[Bioc-devel] Warnings in build for BioCor

Lluís Revilla lluis.revilla at gmail.com
Wed Feb 28 14:43:03 CET 2018

Dear Matthias and Robert,

My namespace doesn't import that package. It is mentioned in the
Description file in Suggests, and on the same vignette it is and loaded but
after the line where the error is reported.
The error is reported on lines 143-148 (BioCor.Rmd) and the library is
loaded on line 260.
But I might end up using the double colon to avoid the error.


On 28 February 2018 at 14:26, Robert Castelo <robert.castelo at upf.edu> wrote:

> Lluis,
> something you can do in you NAMESPACE to follow the advice below from
> Matthias if you are importing the functionality of a whole package is:
> import(pkgyouneed, except=functionmethodyoudefine)
> in this way, you're importing everything except that particular function
> or method that you are defining in your own package.
> cheers,
> robert.
> On 28/02/2018 12:51, Matthias Döring wrote:
>> DearLluis,
>> how is your namespace defined? Do you use 'import' or 'importFrom' to
>> load the package in question? If you are currently using 'import' to load
>> all exports from the package, you could switch to 'importFrom' and exclude
>> the function that causes the problems and then use the double-colon
>> operator when referring to the package's function.
>> Kind regards
>>  Matthias
>> On 02/28/2018 11:31 AM, Lluís Revilla wrote:
>>> Dear bioconductor core,
>>> The development version of my package hosted in Github cannot be build.
>>> It
>>> seems that another package is loaded when it shouldn't and masks the
>>> functions that are used in the vignette. (In case anyone wants to help
>>> here
>>> is the link to the StackOverflow question:
>>> https://stackoverflow.com/q/49002455/2886003)
>>> Additionally the current version hosted in Bioconductor has a warning in
>>> the windows build. Which I hoped to correct for these release.
>>> I don't know if I will find a solution on time for the next release
>>> (which
>>> I expect in three weeks), but I am worried I won't be able to fix it on
>>> time.
>>> The End Of Life page of Bioconductor only talks about errors not
>>> warnings,
>>> and I couldn't find if this has been discussed previously in the
>>> archive. I
>>> would like to know if I can leave the development version as is (until I
>>> find a solution) or should I aim to correct the warning for the next
>>> release?
>>> Many thanks,
>>> Lluís Revilla
>>>     [[alternative HTML version deleted]]
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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