sessionInfo()
## R version 3.3.1 (2016-06-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 14.04.4 LTS
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
##  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
## [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats4    methods   stats     graphics  utils     datasets  grDevices base     
## 
## other attached packages:
##  [1] systemPipeR_1.6.2          ShortRead_1.30.0           GenomicAlignments_1.8.3   
##  [4] SummarizedExperiment_1.2.3 Biobase_2.32.0             BiocParallel_1.6.2        
##  [7] Rsamtools_1.24.0           Biostrings_2.40.2          XVector_0.12.0            
## [10] GenomicRanges_1.24.2       GenomeInfoDb_1.8.1         IRanges_2.6.1             
## [13] S4Vectors_0.10.1           BiocGenerics_0.18.0        BiocStyle_2.0.2           
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.5            lattice_0.20-33        GO.db_3.3.0            digest_0.6.9          
##  [5] plyr_1.8.4             BatchJobs_1.6          backports_1.0.3        RSQLite_1.0.0         
##  [9] evaluate_0.9           ggplot2_2.1.0          zlibbioc_1.18.0        GenomicFeatures_1.24.3
## [13] annotate_1.50.0        Matrix_1.2-6           checkmate_1.8.1        rmarkdown_0.9.6       
## [17] GOstats_2.38.1         splines_3.3.1          stringr_1.0.0          pheatmap_1.0.8        
## [21] RCurl_1.95-4.8         biomaRt_2.28.0         munsell_0.4.3          sendmailR_1.2-1       
## [25] rtracklayer_1.32.1     base64enc_0.1-3        BBmisc_1.9             htmltools_0.3.5       
## [29] fail_1.3               edgeR_3.14.0           codetools_0.2-14       XML_3.98-1.4          
## [33] AnnotationForge_1.14.2 bitops_1.0-6           grid_3.3.1             RBGL_1.48.1           
## [37] xtable_1.8-2           GSEABase_1.34.0        gtable_0.2.0           DBI_0.4-1             
## [41] magrittr_1.5           formatR_1.4            scales_0.4.0           graph_1.50.0          
## [45] stringi_1.1.1          hwriter_1.3.2          genefilter_1.54.2      limma_3.28.14         
## [49] latticeExtra_0.6-28    brew_1.0-6             rjson_0.2.15           RColorBrewer_1.1-2    
## [53] tools_3.3.1            Category_2.38.0        survival_2.39-4        yaml_2.1.13           
## [57] AnnotationDbi_1.34.3   colorspace_1.2-6       knitr_1.13