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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