[Bioc-devel] Warnings in build for BioCor

Martin Morgan martin.morgan at roswellpark.org
Wed Feb 28 21:51:54 CET 2018

On 02/28/2018 09:35 AM, Lluís Revilla wrote:
> 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?

I'm not sure if its documented anywhere; the code here


seems to involve processing all vignettes with a single call to create a 
new process.


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