R help - Dec 2021 - Handling dependencies on Bioconductor packages for packages on CRAN

Dear all

My gRbase package imports the packages from Bioconductor: graph, RBGL and
Rgraphviz

If these packages are not installed, then gRbase can not be installed. The error
message is:

   ERROR: dependency ?graph? is not available for package ?gRbase?

If I, prior to installation, run setRepositories and highlight 'BioC
software', then gRbase installs as it should, because the graph package from
Bioconductor is installed along with it. However, this extra step is an obstacle
to many users of the package which means that either people do not use the
package or people ask questions about this issue on stack overflow, R-help, by
email to me etc. It is not a problem to get the package on CRAN because, I
guess, the CRAN check machines already have the three bioconductor packages
installed.

Therefore, I wonder if there is a way of specifying, in the DESCRIPTION file or
elsewhere, that these packages should be installed automatically from
bioconductor.

An alternative would be if one could force the error message

   ERROR: dependency ?graph? is not available for package ?gRbase?

to be accompanied by a message about what the user then should do.

Any good suggestions? Thanks in advance.

Best regards
S?ren

	[[alternative HTML version deleted]]

I suggest you post this on r-package-devel.  That seems a better fit.

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Sat, Dec 4, 2021 at 7:55 AM S?ren H?jsgaard <sorenh at math.aau.dk>
wrote:
> Dear all
>
> My gRbase package imports the packages from Bioconductor: graph, RBGL and
> Rgraphviz
>
> If these packages are not installed, then gRbase can not be installed. The
> error message is:
>
>    ERROR: dependency ?graph? is not available for package ?gRbase?
>
> If I, prior to installation, run setRepositories and highlight 'BioC
> software', then gRbase installs as it should, because the graph package
> from Bioconductor is installed along with it. However, this extra step is
> an obstacle to many users of the package which means that either people do
> not use the package or people ask questions about this issue on stack
> overflow, R-help, by email to me etc. It is not a problem to get the
> package on CRAN because, I guess, the CRAN check machines already have the
> three bioconductor packages installed.
>
> Therefore, I wonder if there is a way of specifying, in the DESCRIPTION
> file or elsewhere, that these packages should be installed automatically
> from bioconductor.
>
> An alternative would be if one could force the error message
>
>    ERROR: dependency ?graph? is not available for package ?gRbase?
>
> to be accompanied by a message about what the user then should do.
>
> Any good suggestions? Thanks in advance.
>
> Best regards
> S?ren
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

One possibility is to make graph a Suggests: dependency, and preface any code
using it (or, e.g., in an .onLoad function) with

  if (!requireNamespace("graph", quietly = TRUE))
    stop(
      "install the Bioconductor 'graph' package using these
commands\n\n",
      ## standard Bioconductor package installation instructions
      "  if (!requireNamespace('BiocManager', quiety =
TRUE))\n",
      "    install.packages('BiocManager')\n",
      "  BiocManager::install('graph')\n\n"
    )

Use graph:: for any function used in the graph package. The code could be
simplified if BiocManager were an Imports: dependency of your package -- it
would already be installed. The 'Suggests:' dependency would not cause
problems with CRAN, because Suggest'ed packages are available when the
package is built / checked.

The user experience of package installation would be 'non-standard'
(didn't I just install gRbase??), so this is not an ideal solution.

Martin

?On 12/4/21, 10:55 AM, "R-help on behalf of S?ren H?jsgaard"
<r-help-bounces at r-project.org on behalf of sorenh at math.aau.dk>
wrote:

    Dear all

    My gRbase package imports the packages from Bioconductor: graph, RBGL and
Rgraphviz

    If these packages are not installed, then gRbase can not be installed. The
error message is:

       ERROR: dependency ?graph? is not available for package ?gRbase?

    If I, prior to installation, run setRepositories and highlight 'BioC
software', then gRbase installs as it should, because the graph package from
Bioconductor is installed along with it. However, this extra step is an obstacle
to many users of the package which means that either people do not use the
package or people ask questions about this issue on stack overflow, R-help, by
email to me etc. It is not a problem to get the package on CRAN because, I
guess, the CRAN check machines already have the three bioconductor packages
installed.

    Therefore, I wonder if there is a way of specifying, in the DESCRIPTION file
or elsewhere, that these packages should be installed automatically from
bioconductor.

    An alternative would be if one could force the error message

       ERROR: dependency ?graph? is not available for package ?gRbase?

    to be accompanied by a message about what the user then should do.

    Any good suggestions? Thanks in advance.

    Best regards
    S?ren

    	[[alternative HTML version deleted]]

    ______________________________________________
    R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
    https://stat.ethz.ch/mailman/listinfo/r-help
    PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    and provide commented, minimal, self-contained, reproducible code.