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 your annotation hub is out of date.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your annotation hub is out of date.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
Hi,
This array is of type "list" but print() reports otherwise:
a1 <- array(list(1), 2:0)
typeof(a1)
# [1] "list"
a1
# <2 x 1 x 0 array of character>
# [,1]
# [1,]
# [2,]
No such problem with an array of type "logical":
a2 <- array(NA, 2:0)
typeof(a2)
# [1]
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):
>
Hi Martin,
On 09/26/2018 12:41 AM, Martin Maechler wrote:
Hervé Pagès
on Tue, 25 Sep 2018 23:27:19 -0700 writes:
> Hi, Unlike on an atomic matrix, as.vector() doesn't drop
> the "dim" attribute of matrix or array of type "list":
m <- matrix(list(), nrow=2, ncol=3)
m
An alternative might be to find an R package for which the dataset was relevant
to and ask the author if they would be willing to include it in their package.
Personally, I’ve considered soliciting the users of my package to share their
data in my package because every other package for this
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():
With regard to Martin's comment about the strength of (base) R:
I have R code I wrote 15+ years ago that has been used regularly ever since
with only a few minor changes needed due to changes in R. Within that code, I
find particularly impressive for its stability a simple custom GUI that uses
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 Wed, Sep 26, 2018 at 12:04 PM, Joris Meys wrote:
> Hi Thomas,
>
> I would argue that one dataset - even a new one - could be added to another
> package. The pizzapoll doesn't look like a scientific breakthrough, but it
> might be a nice dataset for teaching and/or testing new models. So I see
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
Hi Thomas,
I would argue that one dataset - even a new one - could be added to another
package. The pizzapoll doesn't look like a scientific breakthrough, but it
might be a nice dataset for teaching and/or testing new models. So I see
value in making it available on CRAN one way or another.
If
I want to publish a single dataset, and I am concerned about part of the
CRAN policies. The preamble of the policies [1] says,
> A package's contribution has to be non-trivial
The single dataset [2, 3] is recent and not very widely known.
Is it considered trivial?
If so, what would be a good
> Hervé Pagès
> on Tue, 25 Sep 2018 23:27:19 -0700 writes:
> Hi, Unlike on an atomic matrix, as.vector() doesn't drop
> the "dim" attribute of matrix or array of type "list":
>m <- matrix(list(), nrow=2, ncol=3)
>m
># [,1] [,2] [,3]
># [1,] NULL NULL
Hi,
Unlike on an atomic matrix, as.vector() doesn't drop the "dim"
attribute of matrix or array of type "list":
m <- matrix(list(), nrow=2, ncol=3)
m
# [,1] [,2] [,3]
# [1,] NULL NULL NULL
# [2,] NULL NULL NULL
as.vector(m)
# [,1] [,2] [,3]
# [1,] NULL NULL NULL
#
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