Hi Marcin,
Thanks for providing the details. I was able to reproduce this. The
culprit was the "range" method for CompressedIRangesList objects
defined in the IRanges package. It was attaching the XVector package
to the search path instead of loading its namespace. This is fixed in
IRanges 2.4.1
Dear Herve,
Thank you for your response and apologies for not being sufficiently clear.
> Are you saying that before you add that call, when you install and load
your package BiocGenerics doesn't get attached (only
loaded via a namespace), but after you add the call to genes() and
re-install and
- Original Message -
> From: "Laurent Gatto"
> To: "bioC-devel"
> Sent: Monday, October 19, 2015 3:50:07 PM
> Subject: [Bioc-devel] Bioc 3.2 devel or release
> Dear all,
>
> The Bioconductor build/check results page [1] labels Bioconductor 3.2 as
> devel. Shouldn't 3.2 be release?
>
Dear all,
The Bioconductor build/check results page [1] labels Bioconductor 3.2 as
devel. Shouldn't 3.2 be release?
Laurent
[1] http://bioconductor.org/checkResults/
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Hi Andrzej,
- Original Message -
> From: "Andrzej Oleś"
> To: "bioc-devel"
> Sent: Tuesday, October 13, 2015 5:39:25 AM
> Subject: [Bioc-devel] Bioconductor Workflows: TOC and displaying document
> details
> Hi everyone,
>
> while browsing through http://www.bioconductor.org/help/
Hi Marcin,
On 10/19/2015 05:11 AM, Marcin Cieślik wrote:
Dear Bioc Developers,
I am developing a package that depends on GenomicFeatures which I am adding
to my package using Imports: and import(GenomicFeatures). However, when I
use the "genes" function the "BiocGenerics" package gets attached
Thanks for the quick fix, Dan !
Sonali.
On 10/19/2015 2:24 PM, Dan Tenenbaum wrote:
Hi Sonali,
- Original Message -
From: "Sonali Arora"
To: "bioc-devel"
Sent: Monday, October 19, 2015 12:32:45 PM
Subject: [Bioc-devel] Documentation Section of Package Landing Page messed up
Hi,
I c
Hi Sonali,
- Original Message -
> From: "Sonali Arora"
> To: "bioc-devel"
> Sent: Monday, October 19, 2015 12:32:45 PM
> Subject: [Bioc-devel] Documentation Section of Package Landing Page messed up
> Hi,
>
> I checked this with three browsers on my machine ( Chrome, Firefox and IE)
>
Hi,
I checked this with three browsers on my machine ( Chrome, Firefox and IE)
If a package has multiple vignettes on its package landing page, All
the links for the vignettes are collapsed and displayed next to only one
of them.
This is happening in both devel and release.
For an example, s
Hi Michael,
On 10/17/2015 12:01 PM, Michael Lawrence wrote:
Cool, thanks. So does it make sense to have that as the coercion from
GAlignmentsList to GAlignmentPairs? I can add it, if it seems
reasonable. I'm kind of torn on whether a coercion should discard records.
Right, the coercion won't r
Hi,
I recommend using git cherry-pick as Jim described in other threads.
You might also want to check out Mike's instructions. You'll find all
the links at https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008141.html
Cheers,
Leo
On Mon, Oct 19, 2015 at 5:35 AM, Elena Grassi wrote:
>> Then
Dear Jim,
thanks for the info. So I’ll just lean back and wait.
best,
jo
On 19 Oct 2015, at 13:35, Jim Hester
mailto:james.f.hes...@gmail.com>> wrote:
Rainer,
They are created automatically. There was an error during the update process
for the git mirrors that halted the update. I am worki
Dear Bioc Developers,
I am developing a package that depends on GenomicFeatures which I am adding
to my package using Imports: and import(GenomicFeatures). However, when I
use the "genes" function the "BiocGenerics" package gets attached (I am not
adding BiocGenerics to my Depends:).
Am I missing
Rainer,
They are created automatically. There was an error during the update
process for the git mirrors that halted the update. I am working on it now
and release 3.2 branches for all packages should be available soon.
Sorry for the confusion
Jim
On Oct 19, 2015 5:47 AM, "Rainer Johannes"
wro
Dear all,
somehow my ensembldb package is missing the release-3.2 branch in the
Bioconductor-mirror repository on github. Is there something I should have done
myself? I thought that the branches are created automatically with each new
Bioconductor release.
Thanks for all suggestions and help
> Then I tried forking the repo available from bioconductor-mirror
> (https://github.com/Bioconductor-mirror/GenomicTuples). This resulted
> in an error due to a non-existent devel branch.
Yep, same here. I disabilited the git-svn bridge forked the
Bioconductor-mirror/REPO and cloned it, used upda
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