I've been trying to install the Bioconductor eps package for several days and cannot get it to work. I would be very grateful for any help.
After reading many forum posts and trying several methods, I've installed root version 5.34.36 using the dmg (root_v5.34.36.macosx64-10.11-clang70.dmg) and that works fine when I call root.
I've also set up my .bashrc file as follows, and sourced it before trying to install xps:
# .bashrc export PATH=$PATH:/usr/local/bin # ROOT settings export MACOSX_DEPLOYMENT_TARGET=10.11 export TMPDIR=/Users/sdeproce/temp export DISPLAY=/opt/X11/bin/XQuartz # here you add your path to root export ROOTSYS=/Applications/root_v5.34.36 export PATH=$ROOTSYS/bin:$PATH export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH export DYLD_LIBRARY_PATH=$ROOTSYS/lib:$DYLD_LIBRARY_PATH # Source global definitions if [ -f /etc/bashrc ]; then . /etc/bashrc fi
I've tried installing xps both from the gzipped source and from source using Bioconductor.
In both cases, I get an error message. This is when I use the Bioconductor source installation:
source("http://bioconductor.org/biocLite.R") biocLite("xps", type="source") ... found ROOT version 5.34/36 in directory /Applications/root_v5.34.36 xps configuration error: You must set the shell variable LD_LIBRARY_PATH to the directory where ROOT resides and re-run R CMD INSTALL e.g., (using Bourne shell syntax): export "LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH" R CMD INSTALL xps Please consult the README file for more information ERROR: configuration failed for package ‘xps’ * removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/xps’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/xps’
And this is when I use the .tgz install:
R CMD INSTALL /Users/sdeproce/Downloads/xps_1.34.0.tgz R library(xps) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/xps/libs/xps.so': dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/xps/libs/xps.so, 6): Library not loaded: /usr/local/root/lib/root/libGui.so Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/xps/libs/xps.so Reason: image not found Error: package or namespace load failed for ‘xps’
My session info is:
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.5 (El Capitan) locale:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  BiocInstaller_1.24.0 loaded via a namespace (and not attached):  tools_3.3.1
Thank you very much for any help,