I'm having some problems installing the correct version of bioconductor and upgrading packages.
First, when I run the first command to install bioconductor (
source(...)) I get this:
Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help BiocInstaller version 3.0 is too old for R version 3.2.0; remove.packages("BiocInstaller") then source("http://bioconductor.org/biocLite.R") A new version of Bioconductor is available after installing the most recent version of R; see http://bioconductor.org/install
It doesn't matter if I follow the suggested instructions, it always ends like that.
The second command (
biocLite()) shows this:
BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.0. Old packages: 'AnnotationDbi', 'BiocInstaller', 'GenomeInfoDb' Update all/some/none? [a/s/n]:
When I press "a", the packages are downloaded and apparently installed (although Biocinstaller shows the previous message of being too old) but if I run
biocLite() again in the same R session or a new one, I'm asked again and again. This only happens with those 3 packages.
When I use
biocLite("BiocUpgrade"), the message is:
Error: Bioconductor version 3.0 cannot be upgraded with R version 3.1.0
My version, according to R is:
system x86_64, linux-gnu
svn rev 68180
version.string R version 3.2.0 (2015-04-16)
nickname Full of Ingredients
And the sessionInfo:
R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Arch Linux locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=C  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:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.16.5 loaded via a namespace (and not attached):  tools_3.2.0 tcltk_3.2.0
I ommited the steps where R says it cannot write to "/usr/lib/..." and asks for writing on my personal library located on "~/R/...". Also, I also tried to remove that personal dir to start from zero, restarting the session, the computer...
What can I do to use the latest packages availables?