[R-pkg-devel] Linking Tutorial Site to CRAN Package site.
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 pdf. Can I link to our tutorial site (https://software.klausjung-lab.de/.) under documentation? Sergej [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [EXTERN] Re: [EXTERN] Re: [EXTERN] Re: @doctype is deprecated. need help for r package documentation
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] Re: [R-pkg-devel] [EXTERN] Re: [EXTERN] Re: @doctype is deprecated. need help for r package documentation В Thu, 7 Mar 2024 20:27:29 + "Ruff, Sergej" пишет: > I am refering to Rstudio. I checked the settings and type is set to > "htlm", not text. And I was wondering why the package documentation > opened in a browser when I used @doctype. Do you still have the source package .tar.gz file for which ?bootGSEA would start a browser from inside RStudio? -- Best regards, Ivan [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] [EXTERN] Re: [EXTERN] Re: @doctype is deprecated. need help for r package documentation
yes,
I am refering to Rstudio. I checked the settings and type is set to "htlm", not
text. And I was wondering why the package documentation opened in a browser
when I used @doctype. Maybe it has nothing to do with that but I can´t find the
reason why it opened in the browser in 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 r package documentation
What is a "right side window"? Are you mixing up what R does and what RStudio
does? I think I agree with Ivan that this is a question about the environment
in which you are loading the package rather than anything in the package itself.
On March 7, 2024 11:21:06 AM PST, "Ruff, Sergej"
wrote:
>So, in the previous version of the package when we type ?bootGSEA, it opens
>the documentation in webpage (google, firefox…) and when we type ?pkg-function
>opens to the right side window, but now it just opens in the right side
>window. I was wondering why does it not open in webpage now.
>
>____
>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://github.com/klausjung-hannover/bootGSEA/blob/main/R/bootGSEA.r
>
>
>line 1-31 contains the package information.
>
>
>#' Package contains functions that repeates GSEA using bootstrap samples of
>gene sets. Bootstrap results are
>#' aggregated to a new ranking score. The score can be compared to the gene set
>#' ranking resulting from the standard GSEA.
>#'
>#' So far the functions included in the package are:
>#' \itemize{
>#' \item \code{\link{aggr.boot.GO}} Aggregate boostrap GO analysis
>#' \item \code{\link{aggr.boot.Pathway}} Write a \code{genind} Aggregate
>boostrap pathway analysis
>#' \item \code{\link{aggr.multiomics}} Multiomics Integration analysis
>#' \item \code{\link{boot.GO}} Bootstrap GO analysis
>#' \item \code{\link{boot.pathway}} Bootstrap Pathway analysis
>#' \item \code{\link{compareRank}} Visualisation of bootstrap GO analyses
>#' \item \code{\link{histDiff}} Visualization of difference in ranks
>#' \item \code{\link{plotRank}} Visualisation of bootstrap pathway analyses
>#' }
>#'
>#' \tabular{ll}{
>#' Package: \tab bootGSEA\cr
>#' Type: \tab Package\cr
>#' Version: \tab 1.0\cr
>#' Date: \tab 2024-03-05\cr
>#' License: \tab GPL (>= 3)\cr
>#' }
>#'
>#' @author Shamini Hemandhar Kumar, Klaus Jung
>(\email{shamini.hemandhar.kumar@@tiho-hannover.de})(\email{klaus.jung@@tiho-hannover.de})
>#'
>#' Maintainer: Shamini Hemandhar Kumar
>(\email{shamini.hemandhar.kumar@@tiho-hannover.de})
>#' @aliases bootGSEA
>#' @title Robustness 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 is deprecated. need help for r
>package documentation
>
>Do you have a pointer to the roxygen2 comments that you're using?
>Hadley
>
>On Thu, Mar 7, 2024 at 5:38 AM Ruff, Sergej
>mailto:sergej.r...@tiho-hannover.de>> wrote:
>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) like from
> the before version of the package.
>I tried “_PACKAGE” in the documentation of the package section as @doctype is
>depreceated, but it still doesn’t seem to solve the issue. Do you have any
>idea on this?
>
>
>[[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org<mailto:R-package-devel@r-project.org> mailing
>list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
>--
>http://hadley.nz
>
> [[alternative HTML version deleted]]
>
>__
>R-package-devel@r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-package-devel
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Sent from my phone. Please excuse my brevity.
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Re: [R-pkg-devel] [EXTERN] Re: @doctype is deprecated. need help for r package documentation
So, in the previous version of the package when we type ?bootGSEA, it opens
the documentation in webpage (google, firefox…) and when we type ?pkg-function
opens to the right side window, but now it just opens in the right side window.
I was wondering why does it not open in webpage now.
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://github.com/klausjung-hannover/bootGSEA/blob/main/R/bootGSEA.r
line 1-31 contains the package information.
#' Package contains functions that repeates GSEA using bootstrap samples of
gene sets. Bootstrap results are
#' aggregated to a new ranking score. The score can be compared to the gene set
#' ranking resulting from the standard GSEA.
#'
#' So far the functions included in the package are:
#' \itemize{
#' \item \code{\link{aggr.boot.GO}} Aggregate boostrap GO analysis
#' \item \code{\link{aggr.boot.Pathway}} Write a \code{genind} Aggregate
boostrap pathway analysis
#' \item \code{\link{aggr.multiomics}} Multiomics Integration analysis
#' \item \code{\link{boot.GO}} Bootstrap GO analysis
#' \item \code{\link{boot.pathway}} Bootstrap Pathway analysis
#' \item \code{\link{compareRank}} Visualisation of bootstrap GO analyses
#' \item \code{\link{histDiff}} Visualization of difference in ranks
#' \item \code{\link{plotRank}} Visualisation of bootstrap pathway analyses
#' }
#'
#' \tabular{ll}{
#' Package: \tab bootGSEA\cr
#' Type: \tab Package\cr
#' Version: \tab 1.0\cr
#' Date: \tab 2024-03-05\cr
#' License: \tab GPL (>= 3)\cr
#' }
#'
#' @author Shamini Hemandhar Kumar, Klaus Jung
(\email{shamini.hemandhar.kumar@@tiho-hannover.de})(\email{klaus.jung@@tiho-hannover.de})
#'
#' Maintainer: Shamini Hemandhar Kumar
(\email{shamini.hemandhar.kumar@@tiho-hannover.de})
#' @aliases bootGSEA
#' @title Robustness 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 is deprecated. need help for r
package documentation
Do you have a pointer to the roxygen2 comments that you're using?
