calls install() whose documentation says that its ... > arguments are passed to install.packages() in order to install > dependencies. But I agree that something else seems to be going on here and > that devtools decides the packages can't be installed without running > install.packages(). > > Dan > > > > > > Cheers, > > H. > > > > > > > > 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 > > > > > > > -- > > Hervé Pagès > > > > Program in Computational Biology > > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N, M1-B514 > > P.O. Box 19024 > > Seattle, WA 98109-1024 > > > > E-mail: hpa...@fredhutch.org > > Phone: (206) 667-5791 > > Fax: (206) 667-1319 > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel