* sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

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  methods   base     

other attached packages:
[1] BiocInstaller_1.26.0       ggthemes_3.4.0             tidyr_0.7.0                reshape2_1.4.2             genefilter_1.58.1        
[6] PoiClaClu_1.0.2            RColorBrewer_1.1-2         pheatmap_1.0.8             ggplot2_2.2.1              DESeq2_1.16.1            
[11] SummarizedExperiment_1.6.3 DelayedArray_0.2.7         matrixStats_0.52.2         Biobase_2.36.2             GenomicRanges_1.28.4     
[16] GenomeInfoDb_1.12.2        IRanges_2.10.2             S4Vectors_0.14.3           BiocGenerics_0.22.0        ciiDE_1.0.0              
[21] devtools_1.13.3           

loaded via a namespace (and not attached):
[1] bit64_0.9-7             splines_3.4.0           Formula_1.2-2           assertthat_0.2.0        latticeExtra_0.6-28     blob_1.1.0            
[7] GenomeInfoDbData_0.99.0 RSQLite_2.0             backports_1.1.0         lattice_0.20-35         glue_1.1.1              digest_0.6.12         
[13] XVector_0.16.0          checkmate_1.8.3         colorspace_1.3-2        htmltools_0.3.6         Matrix_1.2-11           plyr_1.8.4            
[19] XML_3.98-1.9            zlibbioc_1.22.0         purrr_0.2.3             xtable_1.8-2            scales_0.5.0            BiocParallel_1.10.1   
[25] git2r_0.19.0            htmlTable_1.9           tibble_1.3.4            annotate_1.54.0         withr_2.0.0             nnet_7.3-12           
[31] lazyeval_0.2.0          survival_2.41-3         magrittr_1.5            crayon_1.3.2            memoise_1.1.0           xml2_1.1.1            
[37] foreign_0.8-69          tools_3.4.0             data.table_1.10.4       stringr_1.2.0           munsell_0.4.3           locfit_1.5-9.1        
[43] cluster_2.0.6           AnnotationDbi_1.38.2    compiler_3.4.0          rlang_0.1.2             grid_3.4.0              RCurl_1.95-4.8        
[49] htmlwidgets_0.9         bitops_1.0-6            base64enc_0.1-3         gtable_0.2.0            DBI_0.7                 roxygen2_6.0.1.9000   
[55] R6_2.2.2                gridExtra_2.2.1         knitr_1.17              bit_1.1-12              commonmark_1.2          Hmisc_4.0-3           
[61] rprojroot_1.2           desc_1.1.1              stringi_1.1.5           Rcpp_0.12.12            geneplotter_1.54.0      rpart_4.1-11          
[67] acepack_1.4.1          