Hadley
On Thu, Mar 7, 2024 at 5:38 AM Ruff, Sergej
mailto:sergej.r...@tiho-hannover.de>> wrote:
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) like from the
before version of the package.
I tried “_PACKAGE” in the documentation of the package section as @doctype is
depreceated, but it still doesn’t seem to solve the issue. Do you have any idea
on this?
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org<mailto:R-package-devel@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
http://hadley.nz
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Re: [R-pkg-devel] [EXTERN] Re: @doctype is deprecated. need help for r package documentation
the package is currently available under:
https://github.com/klausjung-hannover/bootGSEA/blob/main/R/bootGSEA.r
line 1-31 contains the package information.
#' Package contains functions that repeates GSEA using bootstrap samples of
gene sets. Bootstrap results are
#' aggregated to a new ranking score. The score can be compared to the gene set
#' ranking resulting from the standard GSEA.
#'
#' So far the functions included in the package are:
#' \itemize{
#' \item \code{\link{aggr.boot.GO}} Aggregate boostrap GO analysis
#' \item \code{\link{aggr.boot.Pathway}} Write a \code{genind} Aggregate
boostrap pathway analysis
#' \item \code{\link{aggr.multiomics}} Multiomics Integration analysis
#' \item \code{\link{boot.GO}} Bootstrap GO analysis
#' \item \code{\link{boot.pathway}} Bootstrap Pathway analysis
#' \item \code{\link{compareRank}} Visualisation of bootstrap GO analyses
#' \item \code{\link{histDiff}} Visualization of difference in ranks
#' \item \code{\link{plotRank}} Visualisation of bootstrap pathway analyses
#' }
#'
#' \tabular{ll}{
#' Package: \tab bootGSEA\cr
#' Type: \tab Package\cr
#' Version: \tab 1.0\cr
#' Date: \tab 2024-03-05\cr
#' License: \tab GPL (>= 3)\cr
#' }
#'
#' @author Shamini Hemandhar Kumar, Klaus Jung
(\email{shamini.hemandhar.kumar@@tiho-hannover.de})(\email{klaus.jung@@tiho-hannover.de})
#'
#' Maintainer: Shamini Hemandhar Kumar
(\email{shamini.hemandhar.kumar@@tiho-hannover.de})
#' @aliases bootGSEA
#' @title Robustness 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 is deprecated. need help for r
package documentation
Do you have a pointer to the roxygen2 comments that you're using?
Hadley
On Thu, Mar 7, 2024 at 5:38 AM Ruff, Sergej
mailto:sergej.r...@tiho-hannover.de>> wrote:
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) like from the
before version of the package.
I tried “_PACKAGE” in the documentation of the package section as @doctype is
depreceated, but it still doesn’t seem to solve the issue. Do you have any idea
on this?
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org<mailto:R-package-devel@r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
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[R-pkg-devel] @doctype is deprecated. need help for r package documentation
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) like from the before version of the package. I tried �_PACKAGE� in the documentation of the package section as @doctype is depreceated, but it still doesn�t seem to solve the issue. Do you have any idea on this? [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
my bad, I looked at the DESCRIPTIOn fiel again. I assumed that Cluster was a Bioconductor package. I also didn�t see that DeSeq2 was in Suggests. I will follow your advice and try using Bioconductor packages without a conditional function. Sergej Von: 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 Seurat package as an example, because it both lists the > Bioconductor Dependencies under Imports in the DESCRIPTION-File Which packages are you talking about? I don't see any BioConductor dependencies in the Imports list for the current Seurat version. Duncan Murdoch > > and it uses conditional functions to check if those dependencies are > pre-installed. > > > "No, it is a requirement if the package is used but is not listed in > Depends or Imports. > > If the package is in Depends or Imports it is a waste of time to make > the check: it will always succeed." > > > that's what I also thought but I am confused why a package like Seurat > then lists the dependencies in the DESCRIPTION-File and on top of that uses > > conditional functions 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 > *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 anyone uses "Enhances". >> >> >> So, is it just good practice to make a conditional check? > > No, it is a requirement if the package is used but is not listed in > Depends or Imports. > > If the package is in Depends or Imports it is a waste of time to make > the check: it will always succeed. > >> I saw some packages still include it. >> >> >> For example the Seurat package. >> > I don't understand your question here. > > Duncan Murdoch > >> >> Under Utils.R (line 349-379) of the SeuratObject-Package >> (https://cran.r-project.org/src/contrib/Archive/SeuratObject/ >> <https://cran.r-project.org/src/contrib/Archive/SeuratObject/ > <https://cran.r-project.org/src/contrib/Archive/SeuratObject/>>) you will >> find the PackageCheck-function >> >> which used by the Seurat-Package >> (https://cran.r-project.org/src/contrib/Archive/Seurat/ >> <https://cran.r-project.org/src/contrib/Archive/Seurat/ > <https://cran.r-project.org/src/contrib/Archive/Seurat/>>) to check if >> packages are alredy installed. >> >> >> You can find examples for DEseq2 under differential_expression.R >> (starting line 1314 or you cntr+f for packagecheck) in >> the Seurat.package >> (https://cran.r-project.org/src/contrib/Archive/Seurat/ >> <https://cran.r-project.org/src/contrib/Archive/Seurat/ > <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:* 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 >> "mainstream repositories"; I forget what the definition is of that >> (maybe repositories listed in `file.path(R.home(), >> "etc/repositories")`?), but definitely BioConductor is included. >> >>> 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 >> >> No, you don't need to check. If any imported package is not available, >> your package will not load, so errors will happen before you ever get to >> running examples. >> >>> that the Bioconductor dependencies dont cause a rejection from CRAN? >> >> Just make sure they exist on BioC and your code works with them. >> >> Duncan Murdoch >> > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
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 (Bioconductor) packages need to be conditional? Do you
have any experiece regarding Non-CRAN Dependencies
and how to handle them?
