[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1

----- Original Message -----
From: "Florian Hahne" <florian.hahne at novartis.com>
To: "Herv? Pag?s" <hpages at fredhutch.org>, "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Leonardo Collado Torres"
<lcollado at jhu.edu>
Cc: bioc-devel at r-project.org
Sent: Wednesday, November 5, 2014 12:48:23 AM
Subject: Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1

I think there is indeed something more fundamentally broken here:
R.version
               _
platform       x86_64-apple-darwin13.4.0
arch           x86_64
os             darwin13.4.0
system         x86_64, darwin13.4.0
status         Under development (unstable)
major          3
minor          2.0
year           2014
month          10
day            29
svn rev        66895
language       R
version.string R Under development (unstable) (2014-10-29 r66895)
nickname       Unsuffered Consequences

useDevel(TRUE)
Error: 'devel' version already in use

The only problem is that you should not have seen this message, you should instead see a message saying you need a newer version of R to run the devel version of bioconductor. This has been fixed in the release version of BiocInstaller (1.16.1), available later today.
But:

biocinstallRepos()
                                              BioCsoft
           "http://bioconductor.org/packages/3.0/bioc"
                                               BioCann
"http://bioconductor.org/packages/3.0/data/annotation"
                                               BioCexp
"http://bioconductor.org/packages/3.0/data/experiment"
                                             BioCextra
          "http://bioconductor.org/packages/3.0/extra"
                                                  CRAN
                               "http://cran.fhcrc.org"

So I am running R-devel, R thinks that I should already be using the
BiocDevel branch, but the repository is still pointing to
Bioconductor 3.0
After taking a closer look at useDevel() I did this:

assignInNamespace(ns="BiocInstaller", x="IS_USER", value=TRUE)
assignInNamespace(ns="BiocInstaller", x="IS_UPGRADEABLE", value=TRUE)

And behold:
useDevel(TRUE)
Installing package into
?/Users/hahnefl1/software/R/source/R-3-2-0/localPackages?
(as ?lib? is unspecified)
trying URL
'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocInstaller_1.17.1
.tar.gz'
Content type 'application/x-gzip' length 14271 bytes (13 KB)
opened URL
==================================================
downloaded 13 KB

* installing *source* package ?BiocInstaller? ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help
* DONE (BiocInstaller)

The downloaded source packages are in
	?/private/tmp/Rtmp44wF3Y/downloaded_packages?
Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help
'BiocInstaller' changed to version 1.17.1

I couldn't tell how I got my R installation into this seemingly
locked
state, but maybe there should be a force=TRUE option to useDevel for
cases
like this.
Florian

This is NOT what you want. You now have Bioc 3.1 on R 3.1, but Bioc 3.1 is intended to run with R-devel (3.2) only.
Dan

On 04/11/14 20:04, "Herv? Pag?s" <hpages at fredhutch.org> wrote:

Hi,

On 11/02/2014 10:58 PM, Dan Tenenbaum wrote:

----- Original Message -----
From: "Leonardo Collado Torres" <lcollado at jhu.edu>
To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
Cc: bioc-devel at r-project.org
Sent: Sunday, November 2, 2014 9:26:25 PM
Subject: Re: [Bioc-devel] Can't seem to use useDevel();
	biocLite() for
BioC 3.1

Thanks, I incorrectly thought that I was using the same R version
as
the Bioc-build machines since the "r66923" part matched. Now I
realize
that this tag is used in all of the newest R builds at
http://r.research.att.com/.

It's admittedly confusing;
Agreed. But the error message issued by useDevel() in the current
release adds to the confusion:

  > library(BiocInstaller)
  Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for
  help
  > useDevel()
  Error: 'devel' version already in use

What about something like:

  Error: you need R 3.2 to run BioC 'devel' version

Thanks,
H.

the question of whether to use R-devel with Bioc-devel has a
different
answer every six months, but the answer can always be found here:

http://www.bioconductor.org/developers/how-to/useDevel/

Also, when looking at the devel build report, you should probably
focus
more on the version portion of the "R version" column than on the
SVN
revision number.

Dan

On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen
<kasperdanielhansen at gmail.com> wrote:
You should not be using R-3.1.2 patched with the current devel
version of
Bioconductor; use R-devel.

Best,
Kasper

On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres
<lcollado at jhu.edu>
wrote:
Hi,

I can't seem to install devel packages via biocLite() and I
wonder
if
something is broken or if I'm missing something. For example,
take
GenomeInfoDb which is at 1.3.6 and is passing all checks.

The usual code using a fresh R 3.1.2-patched install isn't
working
as
it downloads the latest release version (1.2.2):

source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for
help
## Was expecting 3.1 here
useDevel()
Error: 'devel' version already in use
biocLite('GenomeInfoDb')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R
version
3.1.2.
Installing package(s) 'GenomeInfoDb'
trying URL

'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/Geno
meInfoDb_1.2.2.tgz'
Content type 'application/x-gzip' length 404120 bytes (394 KB)
opened URL
==================================================
downloaded 394 KB

The downloaded binary packages are in

/var/folders/cx/n9s558kx6fb7jf5z_pgszgb80000gn/T//Rtmpxp29xo/downloade
d_packages
sessionInfo()
R version 3.1.2 Patched (2014-11-01 r66923)
## Note that it matches the current R version used by the
Bioc-devel
build machines
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1]
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods
   base

other attached packages:
[1] BiocInstaller_1.16.0 colorout_1.0-2

loaded via a namespace (and not attached):
[1] tools_3.1.2

For my computer it's not problem because I can download the pkg
via
svn and install locally. But it breaks my tests in TravisCI
which
relies on biocLite().

Cheers,
Leo

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--
Herv? Pag?s

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
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Fax:    (206) 667-1319

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[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1

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