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.dun...@gmail.com>
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 <murdoch.dun...@gmail.com>
> *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 <mtmorgan.b...@gmail.com>
>> 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(�<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-boun...@r-project.org> on behalf of
>> Ivan Krylov <krylov.r...@gmail.com>
>> Date: Thursday, March 16, 2023 at 2:15 PM
>> To: Ruff, Sergej <sergej.r...@tiho-hannover.de>
>> Cc: r-package-devel@r-project.org <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 +0000
>> "Ruff, Sergej" <sergej.r...@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
>>
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