Some people is lost even when and how many updates are and differences
between different packages. See this question for instance (
https://www.biostars.org/p/287871/)
Compared to CRAN or PyPi, which don't have release cycles, Bioconductor
workflow is a bit more complicated to learn.
Related to Bi
This makes sense. Windows users won’t be easily able to call variants across
thousands of samples but at least the plotting, impact prediction, etc will
work fine for them.
I will need to define things such that the variant calling is optional, which
is not too absurd — I’ll add loading of MVR
Looks like this has cleared up in the Oct 10 report:
https://www.bioconductor.org/checkResults/release/bioc-LATEST/
We send notifications about failures in release twice a week (Monday and
Thursday). This could have been a transient problem but happened to occur on a
day we send notifications
Sounds good.
I should also mention that Rsamtools has pileup() that is available
on all platforms. Don't know how easy it would be to use to achieve
the kind of variant calling you're doing in MTseeker though...
Cheers,
H.
On 10/11/2018 04:35 AM, Tim Triche, Jr. wrote:
This makes sense. Window
Hello Core team and Maintainers,
We have just launched a new feature to regulate packages on
git.bioconductor.org. The feature gives the core team, the ability to easily
“disable" hooks for each package (software, data-experiment, and workflow) as
needed.
The hooks should be modified using a
Hi,
I am trying to fix bug in my package. However, I got declined message:
git push upstream master
Counting objects: 38, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (26/26), done.
Writing objects: 100% (38/38), 6.16 KiB | 3.08 MiB/s, done.
Total 38 (delta 30),
Hi Jianhong,
I’m looking into it now.
Nitesh
> On Oct 11, 2018, at 1:35 PM, Jianhong Ou, Ph.D. wrote:
>
> Hi,
>
> I am trying to fix bug in my package. However, I got declined message:
>
>
> git push upstream master
>
> Counting objects: 38, done.
>
> Delta compression using up to 8 thr
Nitesh,
I encountered the same issue with CRISPRseek package. Could you please help?
Thanks!
To git.bioconductor.org:packages/CRISPRseek.git
! [remote rejected] master -> master (pre-receive hook declined)
error: failed to push some refs to
'g...@git.bioconductor.org:packages/CRISPRseek.git'
Please try now.
> On Oct 11, 2018, at 1:48 PM, Zhu, Lihua (Julie)
> wrote:
>
> Nitesh,
>
> I encountered the same issue with CRISPRseek package. Could you please help?
> Thanks!
>
> To git.bioconductor.org:packages/CRISPRseek.git
> ! [remote rejected] master -> master (pre-receive hook decl
Thank you Nitesh,
It works now.
Jianhong.
On 10/11/18, 1:53 PM, "Turaga, Nitesh" wrote:
Please try now.
> On Oct 11, 2018, at 1:48 PM, Zhu, Lihua (Julie)
wrote:
>
> Nitesh,
>
> I encountered the same issue with CRISPRseek package. Could you please
help? Than
Nitesh,
Thanks for fixing the issue! It works now.
Best regards,
Julie
On 10/11/18, 1:55 PM, "Bioc-devel on behalf of Jianhong Ou, Ph.D."
wrote:
Thank you Nitesh,
It works now.
Jianhong.
On 10/11/18, 1:53 PM, "Turaga, Nitesh"
wrote
I am the developer of the variancePartition package, and I recently made some
very small changes to the documentation of my package. The latest version
1.10.3 builds correctly on Bioconductor's Windows and OS X machines but fails
on Ubuntu:
http://bioconductor.org/checkResults/release/bioc-LAT
Thanks so much Hervé! That appears to have solved the problem. And I will
definitely keep in mind for the future Michael’s suggestion of duck typing for
matrix-like objects.
All of the best,
Elizabeth
> On Oct 10, 2018, at 9:33 PM, Hervé Pagès wrote:
>
> Hi Elizabeth,
>
> I agree that the s
Hi Gabriel,
I'm not able to reproduce this either. See my sessionInfo()
at the end (obtained after running all the code in the
variancePartition.Rnw vignette).
Did this error just appear today or yesterday, so would follow
your last commit to the RELEASE_3_7 branch? Or did it appear
before e.g.
Thanks for your help. This just showed up last night. I will wait few
more days and see if it continues to be an issue. Also, I’ll add pander
- Gabriel
On 10/11/18, 7:01 PM, "Hervé Pagès" wrote:
>Hi Gabriel,
>
>I'm not able to reproduce this either. See my sessionInfo()
>at the end (obtain
It might make sense to seriously throttle your use of parallel evaluation in
your vignette / example code, perhaps even defaulting to serial evaluation.
This is also relevant to resource use on the build machines. I'm not really
sure of the details but it seems like the problem is that the socke
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