[Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build

From: "Kevin Rue-Albrecht" <kevin.rue at ucdconnect.ie>
To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
Cc: "Robert Castelo" <robert.castelo at upf.edu>, bioc-devel at r-project.org
Sent: Thursday, October 16, 2014 8:07:02 AM
Subject: Re: [Bioc-devel] "'BiocInstaller' package not in repository" error during nightly build


Hi Dan, Robert,


Thanks for the answer and fix, Dan. I thought it might be to do with
the recent release. I just wanted to make sure whether I should be
doing something on my part. Setting the "biocLite" code in my
vignette to "eval=FALSE" crossed my mind, I was just afraid to raise
a warning or something during the build if I had unevaluated code.
Since you say it's fine, then I'll push that with the next
substantial fix. It's added to my GitHub issues to remind me.


Robert, I didn't want to update my local BiocInstaller package, but
thanks for your answer as well. Might be useful in the future for
other types of problems.

Cheers
Kevin






On 16 October 2014 15:34, Dan Tenenbaum < dtenenba at fhcrc.org > wrote:




----- Original Message -----

From: "Robert Castelo" < robert.castelo at upf.edu >
To: "Kevin Rue-Albrecht" < kevin.rue at ucdconnect.ie >
Cc: bioc-devel at r-project.org
Sent: Thursday, October 16, 2014 3:24:32 AM
Subject: Re: [Bioc-devel] "'BiocInstaller' package not in
repository" error during nightly build

hi Kevin,

if you're talking about the devel version of BiocInstaller, the SVN
logs
show a commit yesterday with some correction on the BiocInstaller
package, just svn the last version if you don't want to wait until
the
newer version gets built:

vn export --username readonly --password readonly
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocInstaller
BiocInstaller

and R CMD build and INSTALL this newer version (1.17.1).

Yes, this was an issue with the build system, resolved now.

I wouldn't worry too much about the brand new devel builds; they
usually start off a bit unstable.

BTW, I don't advise that you have an evaluated vignette chunk that
calls biocLite().

Dan

cheers,

robert.

On 10/16/2014 11:45 AM, Kevin Rue-Albrecht wrote:

Hi Bioconductors,

I got the *BUILD* ERROR report below on all platforms last night.

Given the fact that I didn't update my package since the last
(successful)
build, and the error ''BiocInstaller' package not in
repository'',
I have
a feeling this is due to a problem on the build platforms ?
In which case, I wonder how many other packages may be affected
the
same
way. Most of the packages seem fine though.

I can see that the BiocInstaller package got *CHECK* ERROR on all
platforms
in the most recent report. Could that be the origin of the
problem?
In my vignette, I give the typical installation code
"biocLite(GOexpress)"
which likely caused the build error when trying to load the
BiocInstaller
library.

Thanks in advance for advising me

Kind regards,
Kevin


##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD build
--keep-empty-dirs
--no-resave-data GOexpress
###
##############################################################################
##############################################################################


* checking for file ?GOexpress/DESCRIPTION? ... OK
* preparing ?GOexpress?:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Bioconductor version 3.1 (BiocInstaller 1.17.0), ?biocLite for
help

Error: processing vignette 'GOexpress-UsersGuide.Rnw' failed with
diagnostics:
chunk 2
Error : ''BiocInstaller' package not in repository' while trying
http://bioconductor.org/packages/3.1/bioc
Execution halted

--
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550

--

K?vin RUE-ALBRECHT
Wellcome Trust Computational Infection Biology PhD Programme
University College Dublin
Ireland
http://fr.linkedin.com/pub/k%C3%A9vin-rue/28/a45/149/en