[BioC] package xps
Steven
steven.wink at gmail.com
Fri Aug 3 20:08:17 CEST 2012
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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>>>>
>>>>
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