On 10/23/2017 09:59 AM, Elizabeth Purdom wrote:
On Oct 23, 2017, at 3:47 PM, Martin Morgan
<martin.mor...@roswellpark.org <mailto: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.
I can reproduce the error with
clusterExperiment/vignettes master$ R_DEFAULT_PACKAGES= LC_COLLATE=C R
-f clusterExperimentTutorial.R
leading to
> ##
----recallRSEC------------------------------------------------------------
>
rsecFluidigm<-RSEC(rsecFluidigm,isCount=TRUE,combineProportion=0.6,mergeMethod="JC",mergeCutoff=0.05)
Error in validObject(.Object) :
invalid class "ClusterExperiment" object: merge_nodeMerge must be
data.frame with 4 columns and column names equal to:
'Node','Contrast','isMerged','mergeClusterId'
Calls: RSEC ... .local -> new -> initialize -> initialize -> validObject
Execution halted
and then for work inside R
clusterExperiment/vignettes$ R_DEFAULT_PACKAGES= LC_COLLATE=C R
Bioconductor version 3.6 (BiocInstaller 1.27.7), ?biocLite for help
> source("clusterExperimentTutorial.R", echo=TRUE, max=Inf)
Does that set you down the right path?
Martin
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
