Bioconductor fails to install properly because pbkrtest doesn't update correctly. I keep getting a "non-zero exit status" message. Running R 3.2.3 on OS X 10.11.2. I had the same problem with R 3.2.2 before I upgraded. Any idea how to fix?
Output and session info below:
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Old packages: 'pbkrtest'
Update all/some/none? [a/s/n]:
a
There is a binary version available but the source version is later:
binary source needs_compilation
pbkrtest 0.4-2 0.4-3 FALSE
installing the source package ‘pbkrtest’
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 160k 100 160k 0 0 234k 0 --:--:-- --:--:-- --:--:-- 234k
* installing *source* package ‘pbkrtest’ ...
** package ‘pbkrtest’ successfully unpacked and MD5 sums checked
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘stats::sigma’ when loading ‘pbkrtest’
Error : object ‘sigma’ is not exported by 'namespace:stats'
ERROR: lazy loading failed for package ‘pbkrtest’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pbkrtest’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pbkrtest’
The downloaded source packages are in
‘/private/var/folders/ht/1fw_v5ws597bqgkm8dwjnm_80000gn/T/RtmpIJbCeZ/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, repos = repos, :
installation of package ‘pbkrtest’ had non-zero exit status
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.2 (El Capitan)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.20.1
loaded via a namespace (and not attached):
[1] tools_3.2.3
This has also been reported on R-help, where it is probably more appropriate.