[R-pkg-devel] dependency on a bioconductor package
wdunl@p @ending from tibco@com
Fri Oct 5 20:26:54 CEST 2018
It looks like affy is the culprit.
> requiredByCAMERA <- tools::package_dependencies("CAMERA",
> directlyRequired <- tools::package_dependencies(requiredByCAMERA)
> names(directlyRequired)[ vapply(directlyRequired,
function(x)"BiocInstaller"%in%x, FUN.VALUE=NA) ]
 "BiocGenerics" "Biobase" "affyio" "BiocInstaller"
 "methods" "preprocessCore" "stats" "utils"
On Fri, Oct 5, 2018 at 10:58 AM, Morgan, Martin <mtmorgan.bioc using gmail.com>
> (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.
> On 10/5/18 1:35 PM, 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.
>> BiocInstaller has been replaced by the CRAN package BiocManager; the
>>> appropriate way to install Bioconductor packages is
>>> BiocManager::install(). See the vignette at
>>> On 10/5/18 5:36 AM, 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.
>>>> R-package-devel using r-project.org mailing list
>>> R-package-devel using r-project.org mailing list
> R-package-devel using r-project.org mailing list
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