I believe Duncan 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-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 'heavy' package you like, Seurat is a good example; there
are other examples in geospatial or bioinformatics etc
- you can browse _and search_ these to your hearts content
Here is an example of mine. In RcppArmadillo, years ago we (thanks to fine
Google Summer of Code work by Binxiang Ni) added extended support for sparse
matrices pass-through / conversione from R to C++ / Armadillo and back. That
is clearly an optional feature as most uses of (Rcpp)Armadillo use dense
matrices. So all code and test code is _conditional_. File DESCRIPTION has
Suggests: [...], Matrix (>= 1.3.0), [...], reticulate, slam
mostly for tests. I.e. We have very little R code: in one single file
R/SciPy2R.R we switched to doing this via reticulate and opee the function
with
if (!requireNamespace("reticulate", quietly=TRUE)) {
stop("You must install the 'reticulate' package (and have SciPy).",
call.=FALSE)
}
after an actual deprecation warning (as there was scipy converter once).
Similarly, the testsuites in inst/tinytests/* have several
if (!requireNamespace("Matrix", quietly=TRUE)) exit_file("No Matrix
package")
as well as
if (!requireNamespace("reticulate", quietly=TRUE)) exit_file("Package
reticulate missing")
if (!packageVersion("reticulate") >= package_version("1.14"))
exit_file("SciPy not needed on newer reticulate")
and tests for slam (another sparse matrix package besides the functionality
in Matrix).
Hopefully this brief snapshot gives you an idea. There are (likely!!)
thousandss of examples you can browse, and I am sure you will find something.
If you have further (concrete) questions please do not hesitate to use the
resource of this list.
Cheers (or I should say "mit Braunschweiger Gruessen nach Hannover),
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
I took the Seurat package as an example, because it both lists the Bioconductor Dependencies under Imports in the DESCRIPTION-File and it uses conditional functions to check if those dependencies are pre-installed. "No, it is a requirement if the package is used but is not listed in Depends or Imports. If the package is in Depends or Imports it is a waste of time to make the check: it will always succeed." that's what I also thought but I am confused why a package like Seurat then lists the dependencies in the DESCRIPTION-File and on top of that uses conditional functions 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 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 anyone uses "Enhances". > > > So, is it just good practice to make a conditional check? No, it is a requirement if the package is used but is not listed in Depends or Imports. If the package is in Depends or Imports it is a waste of time to make the check: it will always succeed. > I saw some packages still include it. > > > For example the Seurat package. > I don't understand your question here. Duncan Murdoch > > Under Utils.R (line 349-379) of the SeuratObject-Package > (https://cran.r-project.org/src/contrib/Archive/SeuratObject/ > <https://cran.r-project.org/src/contrib/Archive/SeuratObject/>) you will > find the PackageCheck-function > > which used by the Seurat-Package > (https://cran.r-project.org/src/contrib/Archive/Seurat/ > <https://cran.r-project.org/src/contrib/Archive/Seurat/>) to check if > packages are alredy installed. > > > You can find examples for DEseq2 under differential_expression.R > (starting line 1314 or you cntr+f for packagecheck) in > the Seurat.package > (https://cran.r-project.org/src/contrib/Archive/Seurat/ > <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:* 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 > "mainstream repositories"; I forget what the definition is of that > (maybe repositories listed in `file.path(R.home(), > "etc/repositories")`?), but definitely BioConductor is included. > >> 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 > > No, you don't need to check. If any imported package is not available, > your package will not load, so errors will happen before you ever get to > running examples. > >> that the Bioconductor dependencies dont cause a rejection from CRAN? > > Just make sure they exist on BioC and your code works with them. > > Duncan Murdoch > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
Thanks, So is it just necessary for suggested packages. So, is it just good practice to make a conditional check? I saw some packages still include it. For example the Seurat package. Under Utils.R (line 349-379) of the SeuratObject-Package (https://cran.r-project.org/src/contrib/Archive/SeuratObject/) you will find the PackageCheck-function which used by the Seurat-Package (https://cran.r-project.org/src/contrib/Archive/Seurat/) to check if packages are alredy installed. You can find examples for DEseq2 under differential_expression.R (starting line 1314 or you cntr+f 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: 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 "mainstream repositories"; I forget what the definition is of that (maybe repositories listed in `file.path(R.home(), "etc/repositories")`?), but definitely BioConductor is included. > 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 No, you don't need to check. If any imported package is not available, your package will not load, so errors will happen before you ever get to running examples. > that the Bioconductor dependencies dont cause a rejection from CRAN? Just make sure they exist on BioC and your code works with them. Duncan Murdoch [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
I implemented teh limma Bioconductor dependency into the Suggests file and made
it conditionally
Meaning I provided the Description File with
Suggests:
BiocManager,
limma
and created a short function which checks if limma is available
#' Check for package dependency
#'
#' @title Check for 'limma' availability
#' @description checks if the 'limma' package is installed. If not already
installed,
#' limma will be installed automatically.
