Hi Herve,
I reinstalled AnnotationDbi 1.25.17, and now things work flawlessly.
Thank you for your help!
Michael
On 09.04.2014 19:25, Hervé Pagès wrote:
> Hi Michael,
>
> Because of a recent change to IRanges, some information about the
> "as.list" method table is now out-of-sync in your insta
Dear all,
What are your thoughts about adding a new generic to BiocGenerics:
setGeneric("compare", function(x, y, ...) setGeneric("compare"))
I have spotted a couple of existing cases on CRAN (lava (S3) and NMF
(S4) with signature function(object, ...)) and CMA::compare (with a very
different
Update on these tasks.
1) XStringSetList now has an nchar() method (as of Biostrings 2.31.17)
2) restrictToSNV() was removed from VariantAnnotation
3) The following generics and methods for VCF and VRanges have been
added to VariantAnnotation 1.9.50:
isSNV()
isInsertion()
isDeletion()
isInde
Hi Michael,
Because of a recent change to IRanges, some information about the
"as.list" method table is now out-of-sync in your installed
AnnotationDbi (granted it was installed before the new IRanges
propagated to you). Re-installing AnnotationDbi should clear this.
I bumped AnnotationDbi versi
i can't confirm this
> library(GenomicRanges)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clu
Hi Sandro,
According to the release schedule here,
http://bioconductor.org/developers/release-schedule/
it is no longer possible to commit to the 2.13 release branch.
"April 3
Stop release (BioC 2.13) builds. Commits to this branch will be
disabled."
best,
Dan
On Wed, 2014-04-09 at 10:20 +0100
Dear All,
It has been since yesterday I try to commit the changes I made to my
package (VegaMC), but I am not able to commit them.
Here the list of the commando I'm using:
-
svn co https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VegaMC
...
Checked out revision 88652.
- I DO M
Dear Bioc gurus,
Since a few days, QuasR devel (1.3.13 and 1.3.14) is failing on some
unit tests, which turns out to be reproducible independent of QuasR and
might be related to R getting the wrong method for "[[<-".
The following works fine...
library(GenomicRanges)
grl <- GRangesList(r1=GRanges
