[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 1:13:07 PM
> Subject: Re: [Bioc-devel] Challenges with package installation on fresh R
> 
> 
> 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).
> 

After looking at it some more, I observe:

1) It looks like biocLite() does not pass a repositories argument to install_github(). So it's probably best not to biocLite() for anything but the most trivial installations from github, at least for now. So let's try and remove biocLite() from the equation.
2) install_github() seems to have a problem even if you pass it a repos argument. 

For example:

library(BiocInstaller) # to get biocinstallRepos() function
library(devtools)
install_github("vladpetyuk/toypack", dependencies=TRUE, repos=biocinstallRepos())

It says "Skipping 13 packages not available" and lists all the Bioconductor packages it "tried" to install.
The repos argument is supposed to be passed (as part of ...) to install.packages() but install.packages() is never called (I know because I called debug() on it and never got to a debugger).

So I'd say this is either a bug in devtools or a bug in our understanding of how install_github() is supposed to work. 

So I would maybe ask about this at https://github.com/hadley/devtools/issues . 

Dan


> 
> On Thu, Jun 25, 2015 at 1:08 PM, Dan Tenenbaum <
> dtenenba at fredhutch.org > wrote:
> 
> 
> 
> 
> ----- 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
> > > 
> > 
> > 
> 
>