[R] xps installation error on Mac OS X 10.11

[cstrato]

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