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

[Dan Tenenbaum]

----- Original Message -----
> From: "Hervé Pagès" <hpages at fredhutch.org>
> To: "Vladislav Petyuk" <petyuk at gmail.com>, "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: Bioc-devel at 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
> > <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
> >>>>
> >>>
> >>>
> >>
> >
> > 	[[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at 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
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>