On 11/01/2017 07:53 PM, Arman Shahrisa wrote:
I cloned the package into a clean directory.
It helps to be more precise here. Were did you clone the package from?
In the simplest case it would be
git clone g...@git.bioconductor.org:packages/your-package
and you'd have a single remote named
On 11/01/2017 08:54 PM, Vincent Carey wrote:
As I plan to "fix a bug" in release version of BiocSklearn, I tried
%vjcair> git checkout remotes/upstream/RELEASE_3_6
Here is the result; what would I do to make some changes, alter DESCRIPTION
version to 1.0.1, commit and push so that the build sys
As I plan to "fix a bug" in release version of BiocSklearn, I tried
%vjcair> git checkout remotes/upstream/RELEASE_3_6
Here is the result; what would I do to make some changes, alter DESCRIPTION
version to 1.0.1, commit and push so that the build system
has 1.0.1?
Note: checking out 'remotes/up
I cloned the package into a clean directory. Then I followed �New package
workflow� strategy. By checking Description file while switching between
branches, I can easily see the version change which is correct. If I understand
it correctly, GitHub can only contain changes I make to master branch
One possible point of confusion: Laurent's workflow includes maintaining
separate branches "master" and "devel", which he syncs to his own Github
repo and Bioconductor's git repo respectively. However, the
documentation on the bioc website
(https://bioconductor.org/developers/how-to/git/) assum
FYI today's data-experiment builds completed and pcxnData is
green:
https://bioconductor.org/checkResults/3.6/data-experiment-LATEST/pcxnData/
and propagated:
https://bioconductor.org/packages/3.6/data/experiment/html/pcxnData.html
Now the next step is that the software builds will be able
Thanks so much for the help. I did manage to push with the SSH protocol.
Will wait till the next build to see if it went through.
Best
Kushal
On 1 November 2017 at 16:18, Turaga, Nitesh
wrote:
> Hi Kushal,
>
> You also need to use the “SSH” protocol, and not the “HTTPS” protocol.
>
> Your ups
On 1 November 2017 20:36, Arman Shahrisa wrote:
> I'm confused with development process.
>
> At first, I need to have a folder with accepted packaged. Then I need to pull
> origion RELEASE_3_6?
>
> Then in another folder, I need to pull origion master?
No, it all happens in the same folder, but
On 11/01/2017 05:15 PM, Bemis, Kylie wrote:
Yes, the ideal solution seems rather unlikely, but I feel like there must be a
solution better than the current situation.
I’d like to implement some more of the functionality from matrixStats for
‘matter’ matrices, but importing DelayedArray and Del
I suggest that you cc Martin Maechler on this discussion. I happen to be
on the Bioc-devel list but I'm not sure if he is. Although both of us are
still listed as maintainers of the Matrix package, he is, and has been for
several years, the de facto maintainer.
On Wed, Nov 1, 2017 at 4:15 PM Bem
On 11/01/2017 04:42 PM, Gabe Becker wrote:
Arman,
Not on the Bioc team per se, but I would say only have a checkout of the
release branch when you need it, ie a bug is reported, you have fixed it in
devel, and you are ready to push the very narrow bugfix to release. I only
keep "master" checkout
Hi Kushal,
You also need to use the “SSH” protocol, and not the “HTTPS” protocol.
Your upstream should be g...@git.bioconductor.org:packages/CountClust
Best,
Nitesh
> On Nov 1, 2017, at 5:06 PM, Turaga, Nitesh
> wrote:
>
> Hi Kushal,
>
> Can you please try,
>
> ssh -T g...@git.bioc
Yes, the ideal solution seems rather unlikely, but I feel like there must be a
solution better than the current situation.
I’d like to implement some more of the functionality from matrixStats for
‘matter’ matrices, but importing DelayedArray and DelayedMatrixStats solely for
the generic functi
Probably way easier to add the generics to the Matrix package and everyone
just depends on that.
On Wed, Nov 1, 2017 at 1:59 PM, Hervé Pagès wrote:
> That's probably a good idea but a clean solution would need to
> involve all players, including the Matrix package. Right now there
> are conflict
Hi Kushal,
Can you please try,
ssh -T g...@git.bioconductor.org -v
Are you using the correct private key to your corresponding public key on our
machine?
If not, please check the FAQ section
bioconductor.org/developers/how-to/git/faq/ point#15. You can set up a config
file to use th
That's probably a good idea but a clean solution would need to
involve all players, including the Matrix package. Right now there
are conflicts for some S4 generics defined in Matrix and in
BiocGenerics (e.g. rowSums). I'm not sure that moving rowSums from
BiocGenerics to a new MatrixGenerics pack
I think that's a good idea, Kylie.
Pete (DelayedMatrixStats developer)
On Thu., 2 Nov. 2017, 6:09 am Kasper Daniel Hansen, <
kasperdanielhan...@gmail.com> wrote:
> I think it makes sense. A lot of sense. Might be useful to involve Henrik
> (matrixStats) as well.
>
> Who are the players, apart fro
Arman,
Not on the Bioc team per se, but I would say only have a checkout of the
release branch when you need it, ie a bug is reported, you have fixed it in
devel, and you are ready to push the very narrow bugfix to release. I only
keep "master" checkouts of my packages on a permanent basis.
