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

Hi Elizabeth,

Thanks for troubleshooting this.

Note that testing with identical()/checkIdentical() is safer than with 
'any(sort(colnames1) != sort(colnames2))'. The latter won't do the
right thing if 'colnames1' and 'colnames2' have different lengths.

Cheers,
H.


On 10/23/2017 01:06 PM, Elizabeth Purdom wrote:

Dear Martin,

Just for completeness, I figured out the discrepancy and solved my 
problem. In my check, I check that the column names contain the 
expected names and I didn?t want to make the order required in a 
certain way so I used sort -- but only of one side because I naively 
assumed the other side would be fixed:

any(sort(colnames(object at merge_nodeMerge)) != 
c('Contrast','isMerged','mergeClusterId','Node?)

But the different environments are sorting differently!

In my normal interactive R session:

sort(c("Contrast", "isMerged", "mergeClusterId", "Node"))

[1] "Contrast"?????? "isMerged"?????? "mergeClusterId" "Node"

In the build version of R however:
Browse[2]> sort(c("Contrast", "isMerged", "mergeClusterId", "Node"))
[1] "Contrast"?????? "Node"?????????? "isMerged"?????? "mergeClusterId"

Thank you very much for your help in getting an interactive session in 
the build environment!

Elizabeth

On Oct 23, 2017, at 4:35 PM, Martin Morgan 
<martin.morgan at roswellpark.org> wrote:

On 10/23/2017 09:59 AM, Elizabeth Purdom wrote:

On Oct 23, 2017, at 3:47 PM, Martin Morgan 
<martin.morgan at roswellpark.org 
<mailto:martin.morgan at 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



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