Dear Jack,
First, please do not use r-help or r-devel to ask Bioconductor-related
questions, Bioconductor has its own support site for BioC packages:
https://support.bioconductor.org/
Second, please note that ROOT_6.x cannot be used for xps.
In the README file I mention for Yosemite:
ftp://root.cern.ch/root/root_v5.34.30.macosx64-10.10-clang61.tar.gz
However, you can probably also use the newest version:
ftp://root.cern.ch/root/root_v5.34.34.macosx64-10.10-clang61.tar.gz
Before installing ROOT again please make sure to delete all versions of
ROOT that you have already installed.
Best regards,
Christian
On 01/13/16 18:28, Zhu, Jack (NIH/NCI) [E] wrote:
Dear Christian,
Sorry for bothering you, but it looks like I really need your help with
the xps installation on my Mac OS X 10.11 system. I have been
struggling for a few days and tried all the options listed in your
README file:
http://bioconductor.org/packages/devel/bioc/readmes/xps/README
I also read all the online posts related to the xps installation. But
still have problem. By strictly following the instructions, I
re-installed ROOT from both source and binary for Mac OS X 10.11 and
added ROOT environmental variables in my .bashrc (all the four lines).
The ROOT itself seems working totally fine by different tests and the
$ echo $ROOTSYS
/Applications/root_v6.06.00
$ echo $LD_LIBRARY_PATH
/Applications/root_v6.06.00/lib
$ echo $DYLD_LIBRARY_PATH
/Applications/root_v6.06.00
$echo $PATH
/Applications/root_v6.06.00/bin:…
But I always get an error with LD_LIBRARY_PATH when I try to install the
xps package from the source:
-------------------
$R CMD INSTALL -d -l /Users/zhujack/Library/R/3.3/library
xps_1.31.0.tar.gz
found ROOT version 6.06/00 in directory /Applications/root_v6.06.00
xps configuration error:
You must set the shell variable LD_LIBRARY_PATH to the
directory where ROOT resides and re-run R CMD INSTALL
e.g., (using Bourne shell syntax):
export "LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH"
R CMD INSTALL xps
Please consult the README file for more information
ERROR: configuration failed for package ‘xps’
* removing ‘/Users/zhujack/Library/R/3.3/library/xps’
* restoring previous ‘/Users/zhujack/Library/R/3.3/library/xps’
I also tried to add the following line to the /usr/local/bin/R:
LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/Applications/root_v6.06.00/lib"
export LD_LIBRARY_PATH
But I still get the same error. Your help and insigts will be greatly
appreciared.
Jack
> sessionInfo()
R Under development (unstable) (2016-01-11 r69918)
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_1.21.2
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