Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

May 3, 2023 at 11:13 AM To: Dirk Eddelbuettel Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package Thank you, Dirk. I see your dependencies are Suggested. I know that Suggested dependencies should be condit

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

On 4 May 2023 at 09:00, Simon Urbanek wrote: | > On May 4, 2023, at 3:36 AM, Martin Morgan wrote: | > CRAN is fine with Bioconductor Depends: and Imports: dependencies, as previously mentioned. This is because the CRAN maintainers explicitly configure their system to know about Bioconductor pa

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

t; 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-devel@r-project.org > Betreff: Re: [R-pkg-devel] How

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

uettel Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package Thank you, Dirk. I see your dependencies are Suggested. I know that Suggested dependencies should be conditional. Do you know if Non-Cran (Bi

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

: 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

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

w to declare Bioconductor Dependencies in the Description File of my R Package On 03/05/2023 9:17 a.m., Ruff, Sergej wrote: Thanks, So is it just necessary for suggested packages. Those and "Enhances" packages, but hardly anyone uses "Enhances". So, is it just good practi

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

ckage-devel@r-project.org Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package Sergej, Please consider: - there are nearly 20k CRAN packages - all of them are mirrored at https://github.com/cran so you can browse - pick any one &

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

Sergej, Please consider: - there are nearly 20k CRAN packages - all of them are mirrored at https://github.com/cran so you can browse - pick any one 'heavy' package you like, Seurat is a good example; there are other examples in geospatial or bioinformatics etc - you can browse

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

ject.org Betreff: Re: AW: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package On 03/05/2023 9:17 a.m., Ruff, Sergej wrote: > Thanks, > > > So is it just necessary for suggested packages. Those and "Enhances" packages, but hardly an

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

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 03/05/2023 8:00 a.m., Ruff, Sergej wrote: ... [ lines about current solution deleted ] Also for the future - how Do i provide Bioconduct

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package On 03/05/2023 8:00 a.m., Ruff, Sergej wrote: ... [ lines about current solution deleted ] > Also for the future - how Do i provide Bioconductor dependencies as "Imports" > for

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

On 03/05/2023 8:00 a.m., Ruff, Sergej wrote: ... [ lines about current solution deleted ] Also for the future - how Do i provide Bioconductor dependencies as "Imports" for a package that I want to submit to CRAN? Just list it as you would a CRAN package. The CRAN docs talk about "mainstr

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

sure that the Bioconductor dependencies dont cause a rejection from CRAN? Best Regards, Sergej ____________ Von: Ivan Krylov Gesendet: Montag, 20. M�rz 2023 21:08:38 An: Ruff, Sergej Cc: r-package-devel@r-project.org Betreff: Re: [R-pkg-devel] How to declare Bioconductor Depend

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

On Mon, 20 Mar 2023 19:32:03 + "Ruff, Sergej" wrote: > but I thought Notes will also cause rejection when submitting a > package to CRAN. Won´t that be a problem? True, a NOTE during an automatic check may cause a rejection, but you won't get this NOTE there. Automatic CRAN pre-tests are don

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

: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: &

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: > > > "Package suggested but not available for checking: 'limma'". > > > Seems like the functions isnt installing limma. > > Is there something I am missing? No, this is exactly

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

z 2023 17:36:47 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 Hi, My package pliman depends on EBImage which is in Bioconductor. I have created a function check_ebi() <https://g

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

-- From: R-package-devel on behalf of Ruff, Sergej Sent: Friday, March 17, 2023 22:29 To: Simon Urbanek Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Packag

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

kage-devel on behalf of Ruff, Sergej Sent: Friday, March 17, 2023 22:29 To: Simon Urbanek Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package thank, I was wondering if my idea regarding the imple

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

e-devel on behalf of Ruff, Sergej Sent: Friday, March 17, 2023 22:29 To: Simon Urbanek Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package thank, I was wondering if my idea regarding the implementation i

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

Von: Simon Urbanek Gesendet: Freitag, 17. M�rz 2023 22:05:00 An: Ruff, Sergej Cc: Duncan Murdoch; Martin Morgan; Ivan Krylov; r-package-devel@r-project.org Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package Packages can

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

Packages can only be installed from the repositories listed and only CRAN is the default so only CRAN package are guaranteed to work. I'd like to add that the issue below is exactly why, personally, I would not recommend using Bioconductor package as strong dependency (imports/depends), because

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

package", "Functions > for", package name, title or similar. > ------- > > > Duncan Murdoch > >> >> >> Thats the source of my worries. Will the same error appear when CRAN >> checks the examples of my package? Or should I not be worried? &g

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

*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 File of my R Package On 17/03/2023 6:19 a.m.

