From dstr7320 at uni.sydney.edu.au  Thu Jun 12 09:00:14 2014
From: dstr7320 at uni.sydney.edu.au (Dario Strbenac)
Date: Thu, 12 Jun 2014 07:00:14 +0000
Subject: [Rd] do.call Error for Function Not Present When Manually Called
Message-ID: <1402560086387.53754@uni.sydney.edu.au>

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



[Rd] do.call Error for Function Not Present When Manually Called
Dario Strbenac