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

[Hervé Pagès]

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).

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
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