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

[Henrik Bengtsson]

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