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

[Barry Garchow]

Thank you Christian,

It seems that the ROOT package in the Ubuntu repositories is not being actively maintained and is quite buggy.  I installed ROOT from source and was then able to successfully install the xps package. 

Barry

On Jan 12, 2014, at 5:55 PM, cstrato <cstrato at aon.at> wrote:

> 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)