You g
I�m confused with development process.
At first, I need to have a folder with accepted packaged. Then I need to pull
origion RELEASE_3_6?
Then in another folder, I need to pull origion master?
So that by opening each folder, I know what I�m editing.
Also during push, I need to be careful about w
I think it makes sense. A lot of sense. Might be useful to involve Henrik
(matrixStats) as well.
Who are the players, apart from DelayedArray/DelayedMatrixStats and matter?
(and some very old stuff in Biobase which should really be deprecated in
favor of matrixStats).
Best,
Kasper
On Wed, Nov 1,
Just a heads up that we're currently branching the BioC 3.7 annotation
packages. There may be a brief period when biocLite() can't get annotations for
3.7 while the repo is being populated. This should be complete around 4 pm EST.
This only affects people using "devel", i.e., R 3.5 and BioC 3.7.
Hi all,
To continue a variant of this conversation, with the latest BioC release, we
now have quite a few packages that are implementing various matrix-related S4
generic functions, many of them relying on matrixStats as a template.
I was wondering if there is any interest or intention to creat
Thanks for your thorough answer. So, when I’m going to push the first devel
change, the version must be 1.1.1 while bug fixes for the released package will
start from 1.0.1. Am I right?
Best regards,
Arman
From: Shepherd, Lori
Sent: Wednesday, November 1, 2017
Hi Herve,
Thanks for clarifying on the matter. I followed your instructions and did *git
cherry-pick* to make the following changes
- fix a bug in one of the functions
- add a citation
- fix the readme
I bumped the version number from 1.4.0 to 1.4.1 and tried to push to the
release branch, but I
On 11/01/2017 11:14 AM, Arman Shahrisa wrote:
Hi,
There are two GitHub commits for my package �cbaf� by Bioconductor on 30
October.
The interesting thing is the first commit changes version in description file
from
0.99.8 to 1.0.0 while the second one changes 1.0.0 to 1.1.0. Is it correct?
Yes this is correct - Pkg_version x.y.z
We do a version bump on the devel version of the package to make the versioning
consistent with release( y even in release) - hence the first version bump to
1.0.0 - this is now the current release version of your package
The second version bump is t
There are no updates given from that google form.
Did you try to access your package?
> On Nov 1, 2017, at 1:45 PM, Valeriia Sherina wrote:
>
> Dear Bioconductor,
>
> I am a maintainer of the package "nondetecs" on Bioconductor. I know that
> Bioconcuctor transitioned to GitHub submittions. I
Dear Bioconductor,
I am a maintainer of the package "nondetecs" on Bioconductor. I know that
Bioconcuctor transitioned to GitHub submittions. I filled up a form "git /
svn transition: ssh keys" to get access to my package, but since last
Wednesday have not gotten any updates on that.
I am hoping
Hi all,
You may have noticed the devel builds have a lot of red. Part of the problem
is that we currently have no CRAN binaries for Windows or OS X El Capitan built
against R 3.5.
In the BBS code, we are attempting to install CRAN dependencies from "source"
where possible but some packages ar
Yes, I am experiencing the same problem for the EnrichmentBrowser package.
The release package landing page holds all the new stuff, but the vignette
is still the one of the old release.
Best,
Ludwig
--
Dr. Ludwig Geistlinger
eMail: ludwig.geistlin...@bio.ifi.lmu.de
> Dear,
>
> It seems that t
Hi Maren,
pwOmics/vignettes/ contains a pwOmics.bcf file which is
likely to be contamination (looks like an intermediate biber
file). It's never a good idea to put this kind of intermediate
file in git. Please remove and let's see if that solves the problem.
Cheers,
H.
On 11/01/2017 12:33 AM, S
Hi Sokratis,
Not sure why but it seems that for some reason the build machines
didn't manage to install pcxn so far. Until only now. I went on
build machine malbec1 to check whether it managed to install pcxn,
and it seems that it did:
> "pcxn" %in% rownames(installed.packages())
[1] TRUE
A
Dear,
It seems that the 3.6 release contains an old version of the vignette of
MutationalPatterns.
In commit d1c4e14 I pushed updates of the corresponding bioRxiv paper, but the
changes in the vignette haven't made it in.
Should I now bump the release number without making any further changes?
You submitted your key very recently. We process the keys every 24 hours, at
12pm EST.
Please be patient.
Nitesh
> On Oct 31, 2017, at 5:54 PM, Arman Shahrisa
> wrote:
>
> Hi,
>
> I�m the maintainer of the package �cbaf�. It�s a new package for bioc v 3.6.
>
> I�m trying to pull changes t
Could you please provide the full output from the following:
git remote -v
git checkout master
git fetch upstream
git merge upstream/master
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, Ne
Hey all,
After the release I can see the release page of the pcxn package but not
pcxnData package. In the build page it says it cannot find the pcxn package
and fails.
Regards,
Sokratis
On 31 October 2017 at 16:33, Shepherd, Lori
wrote:
> It should be the same and you should be able to see th
Dear Bioconductor developers,
I can't reproduce the error from the OS X server which is
/usr/local/bin/texi2dvi: biber failed
for the pwOmics build report.
Do you have any advice for me, how to fix this?
Additionally, I wan't to point out that the maintenance changed and that I'm the
new main
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