I was trying to use the DECIPHER package today and it was not supporting even the examples in the manual. When I checked, I was using an old version (v 1.16.1). It was strange because I just installed it with:
Thus, I installed manually the more recent version available:
install.packages("~/DECIPHER_2.0.2.tar.gz", repos = NULL, type="source")
And now it seems to be ok with the manual. Why the biocLite function is installing this old version?
> sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.4 LTS locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  stats4 parallel stats graphics grDevices utils datasets  methods base other attached packages:  BiocInstaller_1.20.3 DECIPHER_2.0.2 RSQLite_1.0.0  DBI_0.4-1 Biostrings_2.38.4 XVector_0.10.0  IRanges_2.4.8 S4Vectors_0.8.11 BiocGenerics_0.16.1 loaded via a namespace (and not attached):  zlibbioc_1.16.0 tools_3.3.0
And below you can see the behavior of the biocLite() function with the above 'version setting' (already with the last DECIPHER version):
> biocLite("DECIPHER") BioC_mirror: https://bioconductor.org Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.3.0 (2016-05-03). Installing package(s) ‘DECIPHER’ trying URL 'https://bioconductor.org/packages/3.2/bioc/src/contrib/DECIPHER_1.16.1.tar.gz' Content type 'unknown' length 7621858 bytes (7.3 MB) ================================================== downloaded 7.3 MB
There is just one more recent R version, which is not even launched. I am missing something?