Hi Hervé, Thanks for the suggestion. I actually checked first that they were
the same length, but identical() would be safer and simplify my code. Elizabeth
> On Oct 23, 2017, at 10:40 PM, Hervé Pagès <hpa...@fredhutch.org> 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.
>
> 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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>>
>>
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>>
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>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
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