#' @author Sergej Ruff
#' @importFrom utils install.packages menu
#' @export
#' @keywords internal
check_limma <- function() # Returns TRUE if available, FALSE otherwise
{
if(requireNamespace("limma", quietly=TRUE)) return(TRUE)
if(!interactive()) return(FALSE)
inst <- menu(c("Yes", "No"), title="Package {limma} required but not
installed.\nDo you want to install it now?")
if(inst != 1)
{
message("To run this example, first install {limma} following the
directions at 'https://bioconductor.org/packages/limma'")
return(FALSE)
}
# the following could be wrapped in try and conditionally return TRUE / FALSE
if(!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager", quiet=TRUE)
BiocManager::install("limma", update=FALSE, ask=FALSE, quiet=TRUE)
return(TRUE)
}
In the example field which uses the limma functions I then implemented the
check-function:
if(check_limma()){
group = gl(2, n)
design = model.matrix(~ group)
fit1 = limma::lmFit(X, design)
fit = limma::eBayes(fit1)
### Calculation of confidence intervals
CI = fc_ci(fit=fit, alpha=0.05, method="raw")
head(CI)
CI = fc_ci(fit=fit, alpha=0.05, method="BH")
head(CI)
CI = fc_ci(fit=fit, alpha=0.05, method="BY")
head(CI)
fc_plot(CI, xlim=c(-0.5, 3), ylim=-log10(c(1, 0.0001)), updown="up")
fc_plot(CI, xlim=c(-3, 0.5), ylim=-log10(c(1, 0.0001)), updown="down")
fc_plot(CI, xlim=c(-3, 3), ylim=-log10(c(1, 0.0001)), updown="all")
}
I don�t get any Errors. Thank you R mailing list for providing the tips.
I just wanted to ask, if theres any other way to implement it, since I have
never seen an example field
which has a check-if dependency is available function.
Is there any Improvments i could make or better methods.
Also for the future - how Do i provide Bioconductor 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?
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 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 done with a
full package set: anything from CRAN and BioConductor that runs on a
given operating system can be loaded.
(This differentiates CRAN from, say, PyPI or NPM: the two latter
ecosystems are much larger and are expected to handle conflicting
dependency requirements. CRAN is small enough to be able to enforce the
rule that every package must play well with the latest version of
everything else.)
There's an additional CRAN check called noSuggests
<https://www.stats.ox.ac.uk/pub/bdr/noSuggests/README.txt>. You will
get a NOTE there, but it's expected and won't count against you. The
only way avoid this NOTE there is to not have any packages in Suggests:
(or Enhances:).
--
Best regards,
Ivan
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Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
thanks,
but I thought Notes will also cause rejection when submitting a package to
CRAN. Won´t that be a problem?
My package isn´t new, so it will most likely only be checked by CRAN´s
automatic system.
Von: Ivan Krylov
Gesendet: Montag, 20. März 2023 12:55:58
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:
>
>
> "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 how it's supposed to behave under R CMD check. The
CRAN policy forbids packages to install other packages ("Packages
should not write in the user’s home filespace <...> nor anywhere else
on the file system") except when the user gives permission to do so
("Limited exceptions may be allowed in interactive sessions if the
package obtains confirmation from the user").
Under R CMD check, interactive() is FALSE because there is no user to
ask permission from, so the function correctly decides not to install
the package. The resulting NOTE is the expected result here. The
important part is that your example doesn't crash because it's unable
to load the limma namespace.
--
Best regards,
Ivan
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
I implemented a function to check if limma is available as suggested by Berry
and Tiago.
It works fine when limma is pre-installed.
When Limma is not pre-installed, I get the following Note:
"Package suggested but not available for checking: 'limma'".
Seems like the functions isn't installing limma.
Is there something I am missing? I added BiocManager and limma to the suggests
and utils to Imports.
check_limma <- function() # Returns TRUE if available, FALSE otherwise
{
if(requireNamespace("limma", quietly=TRUE)) return(TRUE)
if(!interactive()) return(FALSE)
inst <- menu(c("Yes", "No"), title="Package {limma} required but not
installed.\nDo you want to install it now?")
if(inst != 1)
{
message("To run this example, first install {limma} following the
directions at 'https://bioconductor.org/packages/limma'")
return(FALSE)
}
# the following could be wrapped in try and conditionally return TRUE / FALSE
if(!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager", quiet=TRUE)
BiocManager::install("limma", update=FALSE, ask=FALSE, 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, 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://github.com/TiagoOlivoto/pliman/blob/e6efc4b6a2396600939e308c235aeb9ab47af375/R/utilities.R#L534>
that is called in .onAttach()
<https://github.com/TiagoOlivoto/pliman/blob/master/R/zzz.R#L36> and checks if
EBImage is installed. If not, the function asks the user to install it. Both
EBImage and BiocManager are listed as suggests
<https://github.com/TiagoOlivoto/pliman/blob/master/DESCRIPTION#L22>
I believe that this could be a possible solution
Best regards,
Olivoto
Em qui., 16 de mar. de 2023 �s 11:18, Ruff, Sergej
mailto:sergej.r...@tiho-hannover.de>> escreveu:
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 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
Can CRAN identify that limma is a Bioconductor-Package and will it Limma
install, when installing my package from CRAN?
[[alternative HTML version deleted]]
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[[alternative HTML version deleted]]
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Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
I implemented Berrys function.
I works fine when limma is pre-installed.
