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

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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