Public | Automated Build

Last pushed: a month 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:
PackageName,Version
AER,1.2-5
Amelia,1.7.4
AnnotationDbi,1.38.1
AnnotationFilter,1.0.0
AnnotationHub,2.8.1
BH,1.62.0-1
BSgenome,1.44.0
Biobase,2.36.2
BiocGenerics,0.22.0
BiocInstaller,1.26.0
BiocParallel,1.10.1
BiocStyle,2.4.0
Biostrings,2.44.1
CompQuadForm,1.4.3
DBI,0.6-1
DESeq2,1.16.1
DEoptimR,1.0-8
DNAcopy,1.50.1
DelayedArray,0.2.6
ExperimentHub,1.2.0
FDb.InfiniumMethylation.hg19,2.2.0
Formula,1.2-1
GENESIS,2.6.0
GEOquery,2.42.0
GGally,1.3.0
GO.db,3.4.1
GSEABase,1.38.0
GWAF,2.2
GWASExactHW,1.01
GWASTools,1.22.0
GenomeInfoDb,1.12.1
GenomeInfoDbData,0.99.0
GenomicAlignments,1.12.1
GenomicFeatures,1.28.2
GenomicRanges,1.28.3
Gviz,1.20.0
Hmisc,4.0-3
IRanges,2.10.2
IlluminaHumanMethylation450kanno.ilmn12.hg19,0.6.0
KEGGgraph,1.34.0
KernSmooth,2.23-15
MASS,7.3-47
MCMCpack,1.3-9
MatchIt,3.0.1
Matching,4.9-2
Matrix,1.2-10
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
R6,2.2.1
RBGL,1.52.0
RColorBrewer,1.1-2
RCurl,1.95-4.8
ROC,1.52.0
RSQLite,1.1-2
Rcpp,0.12.11
RcppArmadillo,0.7.800.2.0
RcppEigen,0.3.3.3.0
Rgraphviz,2.20.0
Rsamtools,1.28.0
S4Vectors,0.14.2
SKAT,1.3.0
SNPRelate,1.10.2
SeqArray,1.16.0
SeqVarTools,1.14.0
ShortRead,1.34.0
SparseM,1.77
SummarizedExperiment,1.6.3
SuppDists,1.1-9.4
TSP,1.1-5
TxDb.Hsapiens.UCSC.hg19.knownGene,3.2.2
VGAM,1.0-3
VariantAnnotation,1.22.1
WGCNA,1.51
XML,3.98-1.7
XVector,0.16.0
Zelig,5.1-1
ZeligChoice,0.9-5
ZeligEI,0.1-1
acepack,1.4.1
affy,1.54.0
affyio,1.46.0
annotate,1.54.0
argparser,0.4
assertthat,0.2.0
backports,1.1.0
base,3.4.0
base64,2.0
base64enc,0.1-3
bdsmatrix,1.3-2
beanplot,1.2
betareg,3.1-0
biomaRt,2.32.0
biovizBase,1.24.0
bitops,1.0-6
bnlearn,4.1.1
bookdown,0.4
boot,1.3-19
bumphunter,1.16.0
caTools,1.17.1
car,2.1-4
censReg,0.5-26
checkmate,1.8.2
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,3.4.0
coxme,2.2-5
cubature,1.3-8
curl,2.6
data.table,1.10.4
datasets,3.4.0
dendextend,1.5.2
devtools,1.13.2
dichromat,2.0-0
digest,0.6.12
diptest,0.75-7
doMC,1.3.4
doParallel,1.0.10
doRNG,1.6.6
dplyr,0.5.0
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,2.0.3
evaluate,0.10
expm,0.999-2
fastcluster,1.1.22
filematrix,1.1.0
fit.models,0.5-14
flexmix,2.3-14
foreach,1.4.3
foreign,0.8-68
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,5.0-0
gclus,1.3.1
gdata,2.17.0
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,0.18.0
githubinstall,0.2.1
glmmML,1.0.2
gmm,1.5-2
gplots,3.0.1
grDevices,3.4.0
grImport,0.9-0
graph,1.54.0
graphics,3.4.0
grid,3.4.0
gridExtra,2.2.1
gsubfn,0.6-6
gtable,0.2.0
gtools,3.5.0
highr,0.6
htmlTable,1.9
htmltools,0.3.6
htmlwidgets,0.8
httpuv,1.3.3
httr,1.2.1
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,1.16
labeling,0.3
lambda.r,1.1.9
lars,1.2
lattice,0.20-35
latticeExtra,0.6-28
lavaan,0.5-23.1097
lazyeval,0.2.0
limma,3.32.2
lme4,1.1-13
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,4.4.5
memoise,1.1.0
metafor,1.9-9
methods,3.4.0
methylumi,2.22.0
mgcv,1.8-17
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
nlme,3.1-131
nloptr,1.0.4
nnet,7.3-12
nor1mix,1.2-2
numDeriv,2016.8-1
openssl,0.9.6
org.Hs.eg.db,3.4.1
parallel,3.4.0
pbivnorm,0.6.0
pbkrtest,0.4-7
pcaMethods,1.68.0
pcaPP,1.9-61
pedigreemm,0.3-3
pkgmaker,0.22
plm,1.6-5
plogr,0.1-1
plotrix,3.6-5
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,1.4.9
pspearman,0.3-0
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,0.8.6
reshape2,1.4.2
rgenoud,5.7-12.4
rhdf5,2.20.0
rlang,0.1.1
rmarkdown,1.5
rngtools,1.2.4
robust,0.4-18
robustbase,0.92-7
rpart,4.1-11
rprojroot,1.2
rrcov,1.4-3
rstudioapi,0.6
rtracklayer,1.36.3
sandwich,2.3-4
scales,0.4.1
seriation,1.2-2
shiny,1.0.3
siggenes,1.50.0
snow,0.4-2
sourcetools,0.1.6
sp,1.2-4
spatial,7.3-11
splines,3.4.0
sqldf,0.4-10
statmod,1.4.29
stats,3.4.0
stats4,3.4.0
stringi,1.1.5
stringr,1.2.0
survey,3.31-5
survival,2.41-3
sva,3.24.0
tcltk,3.4.0
tibble,1.3.3
tidyr,0.6.3
tmvtnorm,1.4-10
tools,3.4.0
trimcluster,0.1-2
truncreg,0.2-4
ucminf,1.1-4
utils,3.4.0
viridis,0.4.0
viridisLite,0.2.0
wateRmelon,1.20.1
whisker,0.3-2
withr,1.0.2
xtable,1.8-2
yaml,2.1.14
zlibbioc,1.22.0
zoo,1.8-0

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robbyjo
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