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) > >