[Bioc-devel] upgrading
Hi Kasper, I also installed a clean devel version today and had no such problems, also https://www.bioconductor.org/developers/how-to/useDevel/ works for me and says that using an R-devel version is necessary to use Bioc-devel. I also get the correct BiocInstaller version:
biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.21.1), R Under development (unstable) (2015-10-19 r69546). Installing package(s) ?IRanges?, ?AnnotationDbi? Warning: dependency ?IRanges? is not available
There is however the IRanges issue I was asking about earlier. Maybe clean the library and try again? Best wishes, Bernd
On Di, 2015-10-20 at 10:55 -0400, Kasper Daniel Hansen wrote:
So I have an R-devel where I have a previous (pre-bioc-3.2) installed
version of BiocInstaller.
1) I re-compile R-devel today.
2) I run
source("http://www.bioconductor.org/biocLite.R")
which gives me BiocInstaller 1.20.0. However, the current one for
Bioc-devel is 1.21.1.
When I try to push to a higher level version, by doing
library(BiocInstaller)
useDevel(TRUE)
I get
useDevel(TRUE)
Error: 'devel' version requires a more recent R If I now try to upgrade I get
biocLite("BiocUpgrade")
Error: Bioconductor version 3.2 cannot be upgraded with R version 3.3.0 This all looks problematic. How to I upgrade to Bioc-devel using R-devel? Btw. there are no instructions anymore at https://www.bioconductor.org/developers/how-to/useDevel/ Best, Kasper [[alternative HTML version deleted]]
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