Dario Strbenac
2014-Jun-12 07:00 UTC
[Rd] do.call Error for Function Not Present When Manually Called
Hello,
The e1071 function naiveBayes gives an error when called by do.call, although it
doesn't give any error if I call it manually.
Browse[1]> trainParams at classifier
function (x, ...)
UseMethod("naiveBayes")
<environment: namespace:e1071>
Browse[1]> trained <- do.call(trainParams at classifier, paramList)
Error in names(dimnames(tables[[i]])) <- c(Yname, colnames(x)[i]) :
'names' attribute [4] must be the same length as the vector [2]
Browse[1]> summary(paramList)
Length Class Mode
925 -none- numeric
37 factor numeric
verbose 1 -none- logical
Browse[1]> class(trainParams at classifier(paramList[[1]], paramList[[2]],
paramList[[3]]))
[1] "naiveBayes"
What is the explanation for this ? I read that the behaviour of do.call is
currently undefined and subject to change.
Browse[1]> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 splines parallel grid stats graphics grDevices
[8] utils datasets methods base
other attached packages:
[1] robustbase_0.91-1 e1071_1.6-3
[3] car_2.0-20 edgeR_3.6.2
[5] statmod_1.4.19 PoiClaClu_1.0.2
[7] lawstat_2.4.1 VGAM_0.9-4
[9] mvtnorm_0.9-99992 sparsediscrim_0.2
[11] MASS_7.3-33 curatedOvarianData_1.2.0
[13] affy_1.40.0 lumiHumanIDMapping_1.10.0
[15] illuminaHumanv3.db_1.20.0 org.Hs.eg.db_2.10.1
[17] RSQLite_0.11.4 DBI_0.2-7
[19] AnnotationDbi_1.24.0 lumi_2.14.2
[21] Biobase_2.22.0 BiocGenerics_0.8.0
[23] limma_3.18.13 ROCR_1.0-5
[25] gplots_2.13.0 gridExtra_0.9.1
[27] ggplot2_1.0.0
loaded via a namespace (and not attached):
[1] affyio_1.30.0 annotate_1.40.1 AnnotationForge_1.4.4
[4] base64_1.1 bdsmatrix_1.3-1 beanplot_1.1
[7] BiocInstaller_1.14.2 biomaRt_2.18.0 Biostrings_2.30.1
[10] bitops_1.0-6 BSgenome_1.30.0 bumphunter_1.2.0
[13] caTools_1.17 class_7.3-10 codetools_0.2-8
[16] colorspace_1.2-4 corpcor_1.6.6 DEoptimR_1.0-1
[19] digest_0.6.4 doRNG_1.6 foreach_1.4.2
[22] gdata_2.13.3 genefilter_1.44.0 GenomicFeatures_1.14.5
[25] GenomicRanges_1.14.4 gtable_0.1.2 gtools_3.4.0
[28] illuminaio_0.4.0 IRanges_1.20.7 iterators_1.0.7
[31] itertools_0.1-3 KernSmooth_2.23-12 labeling_0.2
[34] lattice_0.20-29 locfit_1.5-9.1 Matrix_1.1-3
[37] matrixStats_0.8.14 mclust_4.3 methylumi_2.8.0
[40] mgcv_1.7-29 minfi_1.8.9 multtest_2.18.0
[43] munsell_0.4.2 nleqslv_2.1.1 nlme_3.1-117
[46] nnet_7.3-8 nor1mix_1.1-4 pkgmaker_0.22
[49] plyr_1.8.1 preprocessCore_1.24.0 proto_0.3-10
[52] RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1
[55] registry_0.2 reshape_0.8.5 reshape2_1.4
[58] R.methodsS3_1.6.1 rngtools_1.2.4 Rsamtools_1.14.3
[61] rtracklayer_1.22.7 scales_0.2.4 siggenes_1.36.0
[64] stringr_0.6.2 survival_2.37-7 tcltk_3.1.0
[67] tools_3.1.0 XML_3.98-1.1 xtable_1.7-3
[70] XVector_0.2.0 zlibbioc_1.8.0
--------------------------------------
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
peter dalgaard
2014-Jun-12 09:02 UTC
[Rd] do.call Error for Function Not Present When Manually Called
On 12 Jun 2014, at 09:00 , Dario Strbenac <dstr7320 at uni.sydney.edu.au> wrote:> Hello, > > The e1071 function naiveBayes gives an error when called by do.call, although it doesn't give any error if I call it manually. > > Browse[1]> trainParams at classifier > function (x, ...) > UseMethod("naiveBayes") > <environment: namespace:e1071> > Browse[1]> trained <- do.call(trainParams at classifier, paramList) > Error in names(dimnames(tables[[i]])) <- c(Yname, colnames(x)[i]) : > 'names' attribute [4] must be the same length as the vector [2] > Browse[1]> summary(paramList) > Length Class Mode > 925 -none- numeric > 37 factor numeric > verbose 1 -none- logical > Browse[1]> class(trainParams at classifier(paramList[[1]], paramList[[2]], paramList[[3]])) > [1] "naiveBayes" > > What is the explanation for this ? I read that the behaviour of do.call is currently undefined and subject to change.Read where? Not in the documentation, as far as I can see. Problems with do.call are usually related to lack of lazy evaluation since "args" in do.call is a list of _evaluated_ arguments. You're not giving sufficient context, but I would conjecture that "Yname" is computed via deparse(substitute(Y)) or something like that. If so, you will run into effects like this (notice the y axis title):> x <- rnorm(3) > do.call("plot", list(x))or, possibly the exact problem for you:> y <- rnorm(10) > yname <- function(y)deparse(substitute(y)) > do.call("yname", list(y))[1] "c(-0.750056154880415, -1.70241489930364, 2.36590757548367, -1.3989317670186, " [2] "0.125698210447379, 0.446013380855154, -0.949447325668307, 0.388833055449324, " [3] "1.61595795424046, -0.657071605757215)" in which the "name" of the vector becomes a character vector of length 3, not 1, because of line breaks. Using list(quote(y)) sometimes helps, but you may need some care that y gets evaluated in the correct environment.> > Browse[1]> sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 splines parallel grid stats graphics grDevices > [8] utils datasets methods base > > other attached packages: > [1] robustbase_0.91-1 e1071_1.6-3 > [3] car_2.0-20 edgeR_3.6.2 > [5] statmod_1.4.19 PoiClaClu_1.0.2 > [7] lawstat_2.4.1 VGAM_0.9-4 > [9] mvtnorm_0.9-99992 sparsediscrim_0.2 > [11] MASS_7.3-33 curatedOvarianData_1.2.0 > [13] affy_1.40.0 lumiHumanIDMapping_1.10.0 > [15] illuminaHumanv3.db_1.20.0 org.Hs.eg.db_2.10.1 > [17] RSQLite_0.11.4 DBI_0.2-7 > [19] AnnotationDbi_1.24.0 lumi_2.14.2 > [21] Biobase_2.22.0 BiocGenerics_0.8.0 > [23] limma_3.18.13 ROCR_1.0-5 > [25] gplots_2.13.0 gridExtra_0.9.1 > [27] ggplot2_1.0.0 > > loaded via a namespace (and not attached): > [1] affyio_1.30.0 annotate_1.40.1 AnnotationForge_1.4.4 > [4] base64_1.1 bdsmatrix_1.3-1 beanplot_1.1 > [7] BiocInstaller_1.14.2 biomaRt_2.18.0 Biostrings_2.30.1 > [10] bitops_1.0-6 BSgenome_1.30.0 bumphunter_1.2.0 > [13] caTools_1.17 class_7.3-10 codetools_0.2-8 > [16] colorspace_1.2-4 corpcor_1.6.6 DEoptimR_1.0-1 > [19] digest_0.6.4 doRNG_1.6 foreach_1.4.2 > [22] gdata_2.13.3 genefilter_1.44.0 GenomicFeatures_1.14.5 > [25] GenomicRanges_1.14.4 gtable_0.1.2 gtools_3.4.0 > [28] illuminaio_0.4.0 IRanges_1.20.7 iterators_1.0.7 > [31] itertools_0.1-3 KernSmooth_2.23-12 labeling_0.2 > [34] lattice_0.20-29 locfit_1.5-9.1 Matrix_1.1-3 > [37] matrixStats_0.8.14 mclust_4.3 methylumi_2.8.0 > [40] mgcv_1.7-29 minfi_1.8.9 multtest_2.18.0 > [43] munsell_0.4.2 nleqslv_2.1.1 nlme_3.1-117 > [46] nnet_7.3-8 nor1mix_1.1-4 pkgmaker_0.22 > [49] plyr_1.8.1 preprocessCore_1.24.0 proto_0.3-10 > [52] RColorBrewer_1.0-5 Rcpp_0.11.1 RCurl_1.95-4.1 > [55] registry_0.2 reshape_0.8.5 reshape2_1.4 > [58] R.methodsS3_1.6.1 rngtools_1.2.4 Rsamtools_1.14.3 > [61] rtracklayer_1.22.7 scales_0.2.4 siggenes_1.36.0 > [64] stringr_0.6.2 survival_2.37-7 tcltk_3.1.0 > [67] tools_3.1.0 XML_3.98-1.1 xtable_1.7-3 > [70] XVector_0.2.0 zlibbioc_1.8.0 > > -------------------------------------- > Dario Strbenac > PhD Student > University of Sydney > Camperdown NSW 2050 > Australia > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel-- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com