Dear all, for a package that is already published on CRAN, we plan to include a function that relies on the M3C-package, which is on Bioconductor only. Since this function in M3C is not essential for most other functions of our package, we thought about adding M3C to the "Suggests" field in the DESCRIPTION file, and from the "Writing R Extensions" page we found that we could also add the URL to the "Additional_repositories" field of the DESCRIPTION file (Additional_repositories: https://bioconductor.org/packages/release/bioc/html/M3C.html). Would this be the correct way to conditionally use a package from Bioconductor in own packages? Best Daniel -- _____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Pr?l?, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING
[R-pkg-devel] Conditionally use packages from Bioconductor
3 messages · Daniel Lüdecke, Uwe Ligges
On 05.02.2020 16:05, Daniel L?decke wrote:
Dear all, for a package that is already published on CRAN, we plan to include a function that relies on the M3C-package, which is on Bioconductor only. Since this function in M3C is not essential for most other functions of our package, we thought about adding M3C to the "Suggests" field in the DESCRIPTION file, and from the "Writing R Extensions" page we found that we could also add the URL to the "Additional_repositories" field of the DESCRIPTION file (Additional_repositories: https://bioconductor.org/packages/release/bioc/html/M3C.html).
BioC is a standard repository that you do not need to delcare. Best, Uwe Ligges
Would this be the correct way to conditionally use a package from Bioconductor in own packages? Best Daniel --
_____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Pr?l?, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING ______________________________________________ R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Thanks for the quick reply! I was a bit uncertain about this due to the CRAN check notes from this package: https://cran.r-project.org/web/checks/check_results_BiocManager.html That made me think that the reason why the packages which are not available for testing are hosted on Bioconductor. Daniel -----Urspr?ngliche Nachricht----- Von: Uwe Ligges [mailto:ligges at statistik.tu-dortmund.de] Gesendet: Mittwoch, 5. Februar 2020 16:08 An: Daniel L?decke <d.luedecke at uke.de>; r-package-devel at r-project.org Betreff: Re: [R-pkg-devel] Conditionally use packages from Bioconductor
On 05.02.2020 16:05, Daniel L?decke wrote:
Dear all, for a package that is already published on CRAN, we plan to include a function that relies on the M3C-package, which is on Bioconductor only. Since this function in M3C is not essential for most other functions of our package, we thought about adding M3C to the "Suggests" field in the DESCRIPTION file, and from the "Writing R Extensions" page we found that we could also add the URL to the "Additional_repositories" field of the DESCRIPTION file (Additional_repositories: https://bioconductor.org/packages/release/bioc/html/M3C.html).
BioC is a standard repository that you do not need to delcare. Best, Uwe Ligges
Would this be the correct way to conditionally use a package from Bioconductor in own packages? Best Daniel --
_____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Pr?l?, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING ______________________________________________ R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
-- _____________________________________________________________________ Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Pr?l?, Marya Verdel _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING