[BioC] package xps
Steven
steven.wink at gmail.com
Fri Aug 3 21:01:31 CEST 2012
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=<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
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
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>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>
>>>>>
>>
>
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