[Bioc-devel] Challenges with package installation on fresh R

[Dan Tenenbaum]

----- Original Message -----
> From: "Vladislav Petyuk" <petyuk at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: Bioc-devel at 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 <
> dtenenba at fredhutch.org > wrote:
> 
> 
> 
> 
> 
> 
> ----- Original Message -----
> > From: "Vladislav Petyuk" < petyuk at gmail.com >
> > To: Bioc-devel at 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 at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
>