* 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* Out-of-date packages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
