[BioC] package xps
cstrato
cstrato at aon.at
Fri Aug 3 21:46:52 CEST 2012
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=<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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>>>>>>>
>>>>>>
>>>
>>
>
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