[R-pkg-devel] dependency on a bioconductor package

[William Dunlap]

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

On Fri, Oct 5, 2018 at 10:58 AM, Morgan, Martin <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 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 BiocInstaller has been replaced by the CRAN package BiocManager; the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/vignette
>>> s/BiocManagerhtml
>>>
>>> Martin
>>>
>>>
>>> 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.
>>>>
>>>> https://win-builder.r-project.org/incoming_pretest/LipidMS_1
>>>> .0.0_20181005_103151/Windows/00check.log>
>>>>
>>>> ______________________________________________
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>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>
>>>
>>> ______________________________________________
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>>>
>>
>>
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