[BioC] Problem in generating heatmap after R and Bioconductor Update

[Remo [guest]]

Dear list,
I'm having issues in generating an heatmap which occurred only after the upgrade to ver. 3.1.1
Below you find a very easy example which works in previous R version 3.0.2 but not in ver. 3.1.1 giving the following error.

Error in heatmap.2(t(mtcars), dendrogram = c("col"), Rowv = FALSE, Colv = as.dendrogram(xClust)) :
  Colv dendrogram doesn't match size of x

I've also added sessionInfo() for the NOT WORKING case and WORKING case.

Can anyone help me to understand why a script that was working 2 weeks ago isn't working anymore?

Thanks for your help

Remo


data(mtcars)
mtcars

xDist<-dist(mtcars,method="euclidean")
xClust<-hclust(xDist,method="complete")
plot(xClust,labels=FALSE)

heatmap.2(t(mtcars),
          dendrogram=c("col"),
          Rowv=FALSE,
          Colv=as.dendrogram(xClust))


-- 







__________________________________________________________

Remo Chiozzotto PhD
CNR (National Research Council)
Institute of Agricultural Biology and Biotechnology (IBBA)
Via E. Bassini, 15 - 20133 - Milano (Italy)
Office +39 0223699427 
Lab    +39 0223699426
Fax    +39 0223699411
e-mail: remo.chiozzotto at ibba.cnr.it
skype:  remo.chiozzotto
__________________________________________________________



 -- output of sessionInfo(): 

NOT WORKING

R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8        LC_COLLATE=en_US.UTF-8   
[5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=it_IT.UTF-8       LC_NAME=C                
[9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C      

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] NMF_0.20.5              Biobase_2.24.0          cluster_1.15.2          rngtools_1.2.4          pkgmaker_0.22         
[6] registry_0.2            gplots_2.14.0           edgeR_3.6.4             limma_3.20.8            RColorBrewer_1.0-5    
[11] ShortRead_1.22.0        GenomicAlignments_1.0.1 BSgenome_1.32.0         Rsamtools_1.16.1        GenomicRanges_1.16.3  
[16] GenomeInfoDb_1.0.2      Biostrings_2.32.0       XVector_0.4.0           IRanges_1.22.9          BiocParallel_0.6.1    
[21] BiocGenerics_0.10.0   

loaded via a namespace (and not attached):
[1] BatchJobs_1.2       BBmisc_1.7          bitops_1.0-6        brew_1.0-6          caTools_1.17        checkmate_1.1     
[7] codetools_0.2-8     colorspace_1.2-4    DBI_0.2-7           digest_0.6.4        doParallel_1.0.8    fail_1.2          
[13] foreach_1.4.2       gdata_2.13.3        ggplot2_1.0.0       grid_3.1.1          gridBase_0.4-7      gtable_0.1.2      
[19] gtools_3.4.1        hwriter_1.3         iterators_1.0.7     KernSmooth_2.23-12  lattice_0.20-29     latticeExtra_0.6-26
[25] MASS_7.3-33         munsell_0.4.2       plyr_1.8.1          proto_0.3-10        Rcpp_0.11.2         reshape2_1.4      
[31] RSQLite_0.11.4      scales_0.2.4        sendmailR_1.1-2     stats4_3.1.1        stringr_0.6.2       tools_3.1.1       
[37] xtable_1.7-3        zlibbioc_1.10.0  

WORKING

R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Italian_Italy.1252  LC_CTYPE=Italian_Italy.1252  
[3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C                 
[5] LC_TIME=Italian_Italy.1252   

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets
[8] methods   base    

other attached packages:
 [1] NMF_0.20.5           Biobase_2.22.0       cluster_1.14.4     
 [4] rngtools_1.2.4       pkgmaker_0.22        registry_0.2       
 [7] gplots_2.14.1        RColorBrewer_1.0-5   ShortRead_1.20.0   
[10] Rsamtools_1.14.3     lattice_0.20-24      Biostrings_2.30.1  
[13] GenomicRanges_1.14.4 XVector_0.2.0        IRanges_1.20.6     
[16] BiocGenerics_0.8.0   BiocInstaller_1.12.1 edgeR_3.4.2        
[19] limma_3.18.13      

loaded via a namespace (and not attached):
 [1] bitops_1.0-6        caTools_1.17        codetools_0.2-8   
 [4] colorspace_1.2-4    digest_0.6.4        doParallel_1.0.8  
 [7] foreach_1.4.2       gdata_2.13.3        ggplot2_1.0.0     
[10] grid_3.0.2          gridBase_0.4-7      gtable_0.1.2      
[13] gtools_3.4.1        hwriter_1.3         iterators_1.0.7   
[16] KernSmooth_2.23-10  latticeExtra_0.6-26 MASS_7.3-29       
[19] munsell_0.4.2       plyr_1.8.1          proto_0.3-10      
[22] Rcpp_0.11.2         reshape2_1.4        scales_0.2.4      
[25] stats4_3.0.2        stringr_0.6.2       tools_3.0.2       
[28] xtable_1.7-3        zlibbioc_1.8.0


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