robbyjo/r-mkl-bioconductor repository overview

This version is WITHOUT Java or R-shlib. Refer to robbyjo/r-mkl-shlib-bioconductor R Versions 3.4.0 and 3.4.1 are ready. See tags.

Q: What is the difference between robbyjo/r-mkl-bioconductor with robbyjo/r-mkl-shlib-bioconductor?

A: Both have the same set of libraries. The latter compile R as shared library (hence "shlib"), which allows integration with other languages (e.g., C/C++, Python, Ruby, etc.). The drawbacks are:

1. R developers claim that having shlib enabled will make R run slower. However my limited empirical results say that they are about the same.
2. The shlib enabled version is quite a bit bigger.

Installed R packages (for ver. 3.4.2-16.04-2018.0): Installed packages,Version AER,1.2-5 Amelia,1.7.4 AnnotationDbi,1.38.2 AnnotationFilter,1.0.0 AnnotationHub,2.8.2 BH,1.65.0-1 BSgenome,1.44.2 Biobase,2.36.2 BiocGenerics,0.22.0 BiocInstaller,1.26.1 BiocParallel,1.10.1 BiocStyle,2.4.1 Biostrings,2.44.2 CompQuadForm,1.4.3 DBI,0.7 DESeq2,1.16.1 DEoptimR,1.0-8 DNAcopy,1.50.1 DelayedArray,0.2.7 ExperimentHub,1.2.0 FDb.InfiniumMethylation.hg19,2.2.0 Formula,1.2-2 GENESIS,2.6.1 GEOquery,2.42.0 GGally,1.3.2 GO.db,3.4.1 GSEABase,1.38.2 GWAF,2.2 GWASExactHW,1.01 GWASTools,1.22.0 GenomeInfoDb,1.12.2 GenomeInfoDbData,0.99.0 GenomicAlignments,1.12.2 GenomicFeatures,1.28.5 GenomicRanges,1.28.6 Gviz,1.20.0 Hmisc,4.0-3 IRanges,2.10.4 IlluminaHumanMethylation450kanno.ilmn12.hg19,0.6.0 KEGGgraph,1.38.1 KernSmooth,2.23-15 MASS,7.3-47 MCMCpack,1.4-0 MatchIt,3.0.1 Matching,4.9-2 Matrix,1.2-11 MatrixModels,0.4-1 OrganismDbi,1.18.0 ProtGenerics,1.8.0 R.methodsS3,1.7.1 R.oo,1.21.0 R.utils,2.5.0 R6,2.2.2 RBGL,1.52.0 RColorBrewer,1.1-2 RCurl,1.95-4.8 ROC,1.52.0 RSQLite,2.0 Rcpp,0.12.13 RcppArmadillo,0.7.960.1.2 RcppEigen,0.3.3.3.0 Rgraphviz,2.20.0 Rsamtools,1.28.0 S4Vectors,0.14.6 SKAT,1.3.2.1 SNPRelate,1.10.2 SeqArray,1.16.1 SeqVarTools,1.14.0 ShortRead,1.34.1 SparseM,1.77 SummarizedExperiment,1.6.5 SuppDists,1.1-9.4 TSP,1.1-5 TxDb.Hsapiens.UCSC.hg19.knownGene,3.2.2 VGAM,1.0-4 VariantAnnotation,1.22.3 WGCNA,1.61 XML,3.98-1.9 XVector,0.16.0 Zelig,5.1-4 ZeligChoice,0.9-6 ZeligEI,0.1-2 acepack,1.4.1 affy,1.54.0 affyio,1.46.0 annotate,1.54.0 argparser,0.4 assertthat,0.2.0 backports,1.1.1 base,3.4.2 base64,2.0 base64enc,0.1-3 bdsmatrix,1.3-2 beanplot,1.2 betareg,3.1-0 bindr,0.1 bindrcpp,0.2 biomaRt,2.32.1 biovizBase,1.24.0 bit,1.1-12 bit64,0.9-7 bitops,1.0-6 blob,1.1.0 bnlearn,4.2 bookdown,0.5 boot,1.3-20 bumphunter,1.16.0 caTools,1.17.1 car,2.1-5 censReg,0.5-26 checkmate,1.8.4 chron,2.3-50 class,7.3-14 cluster,2.0.6 coda,0.19-1 codetools,0.2-15 colorspace,1.3-2 compiler,3.4.2 coxme,2.2-5 cubature,1.3-11 curl,2.8.1 data.table,1.10.4 datasets,3.4.2 dendextend,1.5.2 devtools,1.13.3 dichromat,2.0-0 digest,0.6.12 