Dear all,
we're experiencing WARNINGS in xcms on Tokay2 that are all related to links in
Rd files to functions and methods in other packages.
Example:
we have \code{\link[MSnbase]{pickPeaks}} in XCMSnExp-inherited-methods.Rd that
links to the method in MSnbase, that works nicely on Linux and mac
Dear Ruqian,
Yes sir, I have opened the build report which is a link to an HTML page
with details.
But I unable to understand why the WARNING massages are showing.
Three days before the other reviewers had made some comments and asked me
to address
those issues and also told me to solve the NOT
Hi Johannes,
xcms is certainly not alone with the warning, and it was discussed in
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
I think you should be able to get round it by including the name of Rd file
you're linking to e.g. \code{\link[MSnbase:pickpeaks-method]{pickPeaks}}
Thanks Mike,
I somehow missed the discussion you mentioned. I would really not like to
include the name of the Rd file I want to link to. The *default* way that works
on Linux and macOS should also work on Windows - otherwise what's the matter of
the alias? Interestingly, on my Windows test mac
Hi everyone,
I am the developer of package "PowerExplorer", it has been accepted last week,
and now it is visible on Bioconductor git server. However, the package was
developed in my own personal GitHub repository, now I need to move it into our
lab repository. Does anyone have any idea how to
Martin mentioned that he changed the wording in
https://github.com/wch/r-source/commit/cbd7ca1b1aedf0405e11ee2440fbde891cba524e
, so more recently than your version of R-devel.
Mike
On 16 April 2018 at 11:57, Rainer Johannes
wrote:
> Thanks Mike,
>
> I somehow missed the discussion you mentione
Dear Xu,
While you, with your ssh key, keep pushing to the git.bioconductor.org it
doesn't matter where else is stored.
To move a repository within github you need to follow this tutorial:
https://help.github.com/articles/transferring-a-repository-owned-by-your-personal-account/#transferring-to-an
This was also discussed in this thread a few weeks ago
https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013156.html
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
___
If you are still having problems understanding warnings, it is probably
better to use the github issue -- it may take some time to get an
answer, because the reviewers have many responsibilities.
It looks like your 'webhook' is not correct, and that you are not
changing the version of your pac
Thanks for your help, Lluís.
-Xu
From: Lluís Revilla [mailto:lluis.revi...@gmail.com]
Sent: maanantai 16. huhtikuuta 2018 13.48
To: Xu Qiao
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] repository change after package acceptance
Dear Xu,
While you, with your ssh key, keep pushing to t
Yes Bioconductor utilizes the copy on
git.bioconductor.org:packages/PowerExplorer.git so as long as changes are
pushed there - your github repository doesn't matter -
You may have to submit additional ssh-keys to Bioconductor for access; by
default we use ssh keys from the github account that
Dear Martin,
On Mon, 09-April-2018, at 17:35:47, Martin Maechler
wrote:
>> Ramon Diaz-Uriarte
>> on Mon, 9 Apr 2018 16:51:38 +0200 writes:
>
> > Dear Martin,
>
> > On Fri, 06-April-2018, at 18:59:00, Martin Morgan
> > wrote:
> >> On 04/06/2018 10:44 AM, Lluís Revi
And I have now asked this in R-pkg-devel
(https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002617.html), as
suggested by Martin Maechler
(https://stat.ethz.ch/pipermail/bioc-devel/2018-April/013169.html) in the
thread linked by Lori.
But if you can use \link{foo} (instead of \link[pkg]{foo}
dear sir:
contents in GitHub and that in bioconductor are not the same. I want to update
the package to follow the contents in github, but falied:
git remote -v
origin g...@github.com:wind22zhu/BioMedR.git (fetch)
origin g...@github.com:wind22zhu/BioMedR.git (push)
upstream g...@git.biocond
Hi Zhu,
You submitted your keys with the wrong username. Please use your SVN ID “m.zhu”
and resubmit
Best,
Nitesh
> On Apr 16, 2018, at 12:32 PM, Zhu MF wrote:
>
> dear sir:
>
>
> contents in GitHub and that in bioconductor are not the same. I want to
> update the package to follow the co
Dear BioMedR maintainer,
Unfortunately BioMedR was removed from Bioconductor as of Release 3.6 (last
Oct). We reached out several times before the 3.6 release as your package had
been failing since early July 2017. Part of the Bioconductor guidelines require
that packages are actively maintained
Dear Bioc-Devel,
I’ve just updated my package for the upcoming release upstream successfully
using "git push upstream master”.
My current remotes are set to:
origin https://github.com/gmelloni/LowMACA.git (fetch)
origin https://github.com/gmelloni/LowMACA.git (push)
upstreamg...@git.bi
Hi all,
my package recently got accepted and moved to the Bioconductor repository.
Suddenly I get an error during the package build for Linux and OS (the
INSTALL is working). The error occurs during the creation of the
vignette in a chunk. The error was not there before and I can't
reproduce
Hi Kenneth,
I was unable to reproduce the issue that you described in your original
email with a different package (without access to your package).
I ran `devtools::build_vignettes` on the `RaggedExperiment` package
and the vignettes were built without a problem (with pandoc installed):
> devt
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