[BioC] SomaticSignatures: could not find function "motifMatrix"

[Max Salm [guest]]

Dear Sir/Madam,

I have been working through your excellent vignette for the SomaticSignatures package (http://www.bioconductor.org/packages/devel/bioc/vignettes/SomaticSignatures/inst/doc/SomaticSignatures-vignette.html ), but when I reach the motifMatrix step, the function appears to missing. Has motifMatrix been deprecated?

Kind regards,

Max

 -- output of sessionInfo(): 

R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.3.99 BSgenome_1.32.0                   
 [3] SomaticCancerAlterations_1.0.0     stringr_0.6.2                     
 [5] ggplot2_1.0.0                      VariantAnnotation_1.10.5          
 [7] Rsamtools_1.16.1                   Biostrings_2.32.1                 
 [9] XVector_0.4.0                      GenomicRanges_1.16.3              
[11] GenomeInfoDb_1.0.2                 IRanges_1.22.9                    
[13] SomaticSignatures_1.0.1            Biobase_2.24.0                    
[15] BiocGenerics_0.10.0                BiocInstaller_1.14.2              

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.26.0    BatchJobs_1.3           BBmisc_1.7             
 [4] BiocParallel_0.6.1      biomaRt_2.20.0          biovizBase_1.12.1      
 [7] bitops_1.0-6            brew_1.0-6              checkmate_1.1          
[10] cluster_1.15.2          codetools_0.2-8         colorspace_1.2-4       
[13] DBI_0.2-7               dichromat_2.0-0         digest_0.6.4           
[16] doParallel_1.0.8        exomeCopy_1.10.0        fail_1.2               
[19] foreach_1.4.2           Formula_1.1-2           GenomicAlignments_1.0.3
[22] GenomicFeatures_1.16.2  ggbio_1.12.8            grid_3.1.1             
[25] gridBase_0.4-7          gridExtra_0.9.1         gtable_0.1.2           
[28] gtools_3.4.1            Hmisc_3.14-4            iterators_1.0.7        
[31] lattice_0.20-29         latticeExtra_0.6-26     MASS_7.3-33            
[34] munsell_0.4.2           NMF_0.20.5              pcaMethods_1.54.0      
[37] pkgmaker_0.22           plyr_1.8.1              proto_0.3-10           
[40] RColorBrewer_1.0-5      Rcpp_0.11.2             RCurl_1.95-4.1         
[43] registry_0.2            reshape2_1.4            rngtools_1.2.4         
[46] RSQLite_0.11.4          rtracklayer_1.24.2      scales_0.2.4           
[49] sendmailR_1.1-2         splines_3.1.1           stats4_3.1.1           
[52] survival_2.37-7         tools_3.1.1             XML_3.98-1.1           
[55] xtable_1.7-3            zlibbioc_1.10.0 

--
Sent via the guest posting facility at bioconductor.org.