Hi all,

I'm trying to install the xps in R via biocLite('xps') but I'm getting a configuration error:

* installing *source* package ‘xps’ ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... yes
found ROOT version 5.34/30 in directory /usr

...

g++ -I/usr/include -O2 -Wall -fPIC -pthread -m64 -I/usr/include/root -c XPSUtils.cxx
XPSUtils.cxx:76:28: fatal error: TParallelCoord.h: No such file or directory
 #include "TParallelCoord.h"

Root is installed and working, I have tried all the suggestions in this post: [package xps](package xps) but the installation process still can't find the header files (they are located in root/include)

I'm trying to install it on a Ubuntu 16.04 system

Does anyone have a suggestion what else I could try?

Cheers,
Anja

The latest version of xps requires ROOT version 5.34.36, but I think the version in the default Ubuntu repositories is only 5.34.30.  Perhaps this is the source of the error?

Installation instructions are given in a bit more detail in the xps INSTALL file (https://bioconductor.org/packages/release/bioc/install/xps/INSTALL) and you might be able to get a binary of the latest version here

Hi Mike,

I have installed root 6.10.00. I tried the Ubuntu repository version and installed/configured from source. Root is running, and the header files are in the /include folder... I'm wondering if there is something wrong with the way the systems variable is set?

Not sure where the 5.34.30 version is from, but I'm trying 5.34.36 now

Cheers, Anja

Hi Anja,

As Mike has already kindly mentioned, xps requires root_v5.34.36, as you can see
from the INSTALL file: 
   http://bioconductor.org/packages/3.5/bioc/install/xps/INSTALL

It mentions:
   The source code as well as binaries for Linux and Mac OS X can be obtained
   from: https://root.cern.ch/content/release-53436
   
Thus, for Ubuntu 14 and gcc4.8 there is a binary file:
   https://root.cern.ch/download/root_v5.34.36.Linux-ubuntu14-x86_64-gcc4.8.tar.gz

I don't know whether this binary will also run on Ubuntu 16. You can try, otherwise
you need to compile ROOT from source as described in INSTALL:
   https://root.cern.ch/download/root_v5.34.36.source.tar.gz
   
One note: 
Please use only binaries or source from the official ROOT web site, do not install
ROOT from other repositories such as the one from Ubuntu.

In case there are problems with the setting of system variables, there is also
as example '.bashrc' file listed in INSTALL. Although it is for Mac OS X, the
Linux '.bashrc' file may not be much different.

Regards,
Christian

Hi Christian,

I have just installed the version 5.34.36, and when I run root its recognising it as well:

system > root
  *******************************************
  *                                         *
  *        W E L C O M E  to  R O O T       *
  *                                         *
  *   Version   5.34/36      5 April 2016   *
  *                                         *
  *  You are welcome to visit our Web site  *
  *          http://root.cern.ch            *
  *                                         *
  *******************************************

However, trying to install xps, it's stil finding the version 5.34.30. I don't know which variable is pointing to this version, as the system variables in the .bashrc file are pointing to the 5.34.36 version. Btw, I compiled it from source

Cheers,

Anja

Hi Anja,

You have to delete/uninstall root version 5.34.30.

Since I have no experience with Ubuntu and its repository I do not know how you
have to deinstall it.

However, searching the net I found the following link:
https://help.ubuntu.com/community/EnvironmentVariables

In addition to '.bashrc' there are also ~/.bash_profile, and ~/.bash_login, 
and ~/.pam_environment. 

Maybe you need to look in one of these files, too. But the Ubuntu repository may
have its own file.

Best regards,
Christian