[BioC] xps- not being able to load it

cstrato cstrato at aon.at
Wed Mar 27 14:37:17 CET 2013


Dear Andreia,

1, Can you please tell me which file you did download from the ROOT 
web-site or ftp-site?

2, Please tell me how and in which directory you have installed root, 
i.e. which directory does contain the directory 'root'?

3, What do you mean with '. lib/thisroot.sh'? Please note that the 
command mentioned in the README file is '. bin/thisroot.sh'.

4, I have installed root in directory '/Volumes/GigaDrive/ROOT', thus in 
my .bashrc file I have added:
    export ROOTSYS=/Volumes/GigaDrive/ROOT/root
    export PATH=$ROOTSYS/bin:$PATH
    export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH

In order to see if your Mac can start ROOT, type in the terminal:
$ root
You can quit ROOT by typing '.q'

Best regards,
Christian


On 3/27/13 12:39 PM, Andreia Fonseca wrote:
> Dear Steve and Christian,
>
> I have installed root, its in the root, so when I invoke root in a
> terminal it starts but I am getting the same error message in R. When I
> try to make in the terminal
>
> . lib/thisroot.sh
>
> is doesn't find the file.
>
> I am desperate, I have try to install root in different ways, location
> independent and setting the location, and I don't know what to do
> anymore. :(
>
> Thanks
>
> On Wed, Mar 27, 2013 at 11:16 AM, Andreia Fonseca
> <andreia.fonseca at gmail.com <mailto:andreia.fonseca at gmail.com>> wrote:
>
>     dear Christian,
>
>     can you explain me how to set the environment variables? I found the
>     file .bashrc, I understand that I need to add the path  to this
>     file. Is it the /usr/local?
>     Is it like this? $PATH=/usr/local ?
>
>     Thanks for the help
>
>
>     On Tue, Mar 26, 2013 at 6:43 PM, cstrato <cstrato at aon.at
>     <mailto:cstrato at aon.at>> wrote:
>
>         Dear Andreia,
>
>         As Steve has already kindly mentioned, package xps requires
>         installation of the ROOT framework.
>
>         My only additional comment is, that I would suggest to install
>         ROOT not in /usr/local/ which is not visible in the Mac Finder
>         but in any directory you want and which you can also see in the
>         Finder. You need to set the environment variables in '.bashrc'
>         in your home directory.
>
>         Best regards,
>         Christian
>
>
>
>         On 3/26/13 4:50 AM, Andreia Fonseca wrote:
>
>             Dear all,
>
>             I am trying to install xps and I am getting the following error:
>
>             library("xps")
>             Error in dyn.load(file, DLLpath = DLLpath, ...) :
>                 unable to load shared object
>             '/Library/Frameworks/R.__framework/Versions/2.15/__Resources/library/xps/libs/__i386/xps.so':
>
>             dlopen(/Library/Frameworks/R.__framework/Versions/2.15/__Resources/library/xps/libs/__i386/xps.so,
>             6): Library not loaded: /usr/local/root/lib/root/__libGui.so
>                 Referenced from:
>             /Library/Frameworks/R.__framework/Versions/2.15/__Resources/library/xps/libs/__i386/xps.so
>                 Reason: image not found
>             Error: package/namespace load failed for 'xps'
>
>             can someone help?
>
>             I have downloaded the file using biocLite
>
>                 biocLite("xps")
>
>             BioC_mirror: http://bioconductor.org
>             Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R
>             version 2.15.
>             Installing package(s) 'xps'
>             trying URL '
>             http://bioconductor.org/__packages/2.11/bioc/bin/macosx/__leopard/contrib/2.15/xps_1.18.__1.tgz
>             <http://bioconductor.org/packages/2.11/bioc/bin/macosx/leopard/contrib/2.15/xps_1.18.1.tgz>
>             '
>             Content type 'application/x-gzip' length 7208382 bytes (6.9 Mb)
>             opened URL
>             ==============================__====================
>             downloaded 6.9 Mb
>
>             tar: Failed to set default locale
>
>             The downloaded binary packages are in
>
>             /var/folders/mg/__mgYnPlsvH50tWM6oW27ypE+++TI/-__Tmp-//RtmpubosnY/downloaded___packages
>
>             the sessionInfo is the following:
>
>             sessionInfo()
>             R version 2.15.3 (2013-03-01)
>             Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
>             locale:
>             [1] C
>
>             attached base packages:
>             [1] stats     graphics  grDevices utils     datasets
>               methods   base
>
>             other attached packages:
>             [1] affy_1.36.1         Biobase_2.18.0      BiocGenerics_0.4.0
>             BiocInstaller_1.8.3
>
>             loaded via a namespace (and not attached):
>             [1] affyio_1.26.0         preprocessCore_1.20.0 tools_2.15.3
>             zlibbioc_1.4.0
>
>
>             thnaks for the help,
>
>             Andreia
>
>
>
>
>             ------------------------------__------------------------------__------------------------------__-----
>             Andreia J. Amaral, PhD
>             BioFIG - Center for Biodiversity, Functional and Integrative
>             Genomics
>             Instituto de Medicina Molecular
>             University of Lisbon
>             Tel: +352 217500000 (ext. office: 28253)
>             email:andreiaamaral at fm.ul.pt
>             <mailto:email%3Aandreiaamaral at fm.ul.pt> ;
>             andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>
>
>                      [[alternative HTML version deleted]]
>
>             _________________________________________________
>             Bioconductor mailing list
>             Bioconductor at r-project.org <mailto:Bioconductor at r-project.org>
>             https://stat.ethz.ch/mailman/__listinfo/bioconductor
>             <https://stat.ethz.ch/mailman/listinfo/bioconductor>
>             Search the archives:
>             http://news.gmane.org/gmane.__science.biology.informatics.__conductor
>             <http://news.gmane.org/gmane.science.biology.informatics.conductor>
>
>
>
>
>     --
>     ---------------------------------------------------------------------------------------------
>     Andreia J. Amaral, PhD
>     BioFIG - Center for Biodiversity, Functional and Integrative Genomics
>     Instituto de Medicina Molecular
>     University of Lisbon
>     Tel: +352 217500000 (ext. office: 28253)
>     email:andreiaamaral at fm.ul.pt <mailto:email%3Aandreiaamaral at fm.ul.pt>
>     ; andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>
>
>
>
>
> --
> ---------------------------------------------------------------------------------------------
> Andreia J. Amaral, PhD
> BioFIG - Center for Biodiversity, Functional and Integrative Genomics
> Instituto de Medicina Molecular
> University of Lisbon
> Tel: +352 217500000 (ext. office: 28253)
> email:andreiaamaral at fm.ul.pt <mailto:email%3Aandreiaamaral at fm.ul.pt> ;
> andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>



More information about the Bioconductor mailing list