Dear Steven, Good to know that your problem is finally solved. I cc to BioC so that others will know that the problem is solved. Best regards, Christian On 8/3/12 9:01 PM, Steven wrote: > Dan and Christian, thank you so much both of you:) I am really > looking forward to using xps tomorrow, should be able to solve my R > memory problem I'm sure. > > R cannot find the package yet but I gues that's a question of telling > R where to find the library in my home directory? > > Thanks again, you guys are the modern-age-hero's > > Steven > > 2012/8/3 cstrato <cstrato at="" aon.at="">: >> Dear Steven, >> >> Could you please say once again how you did compile root, see: >> http://root.cern.ch/drupal/content/installing-root-source >> >> The location independent installation suggest as 3. step: >> . bin/thisroot.sh >> >> I do not know if this will have any effect, but it may be worth to try. >> >> >> Furthermore, like Dan I do not understand why you need to use sudo. I have >> the feeling that this could be the problem. >> >> Maybe you could try to create a directory for packages in your home >> directory as described in: >> http://cran.r-project.org/doc/manuals/R-admin.html#Installing- packages >> and then do: >> R CMD INSTALL -l /path/to/library xps_1.16.0.tar.gz >> >> Maybe this could solve the problem (at least the problem with sudo)? >> >> P.S.: Thank you, Dan for your help, maybe you have some additional >> suggestions, too. >> >> Best regards, >> Christian >> >> >> >> >> On 8/3/12 8:08 PM, Steven wrote: >>> >>> Hi Dan, >>> >>> >>> I removed the LD_LIBRARY_PATH from the .bashrc file, and ran source >>> ~/.bashrc >>> In /etc/ld.so.conf.d$ I created a ROOF.conf file with the line >>> /home/winks/ROOT/root/lib and ran sudo /sbin/ldconfig >>> >>> Here is the whole output when I try to install in R with biocLite("xps") >>> Still the same error. >>> >>> >>> source("http://bioconductor.org/biocLite.R") >>> BiocInstaller version 1.4.7, ?biocLite for help >>>> >>>> biocLite("xps") >>> >>> BioC_mirror: http://bioconductor.org >>> Using R version 2.15, BiocInstaller version 1.4.7. >>> Installing package(s) 'xps' >>> trying URL >>> 'http://www.bioconductor.org/packages/2.10/bioc/src/contrib/xps_1. 16.0.tar.gz' >>> Content type 'application/x-gzip' length 6686622 bytes (6.4 Mb) >>> opened URL >>> ================================================== >>> downloaded 6.4 Mb >>> >>> * 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... no >>> >>> xps configuration error: >>> >>> You must set the shell variable ROOTSYS to the >>> directory where ROOT resides and re-run R CMD INSTALL >>> e.g., (using Bourne shell syntax): >>> >>> export ROOTSYS=/opt/root >>> export "PATH=$ROOTSYS/bin:$PATH" >>> R CMD INSTALL xps >>> >>> Please consult the README file for more information >>> >>> ERROR: configuration failed for package ?xps? >>> * removing ?/usr/local/lib/R/site-library/xps? >>> >>> The downloaded source packages are in >>> ?/tmp/RtmpWtzvlM/downloaded_packages? >>> Warning message: >>> In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>> installation of package ?xps? had non-zero exit status >>> >>> >>> Thaks again! >>> >>> Steven >>> >>> >>> 2012/8/3 Dan Tenenbaum <dtenenba at="" fhcrc.org="">: >>>> >>>> On Fri, Aug 3, 2012 at 9:19 AM, Steven <steven.wink at="" gmail.com=""> wrote: >>>>> >>>>> Hi Christian, >>>>> >>>>> sorry about that, a bit sloppy of me but I did in fact add all 3 lines: >>>>> export ROOTSYS=~/ROOT/root >>>>> export PATH=$ROOTSYS/bin:$PATH >>>>> export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH >>>>> >>>>> Also it seems the variable has been set correctly based on the "echo" >>>>> output. Makes the error all the stranger. >>>>> >>>>> Could it be that I a installed ubuntu 12:04 with a windows installer >>>>> (Wubi) have anything to do with it? >>>> >>>> >>>> I doubt it. >>>> >>>> There is an alternative to setting LD_LIBRARY_PATH which most modern >>>> linuxes (including Ubuntu) support. Instead of modifying >>>> LD_LIBRARY_PATH, create a file /etc/ld.so.conf.d/ROOT.conf which just >>>> contains: >>>> (assuming your home directory is /home/winks as ~ won't work here): >>>> >>>> /home/winks/ROOT/root/lib >>>> >>>> Then run sudo /sbin/ldconfig to make the system aware of this file. >>>> Try doing this, removing the LD_LIBRARY_PATH from you .bashrc, and >>>> sourcing it again. See if you can now install xps. >>>> >>>> Dan >>>> >>>> >>>> >>>>> >>>>> Best regards, >>>>> Steven >>>>> >>>>> 2012/8/3 cstrato <cstrato at="" aon.at="">: >>>>>> >>>>>> Dear Steven, >>>>>> >>>>>> You mentioned that you added 2 lines to .bashrc. However, the README >>>>>> file >>>>>> says that you need to add the following 3 lines to .bashrc: >>>>>> >>>>>> export ROOTSYS=/root >>>>>> >>>>>> export PATH=$ROOTSYS/bin:$PATH >>>>>> export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH >>>>>> >>>>>> Could you try this setting and let me know? >>>>>> >>>>>> 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 8/3/12 10:55 AM, Steven wrote: >>>>>>> >>>>>>> >>>>>>> 2012/8/3 Steven <steven.wink at="" gmail.com="">: >>>>>>>> >>>>>>>> >>>>>>>> Hi Dan, >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 2012/8/3 Dan Tenenbaum <dtenenba at="" fhcrc.org="">: >>>>>>>>> >>>>>>>>> >>>>>>>>> Hi Steven, >>>>>>>>> >>>>>>>>> On Thu, Aug 2, 2012 at 3:48 PM, Steven <steven.wink at="" gmail.com=""> >>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Hi all, >>>>>>>>>> >>>>>>>>>> I am having trouble getting package xps to work, and would really >>>>>>>>>> appreciate any help I can get. >>>>>>>>>> >>>>>>>>>> I have succesfully installed root_v5.34.01 on my ubuntu 12.04 OS >>>>>>>>>> as described on in the xps package readme file I added ROOTSYS to >>>>>>>>>> PATH >>>>>>>>>> and LD_LIBRARY_PATH by entering these lines in the terminal: >>>>>>>>>> export ROOTSYS=~/ROOT/root (I make a folder ROOT in which I >>>>>>>>>> unpacked >>>>>>>>>> root.) >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Did you just unpack the source tarball of root into /ROOT, or did >>>>>>>>> you >>>>>>>>> install root there? >>>>>>>>> >>>>>>>> I also installed with ./configure linuxx8664gcc >>>>>>>> make >>>>>>>> >>>>>>>> I can run root by typing root. >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>>> export PATH=$ROOTSYS/bin:$PATH >>>>>>>>>> export >>>>>>>>>> LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH >>>>>>>>>> >>>>>>>>>> I also added above 2 lines in .bashrc >>>>>>>>>> >>>>>>>>> >>>>>>>>> Did you source the .bashrc after adding these lines? >>>>>>>>> What happens if you type >>>>>>>>> echo $ROOTSYS >>>>>>>>> at the command line? >>>>>>>>> >>>>>>>> >>>>>>>> I also sourced it. >>>>>>>> by typing echo $ROOTSYS I get: >>>>>>>> winks at ubuntu:~/ROOT/root$ >>>>>>>> >>>>>>>> >>>>>>>>> To make sure root is properly installed, what happens if you do >>>>>>>>> this: >>>>>>>>> >>>>>>>>> $ROOTSYS/bin/root --help >>>>>>>>> You should see a usage message describing the various options for >>>>>>>>> root. >>>>>>>>> >>>>>>>> Indeed I do, this is the output: >>>>>>>> winks at ubuntu:~/ROOT/root$ $ROOTSYS/bin/root --help >>>>>>>> Usage: /home/winks/ROOT/root/bin/root [-l] [-b] [-n] [-q] [dir] >>>>>>>> [[file:]data.root] [file1.C ... fileN.C] >>>>>>>> Options: >>>>>>>> -b : run in batch mode without graphics >>>>>>>> -n : do not