Entering edit mode
8.9 years ago
syrttgump
▴
50
Hi everyone,
I am using the newest version of R and trying to install ggbio, here is my problem:
> biocLite("ggbio")
BioC_mirror: https://bioconductor.org/
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) 'ggbio'
% 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 1259k 100 1259k 0 0 1057k 0 0:00:01 0:00:01 --:--:-- 1057k
* installing *source* package 'ggbio' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'grid::arrow' when loading 'GGally'
Warning: replacing previous import by 'grid::unit' when loading 'GGally'
Warning: replacing previous import by 'ggplot2::unit' when loading 'ggbio'
Warning: replacing previous import by 'ggplot2::arrow' when loading 'ggbio'
Warning: replacing previous import by 'BiocGenerics::Position' when loading 'ggbio'
Creating a new generic function for 'rescale' in package 'ggbio'
Creating a new generic function for 'xlim' in package 'ggbio'
Creating a generic function for 'print' from package 'base' in package 'ggbio'
Warning: 'eval' is deprecated.
Use 'plotIdeogram' instead.
See help("Deprecated")
Error in rematchDefinition(definition, fdef, mnames, fnames, signature) :
arguments (environment) after '...' in the generic must appear in the method, in the same place at the end of the argument list
Error : unable to load R code in package 'ggbio'
ERROR: lazy loading failed for package 'ggbio'
* removing '/usr/local/lib/R/3.2/site-library/ggbio'
The downloaded source packages are in
'/private/var/folders/gb/vd06k92974n6yp3bshy0rh9w0000gn/T/RtmpynGNyF/downloaded_packages'
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
installation of package 'ggbio' had non-zero exit status
The output of session information:
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin15.2.0 (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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.22.2 GenomeInfoDb_1.6.1 IRanges_2.4.6 S4Vectors_0.8.5
[5] BiocGenerics_0.16.1 edgeR_3.12.0 limma_3.26.3 BiocInstaller_1.20.1
loaded via a namespace (and not attached):
[1] zlibbioc_1.16.0 XVector_0.10.0 tools_3.2.3
Hi, you appear to have cross-posted this to the bioconductor message-boards and received an answer (although that answer didn't help me install ggbio)