Hi Valerie,
Thanks for looking into this.
Yes, if I include the bogus 'MYR' in *.tmpl then I am getting the same
error in R-release as well.
To double-check whether it is related to some nodes on our cluster (ours
has different node architectures and the IB interconnect can be flaky at
times),
Hi Raffaele,
This problem should be resolved in devel at this time. Please update to
the latest version of AnnotationDbi (1.27.14) and try again.
Marc
On 09/23/2014 02:36 PM, calogero UNITO wrote:
affaeleaffaeleHi Vincent,
I have further investigated the error I have in the vignette of c
Hi,
Martin and I looked into this a bit. It looks like a problem with
handling an 'undefined error' returned from a worker (i.e., job did not
run). When there is a problem executing the tmpl script no error message
is sent back. The NULL is coerced to simpleError and becomes a problem
downstr
Hi Vincent,
I have further investigated the error I have in the vignette of chimera
devel package .
It is related to the libraries used to access to org.Hs.eg.db in the
devel branch.
In the presence of the following libraries (stable branch):
[1] org.Hs.eg.db_2.14.0 RSQLite_0.11.4 DBI_0.3
Exactly! And re-installing the various packages didn't result in any
version changes, so it's a mystery as to why there was a problem in the
first place.
On Tue, Sep 23, 2014 at 2:24 PM, Hervé Pagès wrote:
> Also note that, according to the sessionInfo() you sent, it seems you
> were using the
Hi Vince,
You raise an important point that a common use of the chipDb objects
will become overly complicated with this change. Especially since chip
platforms should really have an implicit genome that they were designed
for from the get go. And since annotations packages are being build
rig
Also note that, according to the sessionInfo() you sent, it seems you
were using the release. I've no idea how you could get these warnings
with the release since the changes I made recently to AnnotationDbi,
Category, and GOstats are in devel only...
H.
On 09/23/2014 11:05 AM, James W. MacDonal
Never mind. Installing all of GOstats, Category, AnnotationDbi and
ReportingTools fixed the issue.
Thanks,
Jim
On Tue, Sep 23, 2014 at 1:55 PM, James W. MacDonald wrote:
> Hi Herve,
>
> No joy:
>
>
> > biocLite("ReportingTools")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor ver
Hi Herve,
No joy:
> biocLite("ReportingTools")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
3.1.0.
Installing package(s) 'ReportingTools'
trying URL '
http://bioconductor.org/packages/2.14/bioc/src/contrib/ReportingTools_2.4.0.tar.gz
'
Hi Jim,
On 09/23/2014 09:42 AM, James W. MacDonald wrote:
There is an issue on the support site having to do with the inability to
import the summary function from the namespaces from the packages listed in
the subject line. I see the same problem/errors with my affycoretools
package.
When you
Sean, thanks for confirming that it works. /Henrik
On Tue, Sep 23, 2014 at 4:23 AM, Sean Davis wrote:
> Hi, Henrik.
>
> This is the approach that I have been using, also, roughly summarized as:
>
> - git svn clone from bioconductor svn (can take a LONG time, so use git svn
> clone -r 4:HEAD t
There is an issue on the support site having to do with the inability to
import the summary function from the namespaces from the packages listed in
the subject line. I see the same problem/errors with my affycoretools
package.
When you load ReportingTools, you get the following warnings:
Warning
- Original Message -
> From: "Tom Hardcastle"
> To: "Dan Tenenbaum"
> Cc: bioc-devel@r-project.org
> Sent: Tuesday, September 23, 2014 5:57:38 AM
> Subject: Re: [Bioc-devel] Changing the name of a package
>
> Hi Dan,
>
> This seems to have changed the name of the package in the subver
Hi Vincent,
sorry I only realized now that the error was below the deprecate message:
org.Hs.egCHRLOC is deprecated as the data is better accessed from
another location. Please use an appropriate TxDb object or package for
this kind of data.
LaTeX errors:
!pdfTeX error: /usr/bin/pdflatex (f
Hi Dan,
This seems to have changed the name of the package in the subversion
repository, and I can see the build reports - but the html page is still
http://bioconductor.org/packages/devel/bioc/html/riboSeq.html with the
old versions on it, and biocLite won't install riboSeqR if I give it the
Hi, Henrik.
This is the approach that I have been using, also, roughly summarized as:
- git svn clone from bioconductor svn (can take a LONG time, so use git svn
clone -r 4:HEAD to truncate history to rev4 in svn)
- git push to github
- setup git-svn bridge
- work with git as normal
Sean
Of note, this is not an error and seems at this time not even to be a
warning.
A message is emitted indicating the deprecation, so we have a release to
figure out how to deal with the fact that the *CHR/*CHRLOC entities will go
away
in the next release.
There are various possible workarounds. Som
Hi,
I am the maintainer of chimera package and I am getting the following
error in the develop version:
org.Hs.egCHRLOC is deprecated as the data is better accessed from
another location. Please use an appropriate TxDb object or package for
this kind of data.
Could please indicate me which
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