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? I added BiocManager 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 Dependencies in the
Description File of my R Package
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 Package
I would use conditional returns to make the code more readable (see below) and
then run the examples conditionally.
check_limma <- function() # Returns TRUE if available, FALSE otherwise
{
if(requireNamespace("limma", quietly=TRUE)) return(TRUE)
if(!interactive()) return(FALSE)
inst <- menu(c("Yes", "No"), title="Package {limma} required but not
installed.\nDo you want to install it now?")
if(inst != 1)
{
message("To run this example, first install {limma} following the
directions at 'https://bioconductor.org/packages/limma'")
return(FALSE)
}
# the following could be wrapped in try and conditionally return TRUE / FALSE
if(!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager", quiet=TRUE)
BiocManager::install("limma", update=FALSE, ask=FALSE, quiet=TRUE)
return(TRUE)
}
# In the examples:
if(check_limma()){
group = gl(2, n)
design = model.matrix(~ group)
fit1 = limma::lmFit(X, design)
fit = limma::eBayes(fit1)
}
My 2 cents
Berry
-----
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 Package
thank,
I was wondering if my idea regarding the implementation is correct.
I took the idea from Tiago Olivoto and wrote an additional function that checks
if limma is installed.
Here is a mockup based on Tiago�s package:
check_limma<- function(){
if(!requireNamespace("limma", quietly = TRUE)) {
if(interactive() == TRUE){
inst <-
switch(menu(c("Yes", "No"), title = "Package {limma} required but not
installed.\nDo you want to install it now?"),
"yes", "no")
if(inst == "yes"){
if(!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager", quiet = TRUE)
}
BiocManager::install("limma",
update = FALSE,
ask = FALSE,
quiet = TRUE)
} else{
message("To run this example}, first install {limma} following the
directions at 'https://bioconductor.org/packages/limma'")
}
}
}
}
I would add the check in my example before limma functions are used.
### Differential 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
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 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 that makes
the package unusable for most users, as it cannot be installed (without extra
steps they don't know about) since the dependency doesn't exist on CRAN.
If your users are already Bioconductor users by the virtue of the package
application then they already know so it's fine, but then you are probably
better off to have your package on Bioconductor as part of the ecosystem which
is much more streamlined and coordinated.
If it is only suggested (weak dependency) for some optional functionality, then
your
Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
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 Package
I would use conditional returns to make the code more readable (see below) and
then run the examples conditionally.
check_limma <- function() # Returns TRUE if available, FALSE otherwise
{
if(requireNamespace("limma", quietly=TRUE)) return(TRUE)
if(!interactive()) return(FALSE)
inst <- menu(c("Yes", "No"), title="Package {limma} required but not
installed.\nDo you want to install it now?")
if(inst != 1)
{
message("To run this example, first install {limma} following the
directions at 'https://bioconductor.org/packages/limma'")
return(FALSE)
}
# the following could be wrapped in try and conditionally return TRUE / FALSE
if(!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager", quiet=TRUE)
BiocManager::install("limma", update=FALSE, ask=FALSE, quiet=TRUE)
return(TRUE)
}
# In the examples:
if(check_limma()){
group = gl(2, n)
design = model.matrix(~ group)
fit1 = limma::lmFit(X, design)
fit = limma::eBayes(fit1)
}
My 2 cents
Berry
---------
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 Package
thank,
I was wondering if my idea regarding the implementation is correct.
I took the idea from Tiago Olivoto and wrote an additional function that checks
if limma is installed.
Here is a mockup based on Tiago�s package:
check_limma<- function(){
if(!requireNamespace("limma", quietly = TRUE)) {
if(interactive() == TRUE){
inst <-
switch(menu(c("Yes", "No"), title = "Package {limma} required but not
installed.\nDo you want to install it now?"),
"yes", "no")
if(inst == "yes"){
if(!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager", quiet = TRUE)
}
BiocManager::install("limma",
update = FALSE,
ask = FALSE,
quiet = TRUE)
} else{
message("To run this example}, first install {limma} following the
directions at 'https://bioconductor.org/packages/limma'")
}
}
}
}
I would add the check in my example before limma functions are used.
### Differential 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
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 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 that makes
the package unusable for most users, as it cannot be installed (without extra
steps they don't know about) since the dependency doesn't exist on CRAN.
If your users are already Bioconductor users by the virtue of the package
application then they already know so it's fine, but then you are probably
better off to have your package on Bioconductor as part of the ecosystem which
is much more streamlined and coordinated.
If it is only suggested (weak dependency) for some optional functionality, then
your package will work even if the dependency is not installed so all is well.
And if the optional Bioconductor functionality is used you can direct the user
to instructions explaining that Bioconductor is required for that - but the
package has to do that, it is not anything automatic in R.
Cheers,
Simon
> On Mar 18, 2023, at 1:29 AM, Ruff, Sergej
> wrote:
>
> Really.Whats a problem i have when all dependencies arent prei installed. I
> thought the problem would be solved once my package is available on CRAN.
>
>
> Here is a recent question I had regarding the same issue:
>
>
> I am currently working on a r-package. I would lik
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 is correct.
I took the idea from Tiago Olivoto and wrote an additional function that checks
if limma is installed.
Here is a mockup based on Tiago�s package:
check_limma<- function(){
if(!requireNamespace("limma", quietly = TRUE)) {
if(interactive() == TRUE){
inst <-
switch(menu(c("Yes", "No"), title = "Package {limma} required but not
installed.\nDo you want to install it now?"),
"yes", "no")
if(inst == "yes"){
if(!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager", quiet = TRUE)
}
BiocManager::install("limma",
update = FALSE,
ask = FALSE,
quiet = TRUE)
} else{
message("To run this example}, first install {limma} following the
directions at 'https://bioconductor.org/packages/limma'")
}
}
}
}
I would add the check in my example before limma functions are used.
### Differential 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
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 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 that makes
the package unusable for most users, as it cannot be installed (without extra
steps they don't know about) since the dependency doesn't exist on CRAN.
If your users are already Bioconductor users by the virtue of the package
application then they already know so it's fine, but then you are probably
better off to have your package on Bioconductor as part of the ecosystem which
is much more streamlined and coordinated.
If it is only suggested (weak dependency) for some optional functionality, then
your package will work even if the dependency is not installed so all is well.
