[Bioc-devel] How to recreate R CMD BUILD environment in interactive session?

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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