Hi,
I've been using knitcitations for a while to handle citations in HTML
vignettes. I had been using knitcitations::read.bibtex() until I
realized that it no longer reads the entries in the order that were
given in the bib file**. So I made a change and it all works... except
on Windows. I finall
The data definitely does not belong in the software package.
We are a little schizophrenic about Experiment Data at the moment; my
own feeling is that ExperimentHub is the right place, especially for
data over say 10 Mb. This is more labor intensive and harder to version,
but potentially offer
On 10/02/2017 10:50 AM, Bernat Gel wrote:
Don't want to be alarmist, but is there anything in place to prevent a
"malicious agent" inserting a new ssh key to the form and gaining access
to our git repo? Maybe it would be sufficient to send an email to the
maintainer whenever a new key is added
Bioc-devel subscribers!
The 'digest' mode was previously configured to send mail daily, or
whenever the size of the digest exceeded a threshold, whichever came
first. It is now configured to send the digest on a daily basis,
hopefully reducing frequency for those preferring this form of delive
On Mon, Oct 2, 2017 at 3:07 PM, Juan David Henao Sanchez <
judhena...@unal.edu.co> wrote:
> Hi,
>
> I'm trying to clone my package from git.bioconductor.org as:
>
> git clone g...@git.bioconductor.org:packages/coexnet.git
>
> But, I recive the next message:
>
> ==
> Clonar en «coex
You don’t seem to have an SSH public key on our system. Please submit your SSH
public key.
https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform
If you have more questions, bioconductor.org/developers/how-to/git/faq/
Nitesh
> On Oct 2, 2017, at 3:
Hi,
I'm trying to clone my package from git.bioconductor.org as:
git clone g...@git.bioconductor.org:packages/coexnet.git
But, I recive the next message:
==
Clonar en «coexnet»...
Permission denied (publickey).
fatal: Could not read from remote repository.
Please make sure you
Don't want to be alarmist, but is there anything in place to prevent a
"malicious agent" inserting a new ssh key to the form and gaining access
to our git repo? Maybe it would be sufficient to send an email to the
maintainer whenever a new key is added so we have a clue something has
gone wrong
Thank you Martin, that makes sense to me. In this case, the next
package that my lab contribute to bioc I will probably submit it
myself. The structure of a laboratory involves team members coming and
going, and we need to ensure continuous maintenance. This is certainly
an issue that is not relate
Hello Nitesh,
Thank you very much for the support. I totally agree with that.
Best,
Vinicius
On Mon, Oct 2, 2017 at 10:44 AM Turaga, Nitesh <
nitesh.tur...@roswellpark.org> wrote:
> Hi Mauro
>
> Please always forward your git questions to bioc-devel. There is more than
> one person handling the
On 10/02/2017 09:57 AM, m castro wrote:
Hi Nitesh,
Thank you.
In the submission of these packages, Vinicius and Clarice had included
all the team as maintainers (I can confirm in the packages' homepages,
below), not sure why it did not work at that occasion.
We encourage just a single maintai
Hi Mauro,
You should have access to those packages now.
Please let me know if it has worked.
Best,
Nitesh
> On Oct 2, 2017, at 9:57 AM, m castro wrote:
>
> Hi Nitesh,
>
> Thank you.
>
> In the submission of these packages, Vinicius and Clarice had included
> all the team as maintainers (
Hi Nitesh,
Thank you.
In the submission of these packages, Vinicius and Clarice had included
all the team as maintainers (I can confirm in the packages' homepages,
below), not sure why it did not work at that occasion.
http://bioconductor.org/packages/RTNduals/
http://bioconductor.org/packages/
Hi Mauro
Please always forward your git questions to bioc-devel. There is more than one
person handling the issues about git.
RTNsurvival, — Clari Groeneveld is the maintainer hence you don’t have write
access.
RTNduals — Vinicius Chagas is the listed maintainer on our system.
This issue i
Dear Martin and Vincent,
Thanks for your feedback. Here is the current package repository:
https://github.com/gogleva/SecretSanta
I still need to run more tests on mac and clean the code a bit.
But probably this would be sufficient to say whether the package is
compatible with Bioconductor in pri
I'd also comment that if you make the package visible I would be willing to
have a look at the issues involved in porting to windows. No guarantees
but at least get some sense of context.
On Mon, Oct 2, 2017 at 9:04 AM, Martin Morgan wrote:
> I want to add, though, that OS-specific functionalit
I want to add, though, that OS-specific functionality and system
requirements greatly limit the utility of your package and, like the
OS-specific dependencies your package depends on, serves as a kind of
virus that makes any other package that uses yours also not operable on
the unsupported OS.
Dear Lori,
Thanks a lot for the clarification.
I will incorporate os checks in my unit tests and examples.
Thanks,
Anna
On 2 October 2017 at 12:30, Shepherd, Lori
wrote:
> You can still submit to bioconductor despite this limitation. You could
> also do a os check in the examples and tests th
Hi all,
Today I submitted a new package called "pcxn" in bioconductor and I got the
following Abnormal built result:
Warning in fun(libname, pkgname) :
no display name and no $DISPLAY environment variable
Error: processing vignette 'usingPCxNdb.Rnw' failed with diagnostics:
chunk 4 (label = p
You can still submit to bioconductor despite this limitation. You could also
do a os check in the examples and tests that fail on windows and make a comment
that this is the case. If the program is not meant to run in windows there is
options to handle that as well and the review assigned to y
Dear Bioconductor Team,
I have written a package and was planning to submit it to Bioconductor one
day. The package provides a set of wrapper functions around several
existing command line tools to construct scalable and reproducible
pipelines for secretome prediction.
The package requires severa
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