And if the optional Bioconductor functionality is used you can direct the user
to instructions explaining that Bioconductor is required for that - but the
package has to do that, it is not anything automatic in R.
Cheers,
Simon
> On Mar 18, 2023, at 1:29 AM, Ruff, Sergej
> wrote:
>
> Really.Whats a problem i have when all dependencies arent prei installed. I
> thought the problem would be solved once my package is available on CRAN.
>
>
> Here is a recent question I had regarding the same issue:
>
>
> I am currently working on a r-package. I would like to submit my r package to
> CRAN, but I have a question regarding dependency installations on CRAN.
>
> I have almost finished my package, added the required dependencies to the
> NAMESPACE and DESCRIPTION files as Imports, and get no errors or warnings
>
> when running the check in Rstudio. The package runs on the pc, where I�ve
> built the package, but when I install the package on a pc, where the
> dependencies
>
> are not preinstalled, I get the following error:
>
> ERROR:
>
> dependencies 'depth', 'geometry' are not available for package 'packagename'
> * removing
> 'C:/Users/156932/AppData/Local/Programs/R/R-4.2.1/library/packagename'
> Warning in install.packages : installation of package �packagename� had
> non-zero exit status
>
>
> 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.
>
> Now I don�t want to submit my package to CRAN if the end user gets the same
> error message when installing my package.
>
> Question: After I submit my package to CRAN, will CRAN install dependencies
> automatically (via "install.packages()"), resolving the issue I have right
> now?
>
> Or do I have to modify the R-package or the Description-file to make sure my
> Package can install dependencies?
>
> I provided the dependencies to the NAMESPACE-file as @ImportFrom via the
> devtools::document()-function. I added the dependencies to the
> DESCRIPTION-file via usethis::use_package("x",type="Imports").
Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
I will implement the changes you recommended into my package. Thank you for
your help.
I wasn´t ignoring your advice, I am just confused because other sources like
Stackoverflow gave me contradicting information and I wanted to be sure.
I will write if I encounter other problems which fit 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 Dependencies in
the Description File of my R Package
You keep repeating basically the same questions, and appear to be
ignoring the advice you've received. That's partly understandable,
because some of it (what you find in places like StackOverflow) is
wrong, but I think you should trust what I said, and what Ivan, Martin
and Uwe said. Uwe is an authority on CRAN, Martin is an authority on
BioConductor, and Ivan and I are experienced R users.
Duncan Murdoch
On 17/03/2023 8:29 a.m., Ruff, Sergej wrote:
> Really.Whats a problem i have when all dependencies arent prei
> installed. I thought the problem would be solved once my package is
> available on CRAN.
>
>
> Here is a recent question I had regarding the same issue:
>
>
> I am currently working on a r-package. I would like to submit my r
> package to CRAN, but I have a question regarding dependency
> installations on CRAN.
>
> I have almost finished my package, added the required dependencies to
> the NAMESPACE and DESCRIPTION files as Imports, and get no errors or
> warnings
>
> when running the check in Rstudio. The package runs on the pc, where
> I´ve built the package, but when I install the package on a pc, where
> the dependencies
>
> are not preinstalled, I get the following error:
>
> ERROR:
>
> |dependencies 'depth', 'geometry' are not available for package
> 'packagename' * removing
> 'C:/Users/156932/AppData/Local/Programs/R/R-4.2.1/library/packagename'
> Warning in install.packages : installation of package ‘packagename’ had
> non-zero exit status |
>
> 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.
>
> Now I don´t want to submit my package to CRAN if the end user gets the
> same error message when installing my package.
>
> Question: After I submit my package to CRAN, will CRAN install
> dependencies automatically (via "install.packages()"), resolving the
> issue I have right now?
>
> Or do I have to modify the R-package or the Description-file to make
> sure my Package can install dependencies?
>
> I provided the dependencies to the NAMESPACE-file as @ImportFrom via the
> devtools::document()-function. I added the dependencies to the
> DESCRIPTION-file via |usethis::use_package("x",type="Imports")|. The
> Description looks like this:
>
> |License: GPL (>= 3) Encoding: UTF-8 LazyData: true RoxygenNote: 7.2.3
> Imports: depth, geometry, graphics, grDevices, MASS, mvtnorm, nlme, rgl,
> stats|
>
>
>
> So I thought all 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 Bioconductor
> Dependencies in the Description File of my R Package
> On 17/03/2023 6:19 a.m., Ruff, Sergej wrote:
>> In my example I have the following lines:
>>
>>
>> ### Differential expression analysis with limma
>> group = gl(2, n)
>> design = model.matrix(~ group)
>> fit1 = limma::lmFit(X, design)
>> fit = limma::eBayes(fit1)
>>
>> The R CMD Check returns no Errors or Notes if Limma is pre-installed. If
>> limma is not pre-installed I get an error, reminding me that Limma is
>> not available.
>
> That's a problem, and will cause your package to be rejected. It should
> not raise an error during the tests when a suggested package is missing.
> Ivan gave you good advice on how to fix this.
>
> I'd recommend testing your package a few times on Winbuilder and fixing
> things until you get clean results. That won't guarantee acceptance on
> CRAN; new packages get a manual inspection as well, and they'll often
> find some problem that the automatic tests don't find, e.g. stylistic
> issues in the Description field of the DESCRIPTION file. Here's a note
> I received recently when I submitted a n
Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
Really.Whats a problem i have when all dependencies arent prei installed. I
thought the problem would be solved once my package is available on CRAN.
Here is a recent question I had regarding the same issue:
I am currently working on a r-package. I would like to submit my r package to
CRAN, but I have a question regarding dependency installations on CRAN.
