Issues with Somatic Signatures package
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Entering edit mode
ahorn720 ▴ 10
@ahorn720-22603
Last seen 22 months ago

Hello,

Im having trouble running Somatic Signatures in R. I even tried running the example and it gives an error.

> data("sca_mm", package = "SomaticSignatures")
> identifySignatures(sca_mm,5)
Error in (new("standardGeneric", .Data = function (x)  : 
  unused arguments (model = list("NMFstd", 5, 0), method = "random")

Any recommendations on how to fix this error will be greatly appreciated.

Thank you,

Aaron Horning

R Session below:

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] corpcor_1.6.9                     BSgenome.Hsapiens.UCSC.hg38_1.4.1
 [3] BSgenome_1.50.0                   rtracklayer_1.42.2               
 [5] SomaticSignatures_2.18.0          VariantAnnotation_1.28.13        
 [7] Rsamtools_1.34.1                  Biostrings_2.50.2                
 [9] XVector_0.22.0                    SummarizedExperiment_1.12.0      
[11] DelayedArray_0.8.0                BiocParallel_1.16.6              
[13] matrixStats_0.55.0                NMF_0.21.0                       
[15] Biobase_2.42.0                    cluster_2.1.0                    
[17] rngtools_1.4                      pkgmaker_0.27                    
[19] registry_0.5-1                    phangorn_2.5.5                   
[21] ape_5.3                           forcats_0.4.0                    
[23] purrr_0.3.3                       readr_1.3.1                      
[25] tibble_2.1.3                      ggplot2_3.2.1                    
[27] tidyverse_1.3.0                   RColorBrewer_1.1-2               
[29] GenomicRanges_1.34.0              GenomeInfoDb_1.18.2              
[31] IRanges_2.16.0                    S4Vectors_0.20.1                 
[33] BiocGenerics_0.28.0               stringr_1.4.0                    
[35] tidyr_1.0.0                       dplyr_0.8.3                      

loaded via a namespace (and not attached):
  [1] utf8_1.1.4               tidyselect_0.2.5         RSQLite_2.1.2           
  [4] AnnotationDbi_1.44.0     htmlwidgets_1.5.1        grid_3.5.1              
  [7] munsell_0.5.0            codetools_0.2-16         withr_2.1.2             
 [10] colorspace_1.4-1         OrganismDbi_1.24.0       knitr_1.26              
 [13] rstudioapi_0.10          yarrr_0.1.5              GenomeInfoDbData_1.2.0  
 [16] bit64_0.9-7              coda_0.19-3              vctrs_0.2.0             
 [19] generics_0.0.2           xfun_0.11                biovizBase_1.30.1       
 [22] R6_2.4.1                 doParallel_1.0.15        BayesFactor_0.9.12-4.2  
 [25] AnnotationFilter_1.6.0   bitops_1.0-6             reshape_0.8.8           
 [28] assertthat_0.2.1         scales_1.1.0             nnet_7.3-12             
 [31] gtable_0.3.0             swirl_2.4.4              ggbio_1.30.0            
 [34] ensembldb_2.6.8          rlang_0.4.2              MatrixModels_0.4-1      
 [37] zeallot_0.1.0            GlobalOptions_0.1.1      splines_3.5.1           
 [40] lazyeval_0.2.2           acepack_1.4.1            dichromat_2.0-0         
 [43] broom_0.5.2              brew_1.0-6               checkmate_1.9.4         
 [46] BiocManager_1.30.10      yaml_2.2.0               reshape2_1.4.3          
 [49] modelr_0.1.5             GenomicFeatures_1.34.8   backports_1.1.5         
 [52] Hmisc_4.3-0              RBGL_1.58.2              tools_3.5.1             
 [55] gridBase_0.4-7           ellipsis_0.3.0           proxy_0.4-23            
 [58] sessioninfo_1.1.1        Rcpp_1.0.3               plyr_1.8.4              
 [61] base64enc_0.1-3          progress_1.2.2           zlibbioc_1.28.0         
 [64] RCurl_1.95-4.12          prettyunits_1.0.2        rpart_4.1-15            
 [67] pbapply_1.4-2            haven_2.2.0              fs_1.3.1                
 [70] magrittr_1.5             data.table_1.12.6        circlize_0.4.8          
 [73] reprex_0.3.0             pcaMethods_1.74.0        mvtnorm_1.0-11          
 [76] ProtGenerics_1.14.0      hms_0.5.2                xtable_1.8-4            
 [79] XML_3.98-1.20            jpeg_0.1-8.1             readxl_1.3.1            
 [82] gridExtra_2.3            shape_1.4.4              testthat_2.3.0          
 [85] compiler_3.5.1           biomaRt_2.38.0           crayon_1.3.4            
 [88] htmltools_0.4.0          Formula_1.2-3            lubridate_1.7.4         
 [91] DBI_1.0.0                dbplyr_1.4.2             Matrix_1.2-18           
 [94] cli_1.1.0                quadprog_1.5-8           igraph_1.2.4.2          
 [97] pkgconfig_2.0.3          GenomicAlignments_1.18.1 foreign_0.8-72          
[100] xml2_1.2.2               foreach_1.4.7            bibtex_0.4.2            
[103] rvest_0.3.5              digest_0.6.23            graph_1.60.0            
[106] cellranger_1.1.0         fastmatch_1.1-0          htmlTable_1.13.2        
[109] curl_4.2                 gtools_3.8.1             lifecycle_0.1.0         
[112] nlme_3.1-142             jsonlite_1.6             fansi_0.4.0             
[115] pillar_1.4.2             lattice_0.20-38          GGally_1.4.0            
[118] httr_1.4.1               survival_3.1-7           glue_1.3.1              
[121] iterators_1.0.12         bit_1.1-14               stringi_1.4.3           
[124] blob_1.2.0               latticeExtra_0.6-28      memoise_1.1.0  
software error somatic signatures • 213 views
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1
Entering edit mode
@martin-morgan-1513
Last seen 17 days ago
United States

Please verify that your Bioconductor packages are from a consistent version

BiocManager::valid()
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