Too many dependencies? - Githubissues

Apparently, loading scone loads 136 dependent packages!

library(scone)
sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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 
[8] methods   base     

other attached packages:
 [1] scone_1.1.0                bigmemory_4.5.19          
 [3] bigmemory.sri_0.1.3        SummarizedExperiment_1.7.5
 [5] DelayedArray_0.3.16        matrixStats_0.52.2        
 [7] Biobase_2.37.2             GenomicRanges_1.29.6      
 [9] GenomeInfoDb_1.13.4        IRanges_2.11.5            
[11] S4Vectors_0.15.4           BiocGenerics_0.23.0       

loaded via a namespace (and not attached):
  [1] aroma.light_3.7.0        NMF_0.20.6               igraph_1.0.1            
  [4] plyr_1.8.4               lazyeval_0.2.0           shinydashboard_0.6.1    
  [7] splines_3.4.0            BiocParallel_1.11.2      scater_1.5.0            
 [10] ggplot2_2.2.1            gridBase_0.4-7           digest_0.6.12           
 [13] foreach_1.4.3            htmltools_0.3.6          viridis_0.4.0           
 [16] gdata_2.18.0             magrittr_1.5             memoise_1.1.0           
 [19] cluster_2.0.6            doParallel_1.0.10        mixtools_1.1.0          
 [22] limma_3.33.3             Biostrings_2.45.2        annotate_1.55.0         
 [25] bayesm_3.0-2             R.utils_2.5.0            rARPACK_0.11-0          
 [28] prettyunits_1.0.2        colorspace_1.3-2         dplyr_0.7.1             
 [31] tximport_1.5.0           RCurl_1.95-4.8           jsonlite_1.5            
 [34] hexbin_1.27.1            genefilter_1.59.0        bindr_0.1               
 [37] survival_2.41-3          zoo_1.8-0                iterators_1.0.8         
 [40] glue_1.1.1               registry_0.3             gtable_0.2.0            
 [43] zlibbioc_1.23.0          XVector_0.17.0           compositions_1.40-1     
 [46] kernlab_0.9-25           prabclus_2.2-6           DEoptimR_1.0-8          
 [49] scales_0.4.1             DESeq_1.29.0             mvtnorm_1.0-6           
 [52] DBI_0.7                  edgeR_3.19.1             rngtools_1.2.4          
 [55] miniUI_0.1.1             Rcpp_0.12.11             viridisLite_0.2.0       
 [58] xtable_1.8-2             progress_1.1.2           mclust_5.3              
 [61] DT_0.2                   htmlwidgets_0.8          httr_1.2.1              
 [64] FNN_1.1                  gplots_3.0.1             RColorBrewer_1.1-2      
 [67] fpc_2.1-10               modeltools_0.2-21        pkgconfig_2.0.1         
 [70] XML_3.98-1.9             R.methodsS3_1.7.1        flexmix_2.3-14          
 [73] nnet_7.3-12              locfit_1.5-9.1           dynamicTreeCut_1.63-1   
 [76] rlang_0.1.1.9000         reshape2_1.4.2           AnnotationDbi_1.39.1    
 [79] munsell_0.4.3            tools_3.4.0              visNetwork_1.0.3        
 [82] RSQLite_1.1-2            stringr_1.2.0            robustbase_0.92-7       
 [85] caTools_1.17.1           purrr_0.2.2.2            bindrcpp_0.2            
 [88] EDASeq_2.11.0            mime_0.5                 scran_1.5.3             
 [91] R.oo_1.21.0              biomaRt_2.33.3           compiler_3.4.0          
 [94] beeswarm_0.2.3           plotly_4.7.0             tibble_1.3.3            
 [97] statmod_1.4.30           geneplotter_1.55.0       stringi_1.1.5           
[100] GenomicFeatures_1.29.6   RSpectra_0.12-0          lattice_0.20-35         
[103] trimcluster_0.1-2        Matrix_1.2-10            tensorA_0.36            
[106] data.table_1.10.4        bitops_1.0-6             httpuv_1.3.3            
[109] rtracklayer_1.37.2       R6_2.2.2                 latticeExtra_0.6-28     
[112] hwriter_1.3.2            ShortRead_1.35.1         gridExtra_2.2.1         
[115] KernSmooth_2.23-15       vipor_0.4.5              codetools_0.2-15        
[118] boot_1.3-19              energy_1.7-0             MASS_7.3-47             
[121] gtools_3.5.0             assertthat_0.2.0         rhdf5_2.21.2            
[124] rjson_0.2.15             pkgmaker_0.22            RUVSeq_1.11.0           
[127] GenomicAlignments_1.13.2 Rsamtools_1.29.0         GenomeInfoDbData_0.99.1 
[130] diptest_0.75-7           grid_3.4.0               tidyr_0.6.3             
[133] class_7.3-14             segmented_0.5-2.1        shiny_1.0.3             
[136] ggbeeswarm_0.5.3

Is there a way to move some of the Imports: in Suggests: so that we don't pollute so much the R session? (I'm thinking of all the functions in SCONE_DEFAULTS.R for instance).

YosefLab / scone

Too many dependencies? #88