I'm following the steps recommended at
https://bioconductor.org/developers/how-to/git/sync-existing-repositories/
but getting an unexpected error:
bohdankhomtchouk$ git merge upstream/master
merge: upstream/master - not something we can merge
I just updated
Looks like that was the issue, thanks Vincent & Martin!
> hub = AnnotationHub()
snapshotDate(): 2018-08-20
> isDevel()
[1] TRUE
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 1 record
# snapshotDate(): 2018-08-20
# names(): AH63797
# $dataprovider: Ensembl
# $species: Mus
maybe you are not using the 'devel' version of Bioconductor?
On 09/26/2018 03:48 PM, Bohdan Khomtchouk wrote:
Martin, I don't see it unfortunately:
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 0 records
# snapshotDate(): 2018-04-30
But perhaps it needs to be added to
Just did, same result:
> hub = AnnotationHub()
snapshotDate(): 2018-04-30
I re-installed AnnotationHub package as well.
On Wed, Sep 26, 2018 at 1:16 PM Vincent Carey
wrote:
> your annotation hub is out of date. run hub = AnnotationHub() and try
> again
>
> On Wed, Sep 26, 2018 at 3:48 PM,
Hi bioc-devel,
Thanks to Nitesh Turaga we were able to get derfinderData back in
sync. Basically:
* We discarded the previous GitHub repo (deleted forever)
* Re-synced via
http://bioconductor.org/developers/how-to/git/maintain-github-bioc/
* The real issue was a bug in the bump version script
your annotation hub is out of date. run hub = AnnotationHub() and try again
On Wed, Sep 26, 2018 at 3:48 PM, Bohdan Khomtchouk
wrote:
> Martin, I don't see it unfortunately:
>
> > query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
> AnnotationHub with 0 records
> # snapshotDate(): 2018-04-30
>
> But
Martin, I don't see it unfortunately:
> query(hub, "Mus_musculus.GRCm38.93.chr.gtf")
AnnotationHub with 0 records
# snapshotDate(): 2018-04-30
But perhaps it needs to be added to AnnotationHub, because I see other
.chr.gtf files that go up to 86 (while I'm using 93 in this original post):
>
hmm, does it make sense to submit the hg19, hg38, and mm10 HMM CpG island
predictions to AnnotationHub?
R> qhs <- query(ah, "island" )
R> qhs
AnnotationHub with 4 records
# snapshotDate(): 2018-08-20
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# additional mcols():
Yes I was arguing if NEWS.md could be used. Only after Lori reply I
realized the changes don't apply for the next release of Bioconductor.
Anyway, thanks Laurent for the command, and the team for considering it in
its due time.
Lluís
On Wed, 26 Sep 2018 at 13:22, Shepherd, Lori
wrote:
> As
On 09/25/2018 07:07 PM, Christian Mertes wrote:
Hi,
thanks for the answers.
Since we only use 5 functions from the package within one function in our
package, I hoped to get around it by masking this function in a special way.
not sure what that means; better not to be devious if that is
As mentioned by Henrik, The code referenced seems only implemented in R-devel
currently. Bioconductor will look at updating the code we use on our systems
to match when our Bioconductor version is being built against R-devel (after
the October release) .
Lori Shepherd
Bioconductor Core
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