Dear all,I am trying to run
BiocCheck("/home/package_name", list(`no-check-vignettes`=TRUE))
There is no error but I am getting the following warning.
$warning
[1] "The following files are over 5MB in size:
'dataset/Caenorhabditis_elegans.WBcel235.dna.chromosome.I.fa'."
This as well as other
On Fri, Mar 9, 2018 at 12:36 PM, Cook, Malcolm wrote:
> Hi,
>
>
> > -Original Message-
> > From: Bioc-devel On Behalf Of
> > Michael Lawrence
> > Sent: Friday, March 09, 2018 1:49 PM
> > To: Paul Shannon
> > Cc: Gabe Becker ; bioc-devel@r-project.org
> > Subject: Re: [Bioc-devel]
Hi,
> -Original Message-
> From: Bioc-devel On Behalf Of
> Michael Lawrence
> Sent: Friday, March 09, 2018 1:49 PM
> To: Paul Shannon
> Cc: Gabe Becker ; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] IGV - a new package in preparation
>
> Couple of things:
>
> 1) Che
Hello,
Jumping in the conversation perhaps late.
If it helps the effort, below are some IGV related R functions I've used in the
past to good effect communicating with IGV running on local/remote host and
issuing GOTO and Save Snapshot commands.
They use utils::write.socket
One things that he
Yea I wouldn't use JSON, particularly "row-oriented" JSON, as a means of
scalable data transmission.
On Fri, Mar 9, 2018 at 11:57 AM, Paul Shannon
wrote:
> Thanks, Michael.
>
> httpuv, to which Hector made crucial contributions, makes it easy to send
> data directly between R and the browser, us
Thanks, Michael.
httpuv, to which Hector made crucial contributions, makes it easy to send data
directly between R and the browser, using websockets. I resort to files,
however, because when the data, rendered as json, exceeds 500k, the websocket
hangs. I never identified the weak spot. So
Couple of things:
1) Check out epivizr and the surrounding infrastructure (maybe Hector can
chime in). It's able to serve up data directly from R; would be nice if we
could do that with IGV, instead of writing out to files. That would require
it to talk to some standard API, like the old DAS.
2)
Thanks, Levi. Your comments, and Gabe’s are very helpful, getting me to
consider things I have overlooked.
Support for GenomicRanges is essential, as you and Gabe point out.
In all cases IGV will convert a GRanges object to an appropriate track, then
write it out as a temporary file. igv suppo
Keys are processed once a day around 9am EST. You will get an email indicating
if your submission was successful or not.
Valerie
On 03/09/2018 09:11 AM, Obenchain, Valerie wrote:
Nicolas,
You need to follow instructions to submit an SSH key:
https://bioconductor.org/developers/how-to/git/m
Nicolas,
You need to follow instructions to submit an SSH key:
https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
Specifically, you need to fill out this form using n.servant as your username:
https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexeg
Thank you very much Valerie. I take care of that asap.
N
Le 09/03/2018 � 18:11, Obenchain, Valerie a �crit�:
> Nicolas,
>
> You� need to follow instructions to submit an SSH key:
>
> https://bioconductor.org/developers/how-to/git/maintain-github-bioc/
>
> Specifically, you need to fill out this fo
http://bioconductor.org/developers/how-to/git/
> On Mar 9, 2018, at 11:42 AM, Servant Nicolas wrote:
>
> Can anyone help me ?
> If you have any links or tutorial, it would be useful.
> Thanks
>
> Le 06/03/2018 à 10:04, Servant Nicolas a écrit :
>> Dear all,
>>
>> I try a couple of weeks ago t
That sounds like a bug. Thanks for the report, we'll look into it.
Valerie
On 03/09/2018 07:48 AM, Nicolas Descostes wrote:
I mean that on the landing page:
https://bioconductor.org/packages/3.7/bioc/html/ChIPSeqSpike.html
If you click on NEWS
(https://bioconductor.org/packages/3.7/bioc/news/
Thank you very much.
The point is that I cannot checkout because I guess BioC does not know
my SSH keys.
>>git clone g...@git.bioconductor.org:packages/HiTC
Cloning into 'HiTC'...
Permission denied (publickey).
fatal: Could not read from remote repository.
How can I fix this ?
Thanks
Le 09/0
Can anyone help me ?
If you have any links or tutorial, it would be useful.
Thanks
Le 06/03/2018 à 10:04, Servant Nicolas a écrit :
Dear all,
I try a couple of weeks ago to move to git to maintain the HiTC package,
but I did not succeed.
I followed the guidelines here ;
https://bioconductor.or
What do you mean by 'the NEWS file has not been properly updated'? Did you
commit a change before the builds started, bumped the package version and the
package you downloaded with biocLite() was somehow out of date? Or was a
download from the landing page out of date ... ?
Valerie
On 03/09/
Hi Nicolas,
I understand you've been in contact with several people about this. Are you
still having access problems?
Valerie
On 03/06/2018 01:04 AM, Servant Nicolas wrote:
Dear all,
I try a couple of weeks ago to move to git to maintain the HiTC package,
but I did not succeed.
I followed th
The Bioconductor Team is continuing to identify packages that will be
deprecated in the next release to allow for the Bioconductor community to
respond accordingly. The list will be updated monthly.
The current list of deprecated packages is as follows:
Maintainer requested deprecation:
Sof
Hi,
Just a quick follow-on to this.
Cleaning up the Bioconductor GitHub organization that Nitesh describes below is
not related to SSH key errors when accessing packages on git.bioconductor.org.
If you are having SSH key problems please post on bioc-devel and I can hep out.
Previously Nitesh w
On Thu, Mar 8, 2018 at 12:29 AM, Paul Shannon
wrote:
> Thanks, Gabe.
>
> You make an excellent point: bioc objects get first class support. In
> some instance, base R data types deserve that also, and data.frames lead
> the list for me, being useful, concise, universally available, expressive.
>
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