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

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.

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

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