* Out-of-date packages
                     Package                LibPath                                                          Installed     Built   ReposVer    
backports            "backports"            "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.1.0"       "3.4.0" "1.1.1"     
BiocInstaller        "BiocInstaller"        "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.26.0"      "3.4.0" "1.26.1"    
BSgenome             "BSgenome"             "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.44.1"      "3.4.1" "1.44.2"    
caret                "caret"                "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "6.0-76"      "3.4.0" "6.0-77"    
checkmate            "checkmate"            "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.8.3"       "3.4.1" "1.8.4"     
commonmark           "commonmark"           "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.2"         "3.4.0" "1.4"       
crayon               "crayon"               "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.3.2"       "3.4.0" "1.3.4"     
doParallel           "doParallel"           "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.0.10"      "3.4.0" "1.0.11"    
dplyr                "dplyr"                "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.7.2"       "3.4.1" "0.7.4"     
energy               "energy"               "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.7-0"       "3.4.0" "1.7-2"     
gdtools              "gdtools"              "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.1.5"       "3.4.1" "0.1.6"     
GenomicFeatures      "GenomicFeatures"      "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.28.4"      "3.4.0" "1.28.5"    
GenomicRanges        "GenomicRanges"        "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.28.4"      "3.4.1" "1.28.5"    
ggjoy                "ggjoy"                "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.3.0"       "3.4.1" "0.4.0"     
glmnet               "glmnet"               "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "2.0-10"      "3.4.0" "2.0-13"    
gridExtra            "gridExtra"            "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "2.2.1"       "3.4.0" "2.3"       
IRanges              "IRanges"              "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "2.10.2"      "3.4.0" "2.10.3"    
lambda.r             "lambda.r"             "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.1.9"       "3.4.0" "1.2"       
lava                 "lava"                 "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.5"         "3.4.0" "1.5.1"     
limma                "limma"                "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "3.32.5"      "3.4.1" "3.32.7"    
lme4                 "lme4"                 "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.1-13"      "3.4.0" "1.1-14"    
multcomp             "multcomp"             "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.4-6"       "3.4.0" "1.4-7"     
openssl              "openssl"              "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.9.6"       "3.4.0" "0.9.7"     
psych                "psych"                "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.7.5"       "3.4.0" "1.7.8"     
Rcpp                 "Rcpp"                 "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.12.12"     "3.4.1" "0.12.13"   
RcppArmadillo        "RcppArmadillo"        "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.7.900.2.0" "3.4.0" "0.7.960.1.2"
rstudioapi           "rstudioapi"           "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.6"         "3.4.0" "0.7"       
S4Vectors            "S4Vectors"            "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.14.3"      "3.4.0" "0.14.5"    
segmented            "segmented"            "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.5-2.1"     "3.4.0" "0.5-2.2"   
SummarizedExperiment "SummarizedExperiment" "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.6.3"       "3.4.0" "1.6.5"     
svglite              "svglite"              "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.2.0"       "3.4.0" "1.2.1"     
tidyr                "tidyr"                "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.7.0"       "3.4.1" "0.7.1"     
tidyselect           "tidyselect"           "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.1.1"       "3.4.1" "0.2.0"     
                     Repository                                             
backports            "https://cran.rstudio.com/src/contrib"                 
BiocInstaller        "https://bioconductor.org/packages/3.5/bioc/src/contrib"
BSgenome             "https://bioconductor.org/packages/3.5/bioc/src/contrib"
caret                "https://cran.rstudio.com/src/contrib"                 
checkmate            "https://cran.rstudio.com/src/contrib"                 
commonmark           "https://cran.rstudio.com/src/contrib"                 
crayon               "https://cran.rstudio.com/src/contrib"                 
doParallel           "https://cran.rstudio.com/src/contrib"                 
dplyr                "https://cran.rstudio.com/src/contrib"                 
energy               "https://cran.rstudio.com/src/contrib"                 
gdtools              "https://cran.rstudio.com/src/contrib"                 
GenomicFeatures      "https://bioconductor.org/packages/3.5/bioc/src/contrib"
GenomicRanges        "https://bioconductor.org/packages/3.5/bioc/src/contrib"
ggjoy                "https://cran.rstudio.com/src/contrib"                 
glmnet               "https://cran.rstudio.com/src/contrib"                 
gridExtra            "https://cran.rstudio.com/src/contrib"                 
IRanges              "https://bioconductor.org/packages/3.5/bioc/src/contrib"
lambda.r             "https://cran.rstudio.com/src/contrib"                 
lava                 "https://cran.rstudio.com/src/contrib"                 
limma                "https://bioconductor.org/packages/3.5/bioc/src/contrib"
lme4                 "https://cran.rstudio.com/src/contrib"                 
multcomp             "https://cran.rstudio.com/src/contrib"                 
openssl              "https://cran.rstudio.com/src/contrib"                 
psych                "https://cran.rstudio.com/src/contrib"                 
Rcpp                 "https://cran.rstudio.com/src/contrib"                 
RcppArmadillo        "https://cran.rstudio.com/src/contrib"                 
rstudioapi           "https://cran.rstudio.com/src/contrib"                 
S4Vectors            "https://bioconductor.org/packages/3.5/bioc/src/contrib"
segmented            "https://cran.rstudio.com/src/contrib"                 
SummarizedExperiment "https://bioconductor.org/packages/3.5/bioc/src/contrib"
svglite              "https://cran.rstudio.com/src/contrib"                 
tidyr                "https://cran.rstudio.com/src/contrib"                 
tidyselect           "https://cran.rstudio.com/src/contrib"                  

update with biocLite()

* Packages too new for Bioconductor version '3.5'

         Version      LibPath                                                        
roxygen2 "6.0.1.9000" "/Library/Frameworks/R.framework/Versions/3.4/Resources/library"

downgrade with biocLite("roxygen2")

Error: 33 package(s) out of date; 1 package(s) too new