[BioC] 'xps' package installation fails with ROOT installed from the Ubuntu (13.10) repositories

[cstrato]

Dear Barry,

Please note that for the current version of Bioconductor and xps the 
README file says that you need to install 'root_v5.34.05'.

I do not know anything about Ubuntu repositories but I would suggest to 
download the ROOT binary from: ftp://root.cern.ch/root/
There are three 64 bit binaries listed, dependent on the version of gcc, 
i.e.:
root_v5.34.05.Linux-slc5_amd64-gcc4.3.tar.gz
root_v5.34.05.Linux-slc6_amd64-gcc4.4.tar.gz
root_v5.34.05.Linux-slc6_amd64-gcc4.6.tar.gz

You should try to use these binaries, or you need to compile ROOT from 
source.

BTW, the ROOT binaries always contain the '/include' directory, which 
does contain the header files including TParallelCoord.h, so if the 
Ubuntu binary does not contain this directory then it is the fault of 
the repository.

Best regards,
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._



On 1/12/14 10:48 PM, Barry Garchow wrote:
> Hello,
>
> Has anyone sucessfully installed the 'xps' package with ROOT installed
> from the Ubuntu (13.10) repositories (apt-get install root-system)?
>
> ROOT installed from the Ubuntu repositories seems to run ok (no errors
> when starting a ROOT session) but subsequent installation of 'xps' fails...
>
> ****************************************************************************
>  > biocLite("xps")
> * 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 5.34/09 in directory /usr
>
> g++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/include/root -c
> XPSBase.cxx
> g++ -I/include -O2 -Wall -fPIC -pthread -m64 -I/usr/include/root -c
> XPSUtils.cxx
> XPSUtils.cxx:73:28: fatal error: TParallelCoord.h: No such file or directory
>   #include "TParallelCoord.h"
>                              ^
> compilation terminated.
> make: *** [XPSUtils.o] Error 1
> ERROR: compilation failed for package ‘xps’
> * removing ‘/usr/local/lib/R/site-library/xps’
> ********************************************************************************
>
> A system wide search for TParallelCoord.h fails to find the file. The
> package description for 'root-system' says that it installs all ROOT
> files but maybe that isn't correct?
>
> I'd like to avoid compiling ROOT from source if possible so if anyone
> has sucessfully installed the 'xps' package using ROOT from the Ubuntu
> repositories I'd very much appreciate your input.
>
> Thanks!
>
> **********************
> Relevent system info
> **********************
> uname -a
> Linux 3.11.0-12-generic #19-Ubuntu x86_64 x86_64 x86_64 GNU/Linux
>
> $ R
> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
>
>  > source("http://www.bioconductor.org/biocLite.R")
> Bioconductor version 2.13 (BiocInstaller 1.12.0)
>
> $ root
> ROOT 5.34/09 (heads/v5-34-00-patches at v5-34-08-80-g1323c6f, Jul 03 2013,
> 18:18:00 on linuxx8664gcc)