[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 07:09:03 CET 2017

Thanks Hervé.  I can confirm that reinstalling packages from R 3.3.2
to R 3.3.3 solved the problem:

https://github.com/HenrikBengtsson/globals/commit/f9ff3a092d1712258aab2d01277665abec7dfa32

/Henrik

On Thu, Mar 9, 2017 at 5:52 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> 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
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=j-wrwOYdw3tV8MRxh1bTywbrHtZp5MQWTT-07aOoyoE&s=uX9jH2vmSV2vAA029bdUq70SuPUT3jSUd3-cKnR-RA4&e=
>>
>
> --
> 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: hpages at fredhutch.org
> Phone:  (206) 667-5791
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