Re: [Bioc-devel] updating Bioconductor package that is already on Github

2017-09-06 Thread Sean Davis
Hi, Simina. On Tue, Sep 5, 2017 at 11:40 PM, Simina Boca wrote: > Dear all, > > I hope this isn't a duplicate of another question. Here goes: > > - I would like to update my swfdr package, which is already on > Bioconductor. It is also on Github and my submission process was via > opening an iss

Re: [Bioc-devel] updating Bioconductor package that is already on Github

2017-09-06 Thread Shepherd, Lori
Have you submitted your ssh key https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform [https://lh6.googleusercontent.com/aTIh4yWF4TsFYR95qIA_lBuCgvLJ88Q4WzDmdBuie6ndQirxWI0jhfRBF7eO-n3W6SE=w1200-h630-p]

Re: [Bioc-devel] updating Bioconductor package that is already on Github

2017-09-06 Thread Simina Boca
Thank you so much Sean and Lori! For some reason I thought the ssh key part was only relevant if the package was submitted via svn, which is why i had overlooked those instructions initially. Cheers, Simina On Wed, Sep 6, 2017 at 7:01 AM, Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: >

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

2017-09-06 Thread Jim Hester
This mirror could be relatively simply supported by setting up an additional remote in the server side repositories and adding a post-receive hook to each repository that simply pushes to the GitHub mirror remote after commits are received. https://git-scm.com/book/gr/v2/Customizing-Git-Git-Hooks

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

2017-09-06 Thread Robert M. Flight
I agree with Jim. It has been very useful to have the Bioconductor GitHub mirror to examine code, and the CRAN mirror as well. A post-hook to push there would be very useful. -Robert On Wed, Sep 6, 2017 at 11:07 AM Jim Hester wrote: > This mirror could be relatively simply supported by setting

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

2017-09-06 Thread Martin Morgan
On 09/06/2017 11:28 AM, Robert M. Flight wrote: I agree with Jim. It has been very useful to have the Bioconductor GitHub mirror to examine code, and the CRAN mirror as well. A post-hook to push there would be very useful. The mirror causes tremendous confusion on several fronts. The updates c

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

2017-09-06 Thread Turaga, Nitesh
Hi Jim We are more worried about the confusion it creates among the users. Users have tried to push their commits to the bioconductor-mirror instead of the bioconductor git server. Another source of confusion is, some maintainers have forked their packages from the Bioconductor-mirror, and have

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

2017-09-06 Thread Shepherd, Lori
Even before the bioconductor git server, when we still were using svn, users were confused at where to make updates and push changes. Now even more so we have seen several packages try and push to the bioconductor-mirror or change the remotes to point the the mirror locations. It has created

Re: [Bioc-devel] workflow building issues on mac and windows

2017-09-06 Thread Andrzej Oleś
Hi Leo, many thanks for getting back to me! Regarding cross-references: the format wraps around bookdown so the \@ref() syntax is supported in the same way as in other BiocStyle format functions and in BiocWorkflowTools::f1000research. As for the Mac builder issue, the libraries are: > openssl

[Bioc-devel] splitting a Bioconductor package in two

2017-09-06 Thread Stephanie M. Gogarten
Hi, If one wanted to move some code from an existing Bioconductor package into its own, separate package for ease of maintenance, would that constitute a new package submission with the full review process? Or is there some expedited submission available? We are refactoring the GENESIS packa

Re: [Bioc-devel] splitting a Bioconductor package in two

2017-09-06 Thread Michael Lawrence
On Wed, Sep 6, 2017 at 9:07 AM, Stephanie M. Gogarten wrote: > Hi, > > If one wanted to move some code from an existing Bioconductor package into > its own, separate package for ease of maintenance, would that constitute a > new package submission with the full review process? Or is there some > e

Re: [Bioc-devel] Bioconductor package landing pages

2017-09-06 Thread Hervé Pagès
Hi Nima, Normally you have to allow 24 hours or so to see your changes show up on the build report: https://bioconductor.org/checkResults/3.5/data-experiment-LATEST/ and on the package landing page: https://bioconductor.org/packages/3.5/data/experiment/html/biotmleData.html But sometimes m

Re: [Bioc-devel] Problems pushing changes from github to git.bioconductor

2017-09-06 Thread Blattmann Peter
Dear Nitesh, Thank you for spotting that my upstream was wrong and fixing the form. I submitted my key (id_github) last weekend, but I still get stuck when I try to push changes to upstream. I'm not really sure from where the problem comes and if this might be because I have different .ssh ke

Re: [Bioc-devel] Problems pushing changes from github to git.bioconductor

2017-09-06 Thread Blattmann Peter
Dear Nitesh, Here some addition to the previous e-mail. I saw that in the config file there was written by mistake git.bioconductor.com instead of .org. I changed this now, but still it doesn't work. But the ssh connection seems to work fine and it recognizes me as "blattman" (see below).