I have almost finished my package, added the required dependencies to the
NAMESPACE and DESCRIPTION files as Imports, and get no errors or warnings
when running the check in Rstudio. The package runs on the pc, where I´ve built
the package, but when I install the package on a pc, where the dependencies
are not preinstalled, I get the following error:
ERROR:
dependencies 'depth', 'geometry' are not available for package 'packagename'
* removing
'C:/Users/156932/AppData/Local/Programs/R/R-4.2.1/library/packagename'
Warning in install.packages : installation of package ‘packagename’ had
non-zero exit status
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.
Now I don´t want to submit my package to CRAN if the end user gets the same
error message when installing my package.
Question: After I submit my package to CRAN, will CRAN install dependencies
automatically (via "install.packages()"), resolving the issue I have right now?
Or do I have to modify the R-package or the Description-file to make sure my
Package can install dependencies?
I provided the dependencies to the NAMESPACE-file as @ImportFrom via the
devtools::document()-function. I added the dependencies to the DESCRIPTION-file
via usethis::use_package("x",type="Imports"). The Description looks like this:
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
Imports:
depth,
geometry,
graphics,
grDevices,
MASS,
mvtnorm,
nlme,
rgl,
stats
So I thought all 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 Bioconductor Dependencies in the
Description File of my R Package
On 17/03/2023 6:19 a.m., Ruff, Sergej wrote:
> In my example I have the following lines:
>
>
> ### Differential expression analysis with limma
> group = gl(2, n)
> design = model.matrix(~ group)
> fit1 = limma::lmFit(X, design)
> fit = limma::eBayes(fit1)
>
> The R CMD Check returns no Errors or Notes if Limma is pre-installed. If
> limma is not pre-installed I get an error, reminding me that Limma is
> not available.
That's a problem, and will cause your package to be rejected. It should
not raise an error during the tests when a suggested package is missing.
Ivan gave you good advice on how to fix this.
I'd recommend testing your package a few times on Winbuilder and fixing
things until you get clean results. That won't guarantee acceptance on
CRAN; new packages get a manual inspection as well, and they'll often
find some problem that the automatic tests don't find, e.g. stylistic
issues in the Description field of the DESCRIPTION file. Here's a note
I received recently when I submitted a new package (RmdConcord):
The Description field is intended to be a (one paragraph) description of
what the package does and why it may be useful. Please add more details
about the package functionality and implemented methods in your
Description text.
Please always write package names, software names and API (application
programming interface) names in single quotes in title and description.
e.g: --> 'R Markdown'
Please note that package names are case sensitive.
Please do not start the description with "This 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?
>
>
> With regards,
>
>
> Sergej
>
> ----
> *Von:* Duncan Murdoch
> *Gesendet:* Freitag, 17. 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 when running the automatic check.
>>
>>
>> I am worried that my package will be rejected if Limma won�t install from
>> Bioconductor on a clean version of R. Leading to an Error a
Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
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-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 +0000
"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 package using
BiocManager::install('YOUR_PACKAGE', dependencies = TRUE) and have
limma installed too, as Martin Morgan said above in the thread.
> Some recommend adding biocViews:
This field is required on Bioconductor, not CRAN:
https://contributions.bioconductor.org/description.html?q=biocViews#description-biocviews
> some recommend adding Remotes: bioc::limma
Not a standard R/CRAN field, only used by the remotes package:
https://remotes.r-lib.org/articles/dependencies.html
> Others add Biocmanager to the suggests file
I suppose it could help a user who doesn't initially know to use
BiocManager in order to install your package, and could also be used to
install limma on behalf of your users (with their permission!), but
it's additional work, may be hard to get right (see the CRAN policy
about installing packages and touching user files), and is not required
at all.
> What should I add to my Description File to make sure that limma gets
> installed from Bioconductor when needed?
See Martin Morgan's e-mail above in the thread. In short, tell your
users to install your package using BiocManager::install(...,
dependencies = TRUE) if they want limma to work. They are still free to
install.packages() if they don't want limma or can set things up
themselves.
Move limma to Imports (better) or Depends (may be worse)
if you want limma to be always available, at the cost of always
requiring Bioconductor to be set up to have your package installed.
There are other ways besides BiocManager::install(), but they all
depend on the user having set up Bioconductor repos in their R session
somehow, be it BiocManager::repositories() or setRepositories().
--
Best regards,
Ivan
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R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
Thanks.
I would like to ask, if I need to add something to the DESCRIPTION-file when
declaring Bioconductor dependencies for CRAn Submission.
Right now I only listed limma under "suggests".
I asked online and get conflicting answers. Some recommend adding biocViews:
above suggests and some recommend adding
Remotes: bioc::limma
Others add Biocmanager to the suggests file in Addition to limma.
Is that necessary? What should I add to my Description File to make sure that
limma gets installed from Bioconductor when needed?
Von: Ivan 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 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.stats.ox.ac.uk/pub/bdr/noSuggests/README.txt [*]
See WRE 1.1.3.1 for the official guidance on how to handle optional
dependencies that might not be installed:
https://cran.r-project.org/doc/manuals/R-exts.html#Suggested-packages
In short, your code should check the return value of
requireNamespace('limma', quietly = TRUE) before trying to run code
from it. Your code can (and probably should) raise an error if asked to
do something using limma when it's not available, but then in your
tests/vignettes/examples you should check whether limma is available
before trying to run that code.
