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Question: Trouble Downloading "ggbio"
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gravatar for ebkenn07
23 months ago by
ebkenn070
United States
ebkenn070 wrote:

Hi Everyone,

I have been trying to install "ggbio" on a linux server. In order to download the package, I did the following:

 

source("http://bioconductor.org/biocLite.R")

biocLite("ggbio")

 

Upon completion, I get the following warning errors: 

Warning messages:
1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package ‘ggbio’ had non-zero exit status

The transcript associated with the ggbio install:

biocLite("ggbio")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.1.1.
Installing package(s) 'ggbio'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/ggbio_1.14.0.tar.gz'
Content type 'application/x-gzip' length 1521091 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb

* installing *source* package ‘ggbio’ ...
** R
** inst
** preparing package for lazy loading
Error : object ‘latticeGrob’ is not exported by 'namespace:gridExtra'
ERROR: lazy loading failed for package ‘ggbio’
* removing ‘/home/ebcook/R/x86_64-unknown-linux-gnu-library/3.1/ggbio’

 

Here is the session info:

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

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_1.16.5

loaded via a namespace (and not attached):
[1] tools_3.1.1

 

To try and address the problem, I have attempted the following:

1.Update existing packages using biocLite(character())

Running this package was successful, but still did not resolve issues with the "ggbio" install. 

Anyone have any ideas? 

 

ADD COMMENTlink modified 23 months ago • written 23 months ago by ebkenn070

Update your question to provide a more complete transcript, especially where the installation of Matrix and ggbio actually fail; right now you're giving just enough info to know that something unexpected happened, but not enough to know exactly what. Post a comment when you've updated your question.

ADD REPLYlink written 23 months ago by Martin Morgan ♦♦ 20k

Sorry about the lack of information, hopefully the edits will help explain things a bit better. 

ADD REPLYlink written 23 months ago by ebkenn070

The first step is to install a current version of R and Bioconductor packages. You have versions that are out of date by two release cycles.

ADD REPLYlink written 23 months ago by James W. MacDonald45k
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