[Bioc-devel] Warnings in build for BioCor

Martin Morgan martin.morgan at roswellpark.org
Wed Feb 28 14:53:58 CET 2018

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.


> 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

This email message may contain legally privileged and/or...{{dropped:2}}

More information about the Bioc-devel mailing list