[Bioc-devel] Warnings in build for BioCor

Lluís Revilla lluis.revilla at gmail.com
Wed Feb 28 15:35:26 CET 2018

Thanks Martin for looking into it.
I think that is the reason of the problem, the timeline of the errors
building certainly match.
I couldn't find this documented in Writing R Extensions, is this behavior
documented somewhere?


On 28 February 2018 at 15:03, Martin Morgan <martin.morgan at roswellpark.org>

> Actually, looking at your github repository, I see you have two vignettes,
> you have renamed one from vignette2.Rmd to BioCor_advanced.Rmd, and that
> this vignette now collates before the original one. I believe that
> vignettes are built in the same R process, so the packages loaded in the
> first vignette are available (and conflict with) packages loaded in the
> second.
> Martin
> On 02/28/2018 08:53 AM, Martin Morgan wrote:
>> On 02/28/2018 05:31 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)
>> This means that 'another package' is on the search() path. It only gets
>> there if your package attaches it, directly or indirectly. Maybe another
>> package that you attach previously import'ed it, but now depends on it? To
>> narrow this down, step through your vignette code until you see the
>> offending package on the search() path.
>> Maybe you can avoid attaching the intermediate package, or put your
>> package in front of the others on the search path by loading your package
>> last in the vignette.
>> If you're running into these problems, and you're intimately familiar
>> with your package, then one can imagine that users will also run into this
>> problem and the suggestion to mangle your package function names starts to
>> sound appealing.
>>> 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 next Bioconductor release has not been announced (we try to tie these
>> to the R release schedule, and the release of R-3.5 has not yet been
>> announced), but will likely be at the end of April.
>> Martin
>>> 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
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>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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