package xps
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Steven ▴ 110
@steven-5432
Last seen 7.9 years ago
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.) export PATH=$ROOTSYS/bin:$PATH export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH I also added above 2 lines in .bashrc 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 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
xps xps • 1.3k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 17 months ago
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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? > 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? To make sure root is properly installed, what happens if you do this: $ROOTSYS/bin/root --help You should see a usage message describing the various options for root. > > root seems to run fine. > > next, I download xps_1.16.0.tar.gz and run: > sudo R CMD INSTALL xps_1.16.0.tar.gz Why are you using sudo here? Are you running R 2.15? This is the version of R you will need with xps 1.16.0. We recommend you install xps like this, within R: source("http://bioconductor.org/biocLite.R") biocLite("xps") Dan > > > I get the following error message: > > xps configuration error: > > You must set the shell variable ROOTSYS to the > directory where ROOT resides and re-run R CMD INSTALL > e.g., (using Bourne shell syntax): > > export ROOTSYS=/opt/root > export "PATH=$ROOTSYS/bin:$PATH" > R CMD INSTALL xps > > > So apparently ROOTSYS variables are not set right? I tried anything I > could think of but I am lacking in understanding here. > > Thanks alot! > > sincerely > Steven Wink > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Dan, 2012/8/3 Dan Tenenbaum <dtenenba at="" fhcrc.org="">: > Hi Steven, > > On Thu, Aug 2, 2012 at 3:48 PM, Steven <steven.wink at="" gmail.com=""> wrote: >> Hi all, >> >> I am having trouble getting package xps to work, and would really >> appreciate any help I can get. >> >> I have succesfully installed root_v5.34.01 on my ubuntu 12.04 OS >> as described on in the xps package readme file I added ROOTSYS to PATH >> and LD_LIBRARY_PATH by entering these lines in the terminal: >> export ROOTSYS=~/ROOT/root (I make a folder ROOT in which I unpacked root.) > > Did you just unpack the source tarball of root into /ROOT, or did you > install root there? > I also installed with ./configure linuxx8664gcc make I can run root by typing root. > >> export PATH=$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: > > $ROOTSYS/bin/root --help > You should see a usage message describing the various options for root. > Indeed I do, this is the output: winks at ubuntu:~/ROOT/root$ $ROOTSYS/bin/root --help Usage: /home/winks/ROOT/root/bin/root [-l] [-b] [-n] [-q] [dir] [[file:]data.root] [file1.C ... fileN.C] Options: -b : run in batch mode without graphics -n : do not execute logon and logoff macros as specified in .rootrc -q : exit after processing command line macro files -l : do not show splash screen -x : exit on exception dir : if dir is a valid directory cd to it before executing -? : print usage -h : print usage --help : print usage -config : print ./configure options -memstat : run with memory usage monitoring > > >> >> root seems to run fine. >> >> next, I download xps_1.16.0.tar.gz and run: >> sudo R CMD INSTALL xps_1.16.0.tar.gz > > Why are you using sudo here? I normally get acces problems when installing packages in R when I don't initiate R with sudo rights. I didn't try R CMD INSTALL xps_1.16.0.tar.gz without sudo. > > Are you running R 2.15? This is the version of R you will need with xps 1.16.0. No, I am running R version 2.14.1. I installed R version 2.15. Still get the same error, this is the output: checking whether we are using the GNU C compiler... (cached) yes checking whether gcc -std=gnu99 accepts -g... (cached) yes checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed checking for root-config... no xps configuration error: You must set the shell variable ROOTSYS to the directory where ROOT resides and re-run R CMD INSTALL e.g., (using Bourne shell syntax): export ROOTSYS=/opt/root export "PATH=$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:$PATH" >> R CMD INSTALL xps >> >> >> So apparently ROOTSYS variables are not set right? I tried anything I >> could think of but I am lacking in understanding here. >> >> Thanks alot! >> >> sincerely >> Steven Wink >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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2012/8/3 Steven <steven.wink at="" gmail.com="">: > Hi Dan, > > > > > 2012/8/3 Dan Tenenbaum <dtenenba at="" fhcrc.org="">: >> Hi Steven, >> >> On Thu, Aug 2, 2012 at 3:48 PM, Steven <steven.wink at="" gmail.com=""> wrote: >>> Hi all, >>> >>> I am having trouble getting package xps to work, and would really >>> appreciate any help I can get. >>> >>> I have succesfully installed root_v5.34.01 on my ubuntu 12.04 OS >>> as described on in the xps package readme file I added ROOTSYS to PATH >>> and LD_LIBRARY_PATH by entering these lines in the terminal: >>> export ROOTSYS=~/ROOT/root (I make a folder ROOT in which I unpacked root.) >> >> Did you just unpack the source tarball of root into /ROOT, or did you >> install root there? >> > I also installed with ./configure linuxx8664gcc > make > > I can run root by typing root. > > >> >>> export PATH=$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
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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 >
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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? 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 >> >
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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 >>> >>
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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 >>>> >>>
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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/contr ib/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 >>>>> >>>> >
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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_1.1 6.0.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 >>>>>> >>>>> >> >
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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 >>>>>>> >>>>>> >>> >> >
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