--
Best regards,
Ivan
[*] See also:
https://cran.r-project.org/web/checks/check_issue_kinds.html
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Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
In my example I have the following lines: ### Differential expression analysis with limma group = gl(2, n) design = model.matrix(~ group) fit1 = limma::lmFit(X, design) fit = limma::eBayes(fit1) The R CMD Check returns no Errors or Notes if Limma is pre-installed. If limma is not pre-installed I get an error, reminding me that Limma is not available. 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? With regards, Sergej Von: Duncan Murdoch Gesendet: Freitag, 17. 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 when running the automatic check. > > > I am worried that my package will be rejected if Limma won�t install from > Bioconductor on a clean version of R. Leading to an Error and Note during the > check. > > > I am using Limma only for an example in my functions description, not inside > my actual function. > > > How would CRAN�s System handle that when checking my package for submission? If you have it in the Suggests list you should have written your code to work (i.e. not trigger an error) whether it is installed or not, so you shouldn't worry about it. Duncan Murdoch > > > 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-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 of RTIGER, and would be my preferred instruction in a README or > INSTALL file. A complete instruction might be to install your package as if > it were on Bioconductor � > > If (!requireNamepace(�BiocManager�, quietly = TRUE)) > install.packages(�BiocManager�) > BiocManager::install(��) > > It does not make sense to me to have instructions in .onAttach / .onLoad or > in each function for the user to install a �Suggests:� package, when actually > the package is required for use and belongs in Imports: or perhaps Depends:. > > The instruction to use �version = �3.14�� of Bioconductor in the RTIGER > document is not universally correct, since different Bioconductor versions > are tied to specific R versions (see > https://bioconductor.org/about/release-announcements/ ). On one version of R > I am currently using, I get > >> BiocManager::install(version = "3.14") > Error: Bioconductor version '3.14' requires R version '4.1'; use >`BiocManager::install(version = '3.17')` with R version 4.3; see >https://bioconductor.org/install > > The instruction to install a vector of Bioconductor packages is also > unnecessary for Bioconductor packages in the Imports: or Depends: field of > , or if one were to pass the argument `dependencies = TRUE` to > either BiocManager::install() or install.packages() (to get the Suggests: > packages of to be installed, as well as Depends:, Imports: and > LinkingTo:). > > Briefly, installation requires R to know the correct repositories. The command > > BiocManager::repositories() > > Returns a vector of Bioconductor and CRAN repositories relevant to your > version of R. If one is averse to using BiocManager::install(�RTIGER�), a > reasonable alternative, though still requiring that the BiocManager package > is installed, is > > install.packages(�RTIGER�, repos = BiocManager::repositories()) > > Base R also provides a mechanism for specifying Bioconductor repositories, > via `setRepositories()` called before install.packages(). However, this is > not recommended because, as can be seen on the web page mentioned above, > there are two versions of Bioconductor for each version of R � one always > gets the �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 > 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
Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
I was wondering how CRAN will handle Limma when running the automatic check. I am worried that my package will be rejected if Limma won�t install from Bioconductor on a clean version of R. Leading to an Error and Note during the check. I am using Limma only for an example in my functions 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-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 of RTIGER, and would be my preferred instruction in a README or INSTALL file. A complete instruction might be to install your package as if it were on Bioconductor � If (!requireNamepace(�BiocManager�, quietly = TRUE)) install.packages(�BiocManager�) BiocManager::install(��) It does not make sense to me to have instructions in .onAttach / .onLoad or in each function for the user to install a �Suggests:� package, when actually the package is required for use and belongs in Imports: or perhaps Depends:. The instruction to use �version = �3.14�� of Bioconductor in the RTIGER document is not universally correct, since different Bioconductor versions are tied to specific R versions (see https://bioconductor.org/about/release-announcements/ ). On one version of R I am currently using, I get > BiocManager::install(version = "3.14") Error: Bioconductor version '3.14' requires R version '4.1'; use `BiocManager::install(version = '3.17')` with R version 4.3; see https://bioconductor.org/install The instruction to install a vector of Bioconductor packages is also unnecessary for Bioconductor packages in the Imports: or Depends: field of , or if one were to pass the argument `dependencies = TRUE` to either BiocManager::install() or install.packages() (to get the Suggests: packages of to be installed, as well as Depends:, Imports: and LinkingTo:). Briefly, installation requires R to know the correct repositories. The command BiocManager::repositories() Returns a vector of Bioconductor and CRAN repositories relevant to your version of R. If one is averse to using BiocManager::install(�RTIGER�), a reasonable alternative, though still requiring that the BiocManager package is installed, is install.packages(�RTIGER�, repos = BiocManager::repositories()) Base R also provides a mechanism for specifying Bioconductor repositories, via `setRepositories()` called before install.packages(). However, this is not recommended because, as can be seen on the web page mentioned above, there are two versions of Bioconductor for each version of R � one always gets the �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 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 <https://cran.r-project.org/web/packages/policies.html>, but Bioconductor and CRAN are the "mainstream repositories" for the purposes of the following rule: >> Packages on which a CRAN package depends should be available from a >> mainstream repository (Even non-mainstream repositories are allowed for optional dependencies if you follow a few additional rules.) Here's an example of a CRAN package with a strong dependency on a Bioconductor package: <https://CRAN.R-project.org/package=RTIGER>. You can see the extra instructions for installing the Bioconductor dependencies in its README. -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package
thank you. I see you added biocView: below your suggested Dependencies. Is it necessary for CRAN to identify Bioconductor Dependencies and if so, should I add it below or above the suggested packages? Do I also need BiocManager among my Suggests? Last question: How does CRAN work 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 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/zzz.R#L36> and checks if EBImage is installed. If not, the function asks the user to install it. Both EBImage and BiocManager are listed as suggests <https://github.com/TiagoOlivoto/pliman/blob/master/DESCRIPTION#L22> I believe that this could be a possible solution Best regards, Olivoto Em qui., 16 de mar. de 2023 �s 11:18, Ruff, Sergej mailto:sergej.r...@tiho-hannover.de>> escreveu: 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 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 Can CRAN identify that limma is a Bioconductor-Package and will it Limma install, when installing my package from CRAN? [[alternative HTML version deleted]] __ R-package-devel@r-project.org<mailto:R-package-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[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 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 Can CRAN identify that limma is a Bioconductor-Package and will it Limma install, when installing my package from CRAN? [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
