. März 2023 11:14:25
An: Ruff, Sergej; Martin Morgan; Ivan Krylov
Cc: r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the
Description File of my R Package
On 17/03/2023 6:06 a.m., Ruff, Sergej wrote:
> I was wondering how CRAN will handle Limma w
description, not inside my
actual function.
How would CRAN�s System handle that when checking my package for submission?
with regards,
Sergej
Von: Martin Morgan
Gesendet: Donnerstag, 16. M�rz 2023 20:12:51
An: Ivan Krylov; Ruff, Sergej
Cc: r-package-devel@r
from CRAN? Is that
not the case?
Von: Duncan Murdoch
Gesendet: Freitag, 17. März 2023 13:15:28
An: Ruff, Sergej; Martin Morgan; Ivan Krylov
Cc: r-package-devel@r-project.org
Betreff: Re: AW: [R-pkg-devel] How to declare Bioconductor Dependencies in the
Description Fi
that issue.
Thank you for your help.
Regards,
Sergej
Von: Duncan Murdoch
Gesendet: Freitag, 17. März 2023 13:48:21
An: Ruff, Sergej; Martin Morgan; Ivan Krylov
Cc: r-package-devel@r-project.org
Betreff: Re: AW: AW: [R-pkg-devel] How to declare Bioconductor
Thanks,
I thought about changing it to "Imports", but will it cause any issues when
CRAN runs checks on my package and limma isn´t available on CRAN?
Von: Ivan Krylov
Gesendet: Freitag, 17. März 2023 12:31:23
An: Ruff, Sergej
Cc: r-packa
van Krylov
Gesendet: Freitag, 17. März 2023 11:45:57
An: Ruff, Sergej
Cc: r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the
Description File of my R Package
В Fri, 17 Mar 2023 10:19:37 +0000
"Ruff, Sergej" пишет:
> Thats t
al expression analysis with limma
check_limma()
group = gl(2, n)
design = model.matrix(~ group)
fit1 = limma::lmFit(X, design)
fit = limma::eBayes(fit1)
I tried running the R CMD Check but I keep getting 1 error and note.
Is the implementation incorrect?
regards, Sergej
__
:58
An: Ruff, Sergej
Cc: r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the
Description File of my R Package
В Mon, 20 Mar 2023 08:38:41 +
"Ruff, Sergej" пишет:
> When Limma is üre-installed, I get the following Note:
&
iocManager and limma to the suggests
and utils to Imports.
Regards,
Sergej
Von: Ruff, Sergej
Gesendet: Samstag, 18. März 2023 09:56:55
An: Berry Boessenkool; Simon Urbanek
Cc: r-package-devel@r-project.org
Betreff: AW: [R-pkg-devel] How to declare Bioconductor De
quiet=TRUE)
return(TRUE)
}
The check also never brings up the menu to ask me, if limma should be
installed. Is that normal or should I change something about the
function.
Regards,
Sergej
________
Von: Tiago Olivoto
Gesendet: Donnerstag, 16. M�rz 2023 17:36:47
An: Ruff,
thank you, berry for your idea.
Von: Berry Boessenkool
Gesendet: Samstag, 18. März 2023 09:54:45
An: Ruff, Sergej; Simon Urbanek
Cc: r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the
Description File of my R
I am currently building a package which uses the "limma"-package as a
dependency.
I want to submit my package to CRAN.
Do I need to declare Bioconductor-dependencies such as Limma differently in the
Description-File of my Package?
The Check-Function in R shows no Notes, Warnings or Errors,
with Bioconductor Dependencies? Will CRAN
accept limma as a dependency or will my submission be rejected?
Best regards,
Sergej
Von: Tiago Olivoto
Gesendet: Donnerstag, 16. M�rz 2023 17:36:47
An: Ruff, Sergej
Cc: r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] How
onductor dependencies as "Imports"
for a package that I want to submit to CRAN?
Do I need to make that also conditional? I know I should provide Installation
description in a readme fiel but how do I make sure
that the Bioconductor dependencies dont cause a rejection from CRAN?
for packagecheck) in the Seurat.package
(https://cran.r-project.org/src/contrib/Archive/Seurat/)
or for limma (starting line 2292).
Von: Duncan Murdoch
Gesendet: Mittwoch, 3. Mai 2023 14:25:56
An: Ruff, Sergej; Ivan Krylov
Cc: r-package-devel@r-project.org
Betreff
s to check if the package is pre-installed or not. Wouldn't
that make the packagecheck function used by Seurat redundant?
Sergej Ruff
Von: Duncan Murdoch
Gesendet: Mittwoch, 3. Mai 2023 15:29:34
An: Ruff, Sergej; Ivan Krylov
Cc: r-package-devel@r-project.org
B
: Duncan Murdoch
Gesendet: Mittwoch, 3. Mai 2023 17:25:15
An: Ruff, Sergej; Ivan Krylov
Cc: r-package-devel@r-project.org
Betreff: Re: AW: AW: [R-pkg-devel] How to declare Bioconductor Dependencies in
the Description File of my R Package
On 03/05/2023 9:50 a.m., Ruff, Sergej wrote:
> I took the Seu
Murdoch's experience and opinion regarding that topic, but i
take any second and third opinion to be sure.
Thank you for your help.
Sergej
Von: Dirk Eddelbuettel
Gesendet: Mittwoch, 3. Mai 2023 16:22:09
An: Ruff, Sergej
Cc: Duncan Murdoch; Ivan Krylov; r-package
.
Von: Ruff, Sergej
Gesendet: Donnerstag, 7. März 2024 17:56:20
An: Hadley Wickham
Cc: r-package-devel@r-project.org
Betreff: AW: [EXTERN] Re: [R-pkg-devel] @doctype is deprecated. need help for r
package documentation
the package is currently available under:
https
the first place.
Von: Jeff Newmiller
Gesendet: Donnerstag, 7. März 2024 20:57:58
An: r-package-devel@r-project.org; Ruff, Sergej; Hadley Wickham
Cc: r-package-devel@r-project.org
Betreff: [EXTERN] Re: [R-pkg-devel] [EXTERN] Re: @doctype is deprecated. need
help for
Hello,
I need help with a package I am currently developing called bootGSEA.
I noticed that when I try �?bootGSEA� it goes to the help page in R itself but
not to the html page (we had this issue last time as well but we solved it by
adding a documentation to the package itself to the R file)
ess evaluation of gene set enrichment analysis (GSEA)
#' @keywords Robustness GSEA
"_PACKAGE"
Von: Hadley Wickham
Gesendet: Donnerstag, 7. März 2024 16:02:15
An: Ruff, Sergej
Cc: r-package-devel@r-project.org
Betreff: [EXTERN] Re: [R-pkg-devel] @doctype
yes.
I apologize it took so long to reply.
I uploaded the old version of the package to my repo:
https://github.com/SergejRuff/boot
Von: Ivan Krylov
Gesendet: Freitag, 8. März 2024 08:36:43
An: Ruff, Sergej
Cc: r-package-devel@r-project.org
Betreff: [EXTERN
Hello,
I was wondering if its possible to link the toturial site for a package on the
CRAN Cite to the package?
I want to publish the next version of our package.
The CRAN site
(https://cran.r-project.org/web/packages/RepeatedHighDim/index.html) has a
"documentation" part with the refrence
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