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Question: ggbio installation error
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gravatar for syliang
22 months ago by
syliang0
syliang0 wrote:

Hello,

I have trouble to install ggbio in R 3.2.3  via Bioconductor 3.2 on Linux (centOS 6.7) .  Here are the error message, session info, and library path.  R is downloaded from https://cran.r-project.org/src/base/R-3/.  Although there are similar problems with ggbio installation posted at this site, suggestions for the problem don't seem to apply to mine.  Any helps are appreciated. 

 

######## R code for ggbio installation and message #####################

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> biocLite("ggbio")
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) \u2018ggbio\u2019
trying URL 'http://bioconductor.org/packages/3.2/bioc/src/contrib/ggbio_1.18.1.tar.gz'
Content type 'application/x-gzip' length 1289944 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

* installing *source* package \u2018ggbio\u2019 ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by \u2018ggplot2::unit\u2019 when loading \u2018ggbio\u2019
Warning: replacing previous import by \u2018ggplot2::arrow\u2019 when loading \u2018ggbio\u2019
Warning: replacing previous import by \u2018BiocGenerics::Position\u2019 when loading \u2018ggbio\u2019
Creating a new generic function for \u2018rescale\u2019 in package \u2018ggbio\u2019
Creating a new generic function for \u2018xlim\u2019 in package \u2018ggbio\u2019
Creating a generic function for \u2018print\u2019 from package \u2018base\u2019 in package \u2018ggbio\u2019
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 \u2018ggbio\u2019
ERROR: lazy loading failed for package \u2018ggbio\u2019
* removing \u2018/usr/local/lib64/R/library/ggbio\u2019

The downloaded source packages are in
    \u2018/tmp/Rtmp6qKZjg/downloaded_packages\u2019
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package \u2018ggbio\u2019 had non-zero exit status

######### R session info and library path ######################################

> sessionInfo()

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [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_1.20.1

loaded via a namespace (and not attached):
[1] tools_3.2.3

 

> .libPaths()
[1] "/usr/local/lib64/R/library"

 

ADD COMMENTlink written 22 months ago by syliang0
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