Public | Automated Build

Last pushed: 18 days ago
Short Description
R 3.4.x with MKL 2017.3 on Ubuntu Trusty (14.04.5) plus Bioconductor base packages plus plus.
Full Description

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

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