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 <hpa...@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@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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