diptest,0.75-7 doMC,1.3.4 doParallel,1.0.11 doRNG,1.6.6 dplyr,0.7.4 dynamicTreeCut,1.63-1 e1071,1.6-8 edgeR,3.18.1 ei,1.3-3 eiPack,0.1-7 ellipse,0.3-8 ensembldb,2.0.4 evaluate,0.10.1 expm,0.999-2 fastcluster,1.1.24 filematrix,1.1.0 fit.models,0.5-14 flexmix,2.3-14 foreach,1.4.3 foreign,0.8-69 fpc,2.1-10 futile.logger,1.4.3 futile.options,1.0.0 gamlss,5.0-2 gamlss.data,5.0-0 gamlss.dist,5.0-2 gclus,1.3.1 gdata,2.18.0 gdsfmt,1.12.0 gee,4.13-19 geepack,1.2-1 genefilter,1.58.1 geneplotter,1.54.0 ggplot2,2.2.1 git2r,0.19.0 githubinstall,0.2.1 glmmML,1.0.2 glue,1.1.1 gmm,1.6-1 gplots,3.0.1 grDevices,3.4.2 grImport,0.9-0 graph,1.54.0 graphics,3.4.2 grid,3.4.2 gridExtra,2.3 gsubfn,0.6-6 gtable,0.2.0 gtools,3.5.0 highr,0.6 htmlTable,1.9 htmltools,0.3.6 htmlwidgets,0.9 httpuv,1.3.5 httr,1.3.1 hwriter,1.3.2 illuminaio,0.18.0 impute,1.50.1 interactiveDisplayBase,1.14.0 iterators,1.0.8 jsonlite,1.5 kernlab,0.9-25 kinship,1.1.3 kinship2,1.6.4 knitr,1.17 labeling,0.3 lambda.r,1.2 lars,1.2 lattice,0.20-35 latticeExtra,0.6-28 lavaan,0.5-23.1097 lazyeval,0.2.0 limma,3.32.7 lme4,1.1-14 lmtest,0.9-35 locfit,1.5-9.1 logistf,1.22 lpSolve,5.6.13 lubridate,1.6.0 lumi,2.28.0 magrittr,1.5 markdown,0.8 matrixStats,0.52.2 maxLik,1.3-4 mclust,5.3 mcmc,0.9-5 mediation,4.4.6 memoise,1.1.0 metafor,2.0-0 methods,3.4.2 methylumi,2.22.0 mgcv,1.8-22 mice,2.30 mime,0.5 minfi,1.22.1 minqa,1.2.4 miscTools,0.6-22 mlogit,0.2-4 mnormt,1.5-5 modeltools,0.2-21 moments,0.14 msm,1.6.4 multtest,2.32.0 munsell,0.4.3 mvtnorm,1.0-6 ncdf4,1.16 nleqslv,3.3.1 nlme,3.1-131 nloptr,1.0.4 nnet,7.3-12 nor1mix,1.2-3 numDeriv,2016.8-1 openssl,0.9.7 org.Hs.eg.db,3.4.1 parallel,3.4.2 pbivnorm,0.6.0 pbkrtest,0.4-7 pcaMethods,1.68.0 pcaPP,1.9-72 pedigreemm,0.3-3 pkgconfig,2.0.1 pkgmaker,0.22 plm,1.6-5 plogr,0.1-1 plotrix,3.6-6 pls,2.6-0 plyr,1.8.4 prabclus,2.2-6 preprocessCore,1.38.1 prettyunits,1.0.2 progress,1.1.2 proto,1.0.0 pscl,1.5.1 pspearman,0.3-0 purrr,0.2.3 qap,0.1-1 quadprog,1.5-5 quantreg,5.33 quantsmooth,1.42.0 qvalue,2.8.0 randomForest,4.6-12 registry,0.3 reshape,0.8.7 reshape2,1.4.2 rgenoud,5.7-12.4 rhdf5,2.20.0 rlang,0.1.2 rmarkdown,1.6 rngtools,1.2.4 robust,0.4-18 robustbase,0.92-7 robustlmm,2.1-3 rpart,4.1-11 rprojroot,1.2 rrcov,1.4-3 rstudioapi,0.7 rtracklayer,1.36.5 sandwich,2.4-0 scales,0.5.0 seriation,1.2-2 shiny,1.0.5 siggenes,1.50.0 snow,0.4-2 sourcetools,0.1.6 sp,1.2-5 spatial,7.3-11 splines,3.4.2 sqldf,0.4-11 statmod,1.4.30 stats,3.4.2 stats4,3.4.2 stringi,1.1.5 stringr,1.2.0 survey,3.32-1 survival,2.41-3 sva,3.24.4 tcltk,3.4.2 tibble,1.3.4 tidyr,0.7.1 tidyselect,0.2.0 tmvtnorm,1.4-10 tools,3.4.2 trimcluster,0.1-2 truncreg,0.2-4 ucminf,1.1-4 utils,3.4.2 viridis,0.4.0 viridisLite,0.2.0 wateRmelon,1.20.3 whisker,0.3-2 withr,2.0.0 xtable,1.8-2 yaml,2.1.14 zlibbioc,1.22.0 zoo,1.8-0