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

[Dan Tenenbaum]

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Vladislav Petyuk" <petyuk at gmail.com>
> Cc: Bioc-devel at r-project.org
> Sent: Thursday, June 25, 2015 1:08:50 PM
> Subject: Re: [Bioc-devel] Challenges with package installation on fresh R
> 
> 
> 
> ----- 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.

Sorry, I was wrong. We also pass the bioconductor repositories to that command so that dependencies can be installed.

So never mind. We'll keep looking into it.

Dan


> 
> 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
> > > 
> > 
> >
> 
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