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

[Vladislav Petyuk]

Dan, Herve, thanks for taking a look. This gives some leads.

On Thu, Jun 25, 2015 at 7:26 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

>
>
> ----- 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
> > 1100 Fairview Ave. N, M1-B514
> > P.O. Box 19024
> > Seattle, WA 98109-1024
> >
> > E-mail: hpages at fredhutch.org
> > Phone:  (206) 667-5791
> > Fax:    (206) 667-1319
> >
>

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