On 10/23/2017 09:26 AM, Elizabeth Purdom wrote:
Hello,
I am updating an existing package and I am getting an error in running my
vignette (and a similar error in an example in help pages) but ONLY when I run
R CMD BUILD. I can’t recreate the error in any session where I can debug and
figure out what is happening. So my question is how can I recreate the exact
environment of R CMD BUILD that runs the vignette but in an interactive session
so that I can figure out what is going on?
I have tried reproducing the error in other environments:
* Running R —vanilla interactively and trying the code manually
* running purl on my vignette to get pure R code and running just the R code
with R CMD BATCH —vanilla
hint on the specific package and / or error message?
My approach would be to install the package, Stangle / purl the
vignette, and R -f vignette.R, then trim the vignette to a fast
reproducible case. But it sounds like you're doing that...
Martin
* Running R —vanilla interactively and compiling the vignette
But all of the above runs the code without any error.
Furthermore, for some reason TravisCI can build the package without problem nor
does it hit any error in R CMD CHECK with TravisCI so for a long time I assumed
it was some local file or environment on my machine and forgot about it. But
now that I have pushed the changes to Bioconductor, they are getting the same
error about the vignette not building.
By the way, I can’t slowly take back my commands to see what broke it, because
the change was a dramatic one involving redefining my S4 class, so a large
number of things had to be adapted before any code would work and there’s no
way to slowly roll that back.
Most of the posts I have seen about debugging discrepancies between R CMD BUILD
(or equivalently R CMD CHECK) seem to be about namespace issues with other
packages. Of course I can’t be sure since I have a pretty terse error from R
CMD BUILD, but the error that is given is my own error (it’s a check I wrote as
part of the validity check when I updated the class) so it seems unclear how it
would be a namespace error.
Thanks for any suggestions,
Elizabeth Purdom
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