[R-pkg-devel] dependency on a bioconductor package
Morgan, Martin
mtmorg@n@bioc @ending from gm@il@com
Fri Oct 5 20:52:14 CEST 2018
Bioconductor has a release and a devel branch, with the idea that new
features are introduced into 'devel'. The transition to use BiocManager
is a new feature introduced into devel, and BiocInstaller has a
deprecation message added in devel only. It follows that win-builder is
using bioc-devel (this is reasonable; our next release is at the end of
this month), and that we'd look for use of BiocInstaller in devel
packages. affy is itself a 'core team' package, and we have removed use
of BiocInstaller from that.
But let's see... the 'release' branch has
> dput(repos)
c(BioCsoft = "https://bioconductor.org/packages/3.7/bioc", BioCann =
"https://bioconductor.org/packages/3.7/data/annotation",
BioCexp = "https://bioconductor.org/packages/3.7/data/experiment",
BioCworkflows = "https://bioconductor.org/packages/3.7/workflows",
CRAN = "https://cran.rstudio.com")
> db = available.packages(repos=repos)
> revdeps = tools::package_dependencies("LipidMS", db, recursive=TRUE)
> "BiocInstaller" %in% unlist(revdeps)
[1] TRUE
and indeed BiocInstaller is problematic (but BiocInstaller in the
release branch doesn't generate the warning...) (also, I'm not sure
about the '3.5' components of your annotation / experiment repos, these
should be the same as the main repository).
On the other hand in our devel branch
> repos = sub("3.7", "3.8", repos)
> db = available.packages(repos=repos)
> revdeps = tools::package_dependencies("LipidMS", db, recursive=TRUE)
> "BiocInstaller" %in% unlist(revdeps)
[1] FALSE
So at least for packages that are current in CRAN and in the devel
branch of Bioconductor there is no use of BiocInstaller.
I'm not exactly sure where this leaves us...
Martin
On 10/5/18 2:26 PM, William Dunlap wrote:
> It looks like affy is the culprit.
>
> > requiredByCAMERA <- tools::package_dependencies("CAMERA",
> recursive=TRUE)$CAMERA
> > directlyRequired <- tools::package_dependencies(requiredByCAMERA)
> > names(directlyRequired)[ vapply(directlyRequired,
> function(x)"BiocInstaller"%in%x, FUN.VALUE=NA) ]
> [1] "affy"
> > directlyRequired$affy
> [1] "BiocGenerics" "Biobase" "affyio"
> "BiocInstaller" "graphics" "grDevices"
> [7] "methods" "preprocessCore" "stats" "utils"
> "zlibbioc"
> > getOption("repos")
> CRAN
> BioCsoft
> "https://cloud.r-project.org"
> "http://www.bioconductor.org/packages/release/bioc"
> BioCann
> BioCexp
> "http://bioconductor.org/packages/3.5/data/annotation"
> "http://bioconductor.org/packages/3.5/data/experiment"
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com <http://tibco.com>
>
> On Fri, Oct 5, 2018 at 10:58 AM, Morgan, Martin <mtmorgan.bioc using gmail.com
> <mailto:mtmorgan.bioc using gmail.com>> wrote:
>
> (don't forget to 'reply all', so that others may benefit /
> contribute to the conversation).
>
> You or one of the packages your package depends on must Depend: or
> Import: BiocInstaller. If it is your package, then you should no
> longer do so. If it is one of the packages your package depends on,
> then the responsible thing to do is to contact the author of that
> package and indicate that they should update their package to no
> longer depend on BiocInstaller.
>
> I do not know how the CRAN team will view this warning; I would
> guess that, if it is not directly under your control, then they will
> not be overly concerned about it.
>
> Martin
>
> On 10/5/18 1:35 PM, maialba using alumni.uv.es
> <mailto:maialba using alumni.uv.es> wrote:
>
> Hello Morgan,
>
> thank you for the replay but, how should I solve the problem in
> my package? I did install CAMERA using BiocManager in my
> computer and my package works fine. I do not get any warnings
> when I run R CDM check but the problem appears when I try to
> submit it to CRAN.
>
> Maribel
>
>
> BiocInstaller has been replaced by the CRAN package
> BiocManager; the
> appropriate way to install Bioconductor packages is
> BiocManager::install(). See the vignette at
>
> https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManagerhtml
> <https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManagerhtml>
>
> Martin
>
>
> On 10/5/18 5:36 AM, maialba using alumni.uv.es
> <mailto:maialba using alumni.uv.es> wrote:
>
> I do not know how to solve this warning. I guess it
> comes from the package dependency on CAMERA
> (bioconductor) but I can´t solve it.
>
> https://win-builder.r-project.org/incoming_pretest/LipidMS_1.0.0_20181005_103151/Windows/00check.log
> <https://win-builder.r-project.org/incoming_pretest/LipidMS_1.0.0_20181005_103151/Windows/00check.log>>
>
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