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

[Hervé Pagès]

On 10/23/2017 01:42 PM, Martin Morgan wrote:
> On 10/23/2017 04:40 PM, Hervé Pagès wrote:
>> 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.
>
> ...but in this case it sounds like you're aiming for a set comparison,
>
>    setequal(colnames1, colnames2)

Still not 100% safe though. Will give a false positive in the rare
situation where some columns are duplicated ;-)

 > setequal(c("a", "b", "a"), c("b", "a"))
[1] TRUE

H.

>
> Martin
>
>>
>> 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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>>>
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>>
>
>
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-- 
Hervé Pagès

Program in Computational Biology
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