Nitesh,
It works now.
Thanks,
ImmuneSpace Team
On Fri, Oct 13, 2017 at 10:42 AM, Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:
> Please send me a list of commands you have tried. I’d like to see the
> outputs as well.
>
> e.henrich has associated keys to it coming from
> www.github.com
On 10/13/17 3:32 PM, Hervé Pagès wrote:
Hi Stephanie,
Can you provide a little bit more context? Have you observed
conflicts between VariantAnnotation:::asVCF() and other asVCF()
functions defined elsewhere? Any reason why you can't use/import
VariantAnnotation:::asVCF() in your package?
I w
Hi Stephanie,
Can you provide a little bit more context? Have you observed
conflicts between VariantAnnotation:::asVCF() and other asVCF()
functions defined elsewhere? Any reason why you can't use/import
VariantAnnotation:::asVCF() in your package?
Alternatively, have you considered using/defini
Dear Leo,
I'm happy to inform you that the issues with updating workflows have been
resolved. Apart from the problems with the postprocessing step which was
looking for the now disabled mac tar balls, there was also a similar issue
with the bioconductor website building script which prevented the
Can we move the "asVCF" generic to BiocGenerics?
thanks,
Stephanie
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Hi,
we've had binary compiles a while ago, but we were glad
when we could revert that to "normal" compilation a long time ago.
Another observation from years ago was that the linker step
was what took the longest, and even with a precompiled libpwiz.a
this took very long.
Thanks Herve for t
Yes. That is correct.
> On Oct 13, 2017, at 2:59 PM, Matthew Myint wrote:
>
> Hi,
>
> Thanks for the explanation! To clarify, the proper step after the
> first time you helped restore my repository was to change the Github
> branch (with duplicates) to master_deprecated, and switch in the
> r
Hi,
Thanks for the explanation! To clarify, the proper step after the
first time you helped restore my repository was to change the Github
branch (with duplicates) to master_deprecated, and switch in the
restored one as master?
https://www.avast.com/sig-email?utm_medium=email&utm
Hi Matthew,
After closer inspection of “cytofkit”, it was this commit which caused the
duplicates.
commit 4050c245d04af30705245f48931e677a6b4ae159
Merge: 467f659 e6cef6c
Author: Hervé Pagès
Date: Wed Sep 20 13:19:45 2017 -0700
Merge branch 'master' of git.bioconductor.org:packages/cytof
Hi Matthew,
I’ll have to fix your branch again, for this I need some time. Do not push any
more changes.
*When you pull from the upstream (g...@git.bioconductor.org), you are not
supposed to get any duplicate commits.*
If a merge is giving you duplicate commits, it means that you didn’t swit
Hi,
Both your `origin` and `upstream` are set to the same location i.e
g...@git.bioconductor.org:packages/xps.
This is wrong. You want your origin to point to `g...@github.com:cstrato/xps`
You can do this by following the commands,
`git remote set-url origin g...@github.com:cstrato/xp
Dear Martin,
Following your advice
https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
I did the following:
$ cd xps
$ git remote add upstream g...@git.bioconductor.org:packages/xps.git
$ git fetch upstream
Enter passphrase for key '/Users/rabbitus/.ssh/id_rsa':
From git.bi
Please send me a list of commands you have tried. I’d like to see the outputs
as well.
e.henrich has associated keys to it coming from www.github.com/immunespace.keys
Best,
Nitesh
> On Oct 13, 2017, at 1:36 PM, Immune Space wrote:
>
> Hi Nitesh,
>
> We resubmitted the git transition form
Hello everyone,
The new OrgDb and TxDb packages are now available on the devel branch, e.g.,
https://bioconductor.org/packages/devel/data/annotation/html/org.Rn.eg.db.html
https://bioconductor.org/packages/devel/data/annotation/html/TxDb.Rnorvegicus.UCSC.rn5.refGene.html
Updated OrgDb packages:
Package maintainers,
If you haven't already, please update the NEWS files in your packages. This
information will be included in the release announcement. The deadline for
updating NEWS files is Tuesday, October 24:
http://www.bioconductor.org/developers/release-schedule/
Thanks.
Valerie
Th
Hi Matthew,
I remember fixing this repository for you a few weeks ago.
You cannot push branches to the Bioconductor repository, that is in the FAQ,
and documentation.
Can you tell me what exactly are the steps you are trying that, you are getting
duplicate commits again?
Best,
Nitesh
> On
Dear Martin,
On Fri, 13-October-2017, at 12:27:31, Martin Morgan
wrote:
> On 10/12/2017 07:08 AM, Ramon Diaz-Uriarte wrote:
>> Dear All,
>>
>> I have noticed that on the latest build report, a package I maintain,
>> OncoSimulR
>> (http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimul
On 10/12/2017 07:08 AM, Ramon Diaz-Uriarte wrote:
Dear All,
I have noticed that on the latest build report, a package I maintain,
OncoSimulR
(http://bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/veracruz1-buildsrc.html),
I wonder if it is this issue
https://github.com/Bioconduc
Hi, Martin,
now all works great.
Thanks for all.
All the best
Riccardo
On 13/10/17 10:49, Martin Morgan wrote:
On 10/13/2017 04:35 AM, Riccardo Romoli wrote:
Hi bioc-devel,
I am unable to push to g...@git.bioconductor.org to may package called
"flagme".
Please try again -- your public key
On 10/13/2017 04:35 AM, Riccardo Romoli wrote:
Hi bioc-devel,
I am unable to push to g...@git.bioconductor.org to may package called
"flagme".
Please try again -- your public key was associated with the incorrect
svn identifier.
Martin
###
$ git push upstream master
X11 forwarding reque
Hi bioc-devel,
I am unable to push to g...@git.bioconductor.org to may package called
"flagme".
###
$ git push upstream master
X11 forwarding request failed on channel 0
FATAL: W any packages/flagme rromoli DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote
Hi,
Recently I noticed in hindsight that my repository had duplicate
commits, but I missed this during my normal package updating
procedures.
It was odd that the hook didn't reject these, so I made a clean branch
from a commit before the problem occurred and cherry-picking commits
to the present
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