Re: [Bioc-devel] pandoc SSL error on malbec2 and tokay2

2017-09-06 Thread Martin Morgan
On 09/05/2017 10:35 AM, Nan Xiao wrote: Hey Kasper, - I really appreciate your help. Although it didn't help answer the question directly, I think it would still be necessary to clarify some facts: 1. I agree that using "non-standard fonts" could bring better aesthetics for a particula

Re: [Bioc-devel] experimental data packages and git-lfs

2017-09-06 Thread Levi Waldron
Thank you, Nitesh. Is there any difference at all now in how experimental data vs. software packages are tracked and checked? On Tue, Sep 5, 2017 at 8:40 PM, Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > Hi Levi, > > The external_data_store.txt file is not needed anymore. > > The curr

[Bioc-devel] role of replaceSlots in BiocGenerics

2017-09-06 Thread Vincent Carey
Is this the preferred way of adjusting content in a live object? It is not accessible except via ":::" [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

2017-09-06 Thread Jim Hester
I understand the fragmentation concerns, just felt the mirrors should have been maintained at least until a reasonable alternative exists. The diverging history issues should be resolvable by resetting the state to the canonical bioconductor repository and force pushing necessary changes to their

Re: [Bioc-devel] role of replaceSlots in BiocGenerics

2017-09-06 Thread Michael Lawrence
No, the best practice is to just use initialize(). It used to be that replaceSlots() saved some copying, but that's no longer really the case. The only potential benefit is that it can skip validity checks, but usually you want those. Michael On Wed, Sep 6, 2017 at 12:55 PM, Vincent Carey wrote:

Re: [Bioc-devel] role of replaceSlots in BiocGenerics

2017-09-06 Thread Hervé Pagès
Hi, Personally I like replaceSlots() better. Not only because it's more readable but also the fact that you can use initialize() to update an existing object is an undocumented feature so I prefer to not rely on it. Also initialize() is a generic and there could be a method defined for the obje

Re: [Bioc-devel] role of replaceSlots in BiocGenerics

2017-09-06 Thread Vincent Carey
I am getting complaints from CMD check about ::: which seems necessary to use this replaceSlots facility because it is not exported. I will look into initialize, which might work fine for my concern. I cannot remember why I did not just use direct assignment to slots, however. Perhaps I just fou

Re: [Bioc-devel] role of replaceSlots in BiocGenerics

2017-09-06 Thread Michael Lawrence
On Wed, Sep 6, 2017 at 2:23 PM, Hervé Pagès wrote: > Hi, > > Personally I like replaceSlots() better. > > Not only because it's more readable but also the fact that you can use > initialize() to update an existing object is an undocumented feature so > I prefer to not rely on it. > It seems docum

Re: [Bioc-devel] role of replaceSlots in BiocGenerics

2017-09-06 Thread Hervé Pagès
One of the reasons it's not exported is because it started as something kind of experimental and we didn't find a good home for it yet. I could probably move it to S4Vectors where we already have some low-level S4-related utils. Not the best home either but maybe better than in BiocGenerics? IMO

Re: [Bioc-devel] role of replaceSlots in BiocGenerics

2017-09-06 Thread Hervé Pagès
On 09/06/2017 03:53 PM, Hervé Pagès wrote: One of the reasons it's not exported is because it started as something kind of experimental and we didn't find a good home for it yet. I could probably move it to S4Vectors where we already have some low-level S4-related utils. Not the best home either

Re: [Bioc-devel] role of replaceSlots in BiocGenerics

2017-09-06 Thread Hervé Pagès
On 09/06/2017 03:51 PM, Michael Lawrence wrote: On Wed, Sep 6, 2017 at 2:23 PM, Hervé Pagès wrote: Hi, Personally I like replaceSlots() better. Not only because it's more readable but also the fact that you can use initialize() to update an existing object is an undocumented feature so I pref