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

[cstrato]

Dear Barry,

I am glad to hear that you could finally install ROOT and xps.

Best regards,
Christian


On 1/13/14 8:09 PM, Barry Garchow wrote:
> 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)
>
>