[BioC] package xps
cstrato
cstrato at aon.at
Fri Aug 3 20:32:21 CEST 2012
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=<path>/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
>>>>>>>>
>>>>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
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>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>
>
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