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

В Fri, 17 Mar 2023 12:29:51 + "Ruff, Sergej" пишет: > The problem is that a local installation of my package (via USB-stick > for example) can´t install the dependencies from CRAN. > > The package works perfectly fine, if the dependencies are > preinstalled. This is a similar, but different

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

: Martin Morgan Gesendet: Donnerstag, 16. M�rz 2023 20:12:51 An: Ivan Krylov; 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 I would not follow the instructions in RTIGER�s README for inst

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

dependencies would install automatically 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 Biocondu

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

__ Von: Ivan Krylov Gesendet: Freitag, 17. März 2023 12:31:23 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 11:02:18 + "Ruff, Sergej" пишет: I w

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

Ivan Krylov Date: Thursday, March 16, 2023 at 2:15 PM To: Ruff, Sergej Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package On Thu, 16 Mar 2023 17:01:55 + "Ruff, Sergej" wrote: Last que

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

ge-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 11:02:18 + "Ruff, Sergej" пишет: > I would like to ask, if I need to add something to the > DESCRIPTION-file when declaring Biocondu

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

В Fri, 17 Mar 2023 11:02:18 + "Ruff, Sergej" пишет: > I would like to ask, if I need to add something to the > DESCRIPTION-file when declaring Bioconductor dependencies for CRAn > Submission. Strictly speaking, no. Once you list limma under Suggests, it's possible and proper to install your

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

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 + "Ruff, Sergej" пишет: > Thats the source

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 + "Ruff, Sergej" пишет: > Thats the source of my worries. Will the same error appear when CRAN > checks the examples of my package? Or should I not be worried? Yes, part of CRAN checks is running your package without the packages listed under Suggests: https://www

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

. 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

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

old� Bioconductor version, even when a newer version is available. From: R-package-devel on behalf of Ivan Krylov Date: Thursday, March 16, 2023 at 2:15 PM To: Ruff, Sergej Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Descriptio

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

-project.org Betreff: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package I would not follow the instructions in RTIGER�s README for installing Bioconductor packages. BiocManager::install(�RTIGER�) would install both CRAN and Bioconductor dependencies

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

lable. From: R-package-devel on behalf of Ivan Krylov Date: Thursday, March 16, 2023 at 2:15 PM To: Ruff, Sergej Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package On Thu, 16 Mar 2023 17:01:55 + &

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

On Thu, 16 Mar 2023 17:01:55 + "Ruff, Sergej" wrote: > Last question: How does CRAN work with Bioconductor Dependencies? > Will CRAN accept limma as a dependency or will my submission be > rejected? It's not explicitly spelled out in the CRAN policy

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

Thanks Duncan, I'm in the way of a new CRAN submission and I will make sure to call check_ebi() in the body of each function. This should ensure that the check for EBImage will be called even with pliman::object_edge( ... ), for example. Best regards, Olivoto Em qui., 16 de mar. de 2023 às 14:15,

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

> Best regards, > > Sergej > -- > *Von:* Tiago Olivoto > *Gesendet:* Donnerstag, 16. März 2023 17:36:47 > *An:* Ruff, Sergej > *Cc:* r-package-devel@r-project.org > *Betreff:* Re: [R-pkg-devel] How to declare Bioconductor Dependencies in >

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

On 16/03/2023 12:36 p.m., Tiago Olivoto wrote: Hi, My package pliman depends on EBImage which is in Bioconductor. I have created a function check_ebi() < https://github.com/TiagoOlivoto/pliman/blob/e6efc4b6a2396600939e308c235aeb9ab47af375/R/utilities.R#L534> that is called in .onAttach() < https:

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

to declare Bioconductor Dependencies in the Description File of my R Package Hi, My package pliman depends on EBImage which is in Bioconductor. I have created a function check_ebi() <https://github.com/TiagoOlivoto/pliman/blob/e6efc4b6a2396600939e308c235aeb9ab47af375/R/utilities.R#L534>

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

Hi, My package pliman depends on EBImage which is in Bioconductor. I have created a function check_ebi() < https://github.com/TiagoOlivoto/pliman/blob/e6efc4b6a2396600939e308c235aeb9ab47af375/R/utilities.R#L534> that is called in .onAttach() < https://github.com/TiagoOlivoto/pliman/blob/master/R/zz

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

В Thu, 16 Mar 2023 11:09:16 + "Ruff, Sergej" пишет: > The Check-Function in R shows no Notes, Warnings or Errors, but I am > not sure if that means that limma will install when installing my > package from CRAN. > Currently I am declaring limma like this: > > Suggests: > > limma insta

[R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

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, but