[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]]
>
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> --
> ---------------------------------------------------------------------------------------------
> 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>
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