Related to this, running 'biocLite("BiocUpgrade")' with an bioc-3.0
triggers an upgrade to bioc-3.1 which is non-existing.
Best wishes
Julian
On 22.04.2014 14:38, Julian Gehring wrote:
Hi,
Alejandro and I digged deeper into this:
The bug I described before as caused by 'BiocInstaller:::.onLoad' which
sets 'BiocInstaller:::IS_UPGRADEABLE' to TRUE for every bioc release
with an even minor (e.g. 2.12, 2.14). Within the load function,
(BIOC_VERSION$minor %% 2L) == 0L
checks against the minor of the bioc number, which looks
non-informative. Rather, checking if the minor of the 'BiocInstaller'
package is even or odd could be more useful here
(packageVersion("BiocInstaller")$minor %% 2L) == 0L
which is TRUE for stable and FALSE for devel.
Best wishes
Julian
On 17.04.2014 18:50, Steve Lianoglou wrote:
HI,
On Thu, Apr 17, 2014 at 7:09 AM, Julian Gehring
<julian.gehr...@embl.de> wrote:
Hi,
When I run
source("http://bioconductor.org/biocLite.R";)
biocLite("BiocUpgrade")
on a stable R-3.1.0 with bioc 2.14 already installed, bioc wants to
upgrade to bioc 3.0 (devel):
Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for help
Upgrade all packages to Bioconductor version 3.0? [y/n]
Is this intentional? The documentation on the website and ?BiocUpgrade
suggests that it upgrades to the latest bioc 'release'.
Is this some potential weirdness with ?BiocInstaller::useDevel maybe?
-steve
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