execute logon and logoff macros as specified in >>>>>>>> .rootrc >>>>>>>> -q : exit after processing command line macro files >>>>>>>> -l : do not show splash screen >>>>>>>> -x : exit on exception >>>>>>>> dir : if dir is a valid directory cd to it before executing >>>>>>>> >>>>>>>> -? : print usage >>>>>>>> -h : print usage >>>>>>>> --help : print usage >>>>>>>> -config : print ./configure options >>>>>>>> -memstat : run with memory usage monitoring >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> root seems to run fine. >>>>>>>>>> >>>>>>>>>> next, I download xps_1.16.0.tar.gz and run: >>>>>>>>>> sudo R CMD INSTALL xps_1.16.0.tar.gz >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Why are you using sudo here? >>>>>>>> >>>>>>>> >>>>>>>> I normally get acces problems when installing packages in R when I >>>>>>>> don't initiate R with sudo rights. I didn't try R CMD INSTALL >>>>>>>> xps_1.16.0.tar.gz without sudo. >>>>>>> >>>>>>> >>>>>>> I just tried without SUDO rights, and this is the output: >>>>>>> winks at ubuntu:~/ROOT/root$ R CMD INSTALL xps_1.16.0.tar.gz >>>>>>> * installing to library ?/usr/local/lib/R/site-library? >>>>>>> Error: ERROR: no permission to install to directory >>>>>>> ?/usr/local/lib/R/site-library? >>>>>>> >>>>>>> >>>>>>> ps: I also tried installing the recommended way with biocLite -I get >>>>>>> the same ROOTSYS shell variable problem >>>>>>> >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> Are you running R 2.15? This is the version of R you will need with >>>>>>>>> xps >>>>>>>>> 1.16.0. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> No, I am running R version 2.14.1. >>>>>>>> I installed R version 2.15. >>>>>>>> >>>>>>>> Still get the same error, this is the output: >>>>>>>> >>>>>>>> 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... no >>>>>>>> >>>>>>>> xps configuration error: >>>>>>>> >>>>>>>> You must set the shell variable ROOTSYS to the >>>>>>>> directory where ROOT resides and re-run R CMD INSTALL >>>>>>>> e.g., (using Bourne shell syntax): >>>>>>>> >>>>>>>> export ROOTSYS=/opt/root >>>>>>>> export "PATH=$ROOTSYS/bin:$PATH" >>>>>>>> R CMD INSTALL xps >>>>>>>> >>>>>>>> Please consult the README file for more information >>>>>>>> >>>>>>>> ERROR: configuration failed for package ?xps? >>>>>>>> * removing ?/usr/local/lib/R/site-library/xps? >>>>>>>> >>>>>>>> >>>>>>>> Thanks so far for your help! >>>>>>>> >>>>>>>> Steven >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> We recommend you install xps like this, within R: >>>>>>>>> >>>>>>>>> source("http://bioconductor.org/biocLite.R") >>>>>>>>> biocLite("xps") >>>>>>>>> >>>>>>>>> Dan >>>>>>>>> >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> I get the following error message: >>>>>>>>>> >>>>>>>>>> xps configuration error: >>>>>>>>>> >>>>>>>>>> You must set the shell variable ROOTSYS to the >>>>>>>>>> directory where ROOT resides and re-run R CMD INSTALL >>>>>>>>>> e.g., (using Bourne shell syntax): >>>>>>>>>> >>>>>>>>>> export ROOTSYS=/opt/root >>>>>>>>>> export "PATH=$ROOTSYS/bin:$PATH" >>>>>>>>>> R CMD INSTALL xps >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> So apparently ROOTSYS variables are not set right? I tried anything >>>>>>>>>> I >>>>>>>>>> could think of but I am lacking in understanding here. >>>>>>>>>> >>>>>>>>>> Thanks alot! >>>>>>>>>> >>>>>>>>>> sincerely >>>>>>>>>> Steven Wink >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioconductor mailing list >>>>>>>>>> Bioconductor at r-project.org >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>> Search the archives: >>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>> >>>>>> >>> >> >