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

[Gabe Becker]

FYI, that seems to be a locale issue, as the locale defines the sort order.

The first one is sorting alphabetically in a case-insensitive manner, eg
aAbBcC etc, the second is sorting in a case sensitive manner, where capital
letters all come before lower-case letters, e.g. ABC...YZabc...

You can see what locale you're in via Sys.getlocale() or see it in your
sessionInfo under the locale heading.

Best,
~G

On Mon, Oct 23, 2017 at 1:06 PM, Elizabeth Purdom <epurdom at stat.berkeley.edu
> 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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-- 
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research

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