c2d4u Update: Adding New Bioconductor Release

Thu, 31 May 2018 15:12:00 -0500

When R 3.5 was released, the good folks at the Bioconductor project also released a new version, 3.7. Since I was rebuilding for R 3.5, I didn’t immediately include the updates to Bioconductor in my builds. I have now taken the time to include the update, so there are an additional 83 updated/new packages on c2d4u. (3.4 or 3.5 versions)

My PPAs do not provide all the Bioconductor packages. Some are included in a CRAN Task View, therefore they are included in c2d4u. Others are included in Ubuntu Universe, and with the move to R 3.5, I have made an attempt to rebuild those for compatibility.

Some of the packages (BiocInstaller for example) require R 3.5. Obviously, these do not build against R 3.4, but older versions of the packages are available on the PPAs. If you want to use Bioconductor 3.7, I highly suggest upgrading to R 3.5.

package	version
quantreg	5.36
data.table	1.11.4
purrr	0.2.5
bit	1.1-14
BiocGenerics	0.26.0
graph	1.58.0
RBGL	1.56.0
rJava	0.9-10
plotrix	3.7-2
sbgcop	0.980
energy	1.7-4
impute	1.54.0
MassSpecWavelet	1.46.0
metaLik	0.43.0
apcluster	1.4.7
mritc	0.5-1
Rgraphviz	2.24.0
surveillance	1.16.1
CellNOptR	1.26.0
CNORode	1.22.0
MEIGOR	1.14.0
limma	3.36.1
qvalue	2.12.0
edgeR	3.22.2
Biobase	2.40.0
ChainLadder	0.2.6
HardyWeinberg	1.6.1
zlibbioc	1.26.0
snpStats	1.30.0
ranger	0.10.0
RWeka	0.4-38
stargazer	5.2.2
joint.Cox	2.15
EBImage	4.22.0
GEOquery	2.48.0
GEOmetadb	1.42.0
preprocessCore	1.42.0
multtest	2.36.0
S4Vectors	0.18.2
IRanges	2.14.10
AnnotationDbi	1.42.1
annotate	1.58.0
genefilter	1.62.0
GSEABase	1.42.0
robCompositions	2.0.8
pdftools	1.8
tidytext	0.1.9
CDM	6.3-45
mipfp	3.2
simPop	1.1.1
hypervolume	2.0.9
XVector	0.20.0
Biostrings	2.48.0
Rhdf5lib	1.2.1
rhdf5	2.24.0
biomformat	1.8.0
phyloseq	1.24.0
catR	3.14
rlang	0.2.1
soiltexture	1.4.6
rsurface	1.1.0
occ	1.1
GenomeInfoDbData	1.1.0
GenomeInfoDb	1.16.0
illuminaio	0.22.0
GenomicRanges	1.32.3
BeadDataPackR	1.32.0
BiocInstaller	1.30.0
affyio	1.50.0
beadarray	2.30.0
affy	1.58.0
Icens	1.52.0
joineRML	0.4.2
rstpm2	1.4.2
SemiMarkov	1.4.4
survcomp	1.30.0
ramcmc	0.1.0-1
bestglm	0.37
splusTimeSeries	1.5.0-75
tsibble	0.3.0
abbyyR	0.5.4
rdatacite	0.4.0
servr	0.10

Bioconductor on R Ubuntu Blog

c2d4u Update: Adding New Bioconductor Release