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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