Dear Bioc developers,
I recently had a package accepted that passed the build system during review.
One week after acceptance, there were compilation problems on Windows. In the
next build, the problems disappeared. Now, they're back again:
http://bioconductor.org/checkResults/devel/bioc-LATEST
Dear Bioc developers,
I am currently working on a package for network analysis, and one of the main
functions takes a long time to run in real data sets. Rewriting it in Julia
leads to a dramatic reduction in runtime, so I think it could be a feasible
solution.
I know there are some guidelines
ub.io
De: Spencer Nystrom
Enviado: terça-feira, 24 de agosto de 2021 09:19
Para: Fabricio de Almeida
Cc: Hervé Pagès ; bioc-devel@r-project.org
Assunto: Re: [Bioc-devel] External dependencies and reproducibility in all
platforms
Hi Fabricio,
For another bit of practical advic
/UENF -
RJ/Brazil)
Personal website: https://almeidasilvaf.github.io
De: Hervé Pagès
Enviado: segunda-feira, 23 de agosto de 2021 19:49
Para: Fabricio de Almeida ;
bioc-devel@r-project.org
Assunto: Re: [Bioc-devel] External dependencies and reproducibility in
(LQFPP/CBB/UENF -
RJ/Brazil)
Personal website: https://almeidasilvaf.github.io
De: Hervé Pagès
Enviado: segunda-feira, 23 de agosto de 2021 18:53
Para: Fabricio de Almeida ;
bioc-devel@r-project.org
Assunto: Re: [Bioc-devel] External dependencies and
: https://almeidasilvaf.github.io
De: Hervé Pagès
Enviado: segunda-feira, 23 de agosto de 2021 16:57
Para: Fabricio de Almeida ;
bioc-devel@r-project.org
Assunto: Re: [Bioc-devel] External dependencies and reproducibility in all
platforms
Hi Fabricio,
If your
Dear Bioc developers,
I am writing a package that contains external dependencies, and I'd like to
know what are the best practices to submit this kind of package to Bioconductor.
The external dependencies are standard RNA-seq analysis algorithms, such as
SRAtoolkit, STAR and salmon. I have seen
Dear Bioc developers,
I submitted a package 3 days ago and the build report returned TIMEOUT for
Windows and macOS.
Then I included donttest{} in the example for a function that was taking too
long to run, but now it is returning ERROR
(http://bioconductor.org/spb_reports/cageminer_buildrepor
CNPq: http://lattes.cnpq.br/3119358824056108
Personal website: https://almeidasilvaf.github.io/home/
De: Vincent Carey
Enviado: segunda-feira, 5 de julho de 2021 07:56
Para: Fabricio de Almeida
Cc: bioc-devel@r-project.org
Assunto: Re: [Bioc-devel] Package did
Hi, all.
I pushed a simple bug fix to my package BioNERO on Friday, but the Bioc page
still shows "Updated before release" (see
https://bioconductor.org/packages/release/bioc/html/BioNERO.html). I know it
can take up to 48 hours for the changes to be visible, but I pushed more than
48 hours ag
rent Gatto
Enviado: quinta-feira, 1 de julho de 2021 12:32
Para: Fabricio de Almeida ;
bioc-devel@r-project.org
Assunto: Re: Question on copyright in Bioc vignette
Dear Fabrício,
As far as I know, there's no explicit license on the documentation of a
package, and I'm not sure the
Hi, all.
I am writing a vignette for a package I plan to submit next week, and I would
like to include a figure explaining the package's algorithm. However, I would
also like to include this figure in the paper that describes the package. Does
anyone know if including the same figure in the vig
Tiphaine, did you remember to bump package version in your DESCRIPTION file
after making the changes?
=
Fabr�cio de Almeida Silva
Undergraduate degree in Biological Sciences (UENF)
MSc. candidate in Plant Biotechnology (PGBV/UENF - RJ/Brazil)
Laborat�rio de Qu�mica e
Hi, all.
I have recently had a problem with my machine and I had to format it, but I
didn't copy my SSH key. Now, I am using a different machine and I want to push
bug fixes in my package to Bioc. I have already pushed it my GitHub repo, but I
couldn't push to Bioc. Do I have to create a new SS
-
RJ/Brazil)
Lattes CNPq: http://lattes.cnpq.br/3119358824056108
Personal website: https://almeidasilvaf.github.io/home/
De: Kern, Lori
Enviado: quarta-feira, 5 de maio de 2021 13:59
Para: Fabricio de Almeida ;
bioc-devel@r-project.org
Assunto: Re: Fixing build
Hi, all.
I've noticed that my package has returned an error in the Bioc build
(https://bioconductor.org/packages/devel/bioc/html/BioNERO.html). As it was
accepted last month and this will be my first change to the package after
acceptance, I would like to check some things:
1. Can I change
cnpq.br/3119358824056108
Personal website:
https://almeidasilvaf.github.io/home/<https://almeidasilvaf.github.io/almeida-silvaf/>
____
De: Bioc-devel em nome de Fabricio de
Almeida
Enviado: quarta-feira, 3 de março de 2021 07:45
Para: bioc-devel
Assunto: [Bioc-dev
Hi, all.
I am testing my package on Windows, Linux and MacOS with GitHub Actions using
biocthis. The package passes all checks with devtools::check(vignettes=FALSE)
followed by BiocCheck::BiocCheck(), but when I build the vignettes, it exceeds
the maximum package size.
On building with devtool
Hi all,
I will submit a package to Bioconductor in the next few days, but I would like
to know the submission deadline for my package to be included in the next Bioc
release.
Last year, new Bioconductor versions were released on April 28 and October 28.
What about this year? I searched it ever
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