[Bioc-devel] Bioconductor and R 3.3.3: Error in c(x, values) : could not find symbol "recursive" in environment of the generic function

Fri Mar 10 02:52:53 CET 2017

Hi Henrik,

See here for similar problems reported earlier on our support site:

   https://support.bioconductor.org/p/93347/#93373
   https://support.bioconductor.org/p/93590/#93595

I think you need to reinstall your packages after updating to R 3.3.

API compatibility across minor R releases is a myth :-/

H.

On 03/09/2017 05:38 PM, Henrik Bengtsson wrote:
> Hi. FYI / Is anyone else experiencing:
>
> Error in c(x, values) :
>   could not find symbol "recursive" in environment of the generic function
>
> errors for some Bioconductor packages when running under R 3.3.3 while
> they don't occur with R 3.3.2?  This seems realted to the following R
> 3.3.3 NEWS entry:
>
> c()'s argument use.names is documented now, as belonging to the (C
> internal) default method. In “parallel”, argument recursive is also
> moved from the generic to the default method, such that the formal
> argument list of base generic c() is just (...).
>
> One quick example is:
>
> $ R --vanilla
>> example("callLOH", package = "PureCN")
> [...]
>> head(callLOH(purecn.example.output))
> Error in c(x, values) :
>   could not find symbol "recursive" in environment of the generic function
>
>> traceback()
> 24: c(x, values)
> 23: append(mcols(gr), slot(x, "fixed"))
> 22: append(mcols(gr), slot(x, "fixed"))
> 21: .local(x, ...)
> 20: rowRanges(x)
> 19: rowRanges(x)
> 18: (function (x, ...)
>     standardGeneric("start"))(x = rowRanges(x), ... = ...)
> 17: do.call(start, list(x = rowRanges(x), ... = ...))
> 16: do.call(start, list(x = rowRanges(x), ... = ...))
> 15: start(res$input$vcf)
> 14: start(res$input$vcf)
> 13: split(start(res$input$vcf), as.character(seqnames(res$input$vcf)))
> 12: vapply(split(start(res$input$vcf), as.character(seqnames(res$input$vcf))),
>         function(x) c(min(x), max(x)), c(min = double(1), max = double(1)))
> 11: t(vapply(split(start(res$input$vcf), as.character(seqnames(res$input$vcf))),
>         function(x) c(min(x), max(x)), c(min = double(1), max = double(1))))
> 10: withCallingHandlers(expr, warning = function(w)
> invokeRestart("muffleWarning"))
> 9: suppressWarnings(t(vapply(split(start(res$input$vcf),
> as.character(seqnames(res$input$vcf))),
>        function(x) c(min(x), max(x)), c(min = double(1), max = double(1)))))
> 8: .getArmLocations(res)
> 7: callLOH(purecn.example.output)
> 6: head(callLOH(purecn.example.output)) at Rex657e3e41cba7#8
> 5: eval(expr, envir, enclos)
> 4: eval(ei, envir)
> 3: withVisible(eval(ei, envir))
> 2: source(tf, local, echo = echo, prompt.echo = paste0(prompt.prefix,
>        getOption("prompt")), continue.echo = paste0(prompt.prefix,
>        getOption("continue")), verbose = verbose, max.deparse.length = Inf,
>        encoding = "UTF-8", skip.echo = skips, keep.source = TRUE)
> 1: example("callLOH", package = "PureCN")
>
>> sessionInfo()
> R version 3.3.3 (2017-03-06)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.2 LTS
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] PureCN_1.2.3               VariantAnnotation_1.20.2
>  [3] Rsamtools_1.26.1           Biostrings_2.42.1
>  [5] XVector_0.14.0             SummarizedExperiment_1.4.0
>  [7] Biobase_2.34.0             GenomicRanges_1.26.3
>  [9] GenomeInfoDb_1.10.3        IRanges_2.8.1
> [11] S4Vectors_0.12.1           BiocGenerics_0.20.0
> [13] DNAcopy_1.48.0
>
> loaded via a namespace (and not attached):
>  [1] Rcpp_0.12.9              AnnotationDbi_1.36.2     GenomicAlignments_1.10.0
>  [4] zlibbioc_1.20.0          BiocParallel_1.8.1       BSgenome_1.42.0
>  [7] lattice_0.20-34          tools_3.3.3              grid_3.3.3
> [10] data.table_1.10.4        DBI_0.6                  digest_0.6.12
> [13] Matrix_1.2-8             RColorBrewer_1.1-2       rtracklayer_1.34.2
> [16] bitops_1.0-6             biomaRt_2.30.0           RCurl_1.95-4.8
> [19] memoise_1.0.0            RSQLite_1.1-2            GenomicFeatures_1.26.3
> [22] XML_3.98-1.5
>
>
> Exact same call works with:
>
>> sessionInfo()
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> I see this type of error message running R CMD check on:
>
> * PureCN_1.2.3.tar.gz
> * Repitools_1.20.0.tar.gz
>
> I probably have installed most of the dep packages on R 3.3.2 and then
> upgraded to R 3.3.3.
>
> Over and out,
>
> Henrik
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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