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
https://github.com/wch/r-source/blob/trunk/src/library/tools/R/build.R#L315-L324
seems to involve processing all vignettes with a single call to create a
new process.
Martin
Lluís
On 28 February 2018 at 15:03, Martin Morgan
<martin.mor...@roswellpark.org <mailto:martin.mor...@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
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