xps installation error on Mac OS X 10.11

cstrato

Wed, Jan 13, 2016 9:57 AM

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