[Bioc-devel] Warnings in build for BioCor

Martin Morgan martin.morgan at roswellpark.org
Wed Feb 28 15:03:17 CET 2018

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.


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
>>     [[alternative HTML version deleted]]
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