Hello,
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:
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 2.0
year 2015
month 04
day 16
svn rev 68180
language R
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: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.16.5 loaded via a namespace (and not attached): [1] 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?
Thank you.
Try starting R like this:
R --vanillabefore running theremove.packages("BiocInstaller")command.Same thing. Tried with
R --vanilla,remove.packages, restarting session (with and without--vanillaflag),source && biocLite. Also without restarting session.EDIT: seems I have those packages on /usr/lib/R/library. I'm going to try to remove them with
sudo R --vanilla and see what happens.Well, that was it. Seems like in a previous life I installed bioconductor with root privileges and forgot about it, my fault. Sorry for the trouble and thank you for your help :)
I'm having the same issue it seems. After reading your post, I make the calls R --vanilla, remove.packages, source & biocLite. What do you mean when you say you "have those packages on ...". I understand writing to /usr/lib/R/library is sudo protected. What packages are you talking about? Are you saying remove.packages wasn't actually removing the packages because they were sudo-protected?
You could try starting R as root and then removing the packages. Be sure to restart R (as a regular user) before trying to reinstall anything.
Just tested that and it seems that indeed,
remove.packages()has this wonderful feature that it doesn't say a word when it actually fails to properly remove a package because of insufficient privileges! :-/H.