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@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.mor...@roswellpark.org>
wrote:
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
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