> On Oct 23, 2017, at 3:47 PM, Martin Morgan <martin.mor...@roswellpark.org>
> wrote:
>
> 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
>
Yes, that is what I tried but did not get the error from the R code.
And I apologize, it’s the `clusterExperiment` package. My error was so specific
to the class created by my package that I didn’t think it would be useful, but
here is the relevant error message:
Quitting from lines 271-272 (clusterExperimentTutorial.Rmd)
Error: processing vignette 'clusterExperimentTutorial.Rmd' failed with
diagnostics:
invalid class "ClusterExperiment" object: merge_nodeMerge must have 4 columns
and column names equal to: 'Node','Contrast','isMerged','mergeClusterId'
Execution halted
I would note that my vignette calls an object that is saved as a data object as
part of my package to speed up compilation. But I experimented and you can also
switch it so that it creates the object from scratch and doesn’t load the
object, and it runs into the same error. There is a `LazyData: false` in my
DESCRIPTION File, because I was having problems with my R data object, because
it is of the class I make with my package, and without the package loaded there
was some problem loading it.
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