Hi Martin
to come back to the original trigger for this thread: it was not concerns for
reproducibility, but the fact that a Bioc package in the current release
stopped working because a CRAN package has changed in the meanwhile.
What’s the most practical solution to this specific problem?
Wolfgang,
Alejandro did not have a problem with the current release, but with the
most recent prior release. His issue is precisely because it is no longer
the current (stable) release.
Kasper
On Thu, Apr 24, 2014 at 3:05 PM, Wolfgang Huber whu...@embl.de wrote:
Hi Martin
to come back to
Hi Gabe,
The getAnnMap function doesn't care if the annotation package is an old
style env or a db. In other words, the error you see is because you
don't have KEGG.db installed, not because of a bug in the annotation
package:
annotate:::getAnnMap(PATHID2NAME, KEGG, load = TRUE)
KEGG.db
Ah. I assumed that because I was able to generate the object I had all the
software necessary to summarize it.
Counter-intuitive but my mistake.
Thanks for the quick response,
~G
On Thu, Apr 24, 2014 at 6:58 AM, James W. MacDonald jmac...@uw.edu wrote:
Hi Gabe,
The getAnnMap function
Hi all,
Just saw this tangentially related link to packrat which seems something
analogous to a virtualenv (of sorts) for R by the Rstudio folks, which I
thought might be useful
It actually doesn't solve anybody's problem here, but as I said ...
tangential :-)
http://rstudio.github.io/packrat/
I just 'delete-and-re-create' the git svn bridge for 'flowViz', but it
is still not working (I've tried to 'recreate' the bridge many times)
Does anyone else experience the same lately since the bioc 2.14 release?
Mike
___
Bioc-devel@r-project.org
Hi Mike,
- Original Message -
From: Mike wjia...@fhcrc.org
To: bioc-devel@r-project.org
Sent: Thursday, April 24, 2014 11:14:22 AM
Subject: [Bioc-devel] git svn bridge is broken
I just 'delete-and-re-create' the git svn bridge for 'flowViz', but
it
is still not working (I've
I wonder whether the software that makes the package landing pages (e.g.:
http://bioconductor.org/packages/release/bioc/html/minfi.html ) could be
tweaked to display the actual citation suggested in a package CITATION file.
Right now, it says 'To cite this package in a publication, start R and
+1. this will be a good motivation for maintainers to get the CITATION
entry right.
On Thu, Apr 24, 2014 at 3:39 PM, Wolfgang Huber whu...@embl.de wrote:
I wonder whether the software that makes the package landing pages (e.g.:
http://bioconductor.org/packages/release/bioc/html/minfi.html )
Agreed. Would be nice if the build system could detect changes to CITATION
and update the web page accordingly. Must already happen for DESCRIPTION.
On Thu, Apr 24, 2014 at 1:44 PM, Vincent Carey
st...@channing.harvard.eduwrote:
+1. this will be a good motivation for maintainers to get the
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