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

Uwe Ligges ||gge@ @end|ng |rom @t@t|@t|k@tu-dortmund@de
Fri Mar 17 13:45:44 CET 2023 

The user should set the CRAN+BioC via setRepositories() and then run 
install.packages() will install all dependencies automatically.
Of course, if you install from a local repository without the required 
packages or from a USB drive, R cannot resolve dependencies.

Best,
Uwe Ligges



On 17.03.2023 13:29, 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 <murdoch.duncan using gmail.com>
> Gesendet: Freitag, 17. März 2023 13:15:28
> An: Ruff, Sergej; Martin Morgan; Ivan Krylov
> Cc: r-package-devel using 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 <murdoch.duncan using gmail.com>
>> *Gesendet:* Freitag, 17. März 2023 11:14:25
>> *An:* Ruff, Sergej; Martin Morgan; Ivan Krylov
>> *Cc:* r-package-devel using 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 <mtmorgan.bioc using gmail.com>
>>> Gesendet: Donnerstag, 16. M�rz 2023 20:12:51
>>> An: Ivan Krylov; Ruff, Sergej
>>> Cc: r-package-devel using 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(�<your package>�)
>>>
>>> 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/
>> <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 <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 <your package>, or if one were to pass the argument `dependencies = TRUE` to either BiocManager::install() or install.packages()  (to get the Suggests: packages of <your package> 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 <r-package-devel-bounces using r-project.org> on behalf of Ivan Krylov <krylov.r00t using gmail.com>
>>> Date: Thursday, March 16, 2023 at 2:15 PM
>>> To: Ruff, Sergej <Sergej.Ruff using tiho-hannover.de>
>>> Cc: r-package-devel using r-project.org <r-package-devel using 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 +0000
>>> "Ruff, Sergej" <Sergej.Ruff using tiho-hannover.de> 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
>> <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
>> <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 using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
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