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 |