[BioC] xps- not being able to load it
cstrato
cstrato at aon.at
Wed Mar 27 15:31:29 CET 2013
Dear Andreia,
As I have mentioned earlier I do recommend NOT to install ROOT in
'/usr/local'. This results often in problems.
Please install ROOT in a directory which can be seen in the Finder, e.g.
in directory 'ROOT' in your home directory, i.e.
'/Users/andreia/ROOT'.Since you are have downloaded the source file for
compilation, please unpack the source in this directory and then do:
$ cd root
$ ./configure macosx64
$ make
$ . bin/thisroot.sh
Usually I add the following commands to .bashrc before I compile ROOT,
i.e. in your case:
export ROOTSYS=/Users/andreia/ROOT/root
export PATH=$ROOTSYS/bin:$PATH
export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
BTW, which version of Mac OS X are you using and which version of ROOT
did you compile?
Best regards,
Christian
On 3/27/13 2:57 PM, Andreia Fonseca wrote:
> Dear Christian,
>
> I have downloaded the advised version
>
> http://root.cern.ch/drupal/content/production-version-534
>
> it is saved in my Downloads directory
>
> then I have unpacked using the following command:
>
> $gzip -dc root_<version>.source.tar.gz| tar -xf -
>
>
> after unpacking I went to the directory root and did
>
> $./configure --prefix=/usr/local
>
> then
>
> $make
>
> then
>
> $make install
>
> I have tried the other way without setting the location but it did not work.
>
>
> then I tried ldconfig but it doesn't work, mac doesn't know this command.
>
> I also tried
>
> . bin/thisroot.sh
>
> but it still gives error in R
>
>
> I have found the file bashrc in /etc/bashrc but is read only and even making sudo I can not edit it. Is this the file or should I create another bashrc somewhere else?
> Thanks for the help.
>
>
>
>
> On Wed, Mar 27, 2013 at 1:37 PM, cstrato <cstrato at aon.at
> <mailto:cstrato at aon.at>> wrote:
>
> Dear Andreia,
>
> 1, Can you please tell me which file you did download from the ROOT
> web-site or ftp-site?
>
> 2, Please tell me how and in which directory you have installed
> root, i.e. which directory does contain the directory 'root'?
>
> 3, What do you mean with '. lib/thisroot.sh'? Please note that the
> command mentioned in the README file is '. bin/thisroot.sh'.
>
> 4, I have installed root in directory '/Volumes/GigaDrive/ROOT',
> thus in my .bashrc file I have added:
> export ROOTSYS=/Volumes/GigaDrive/__ROOT/root
> export PATH=$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>
> <mailto: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>
> <mailto: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>
>
>
> <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>
> <mailto:email%3Aandreiaamaral at __fm.ul.pt
> <mailto:email%253Aandreiaamaral at fm.ul.pt>> ;
> andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>
> <mailto:andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>__>
>
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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>
> <mailto:email%3Aandreiaamaral at __fm.ul.pt
> <mailto:email%253Aandreiaamaral at fm.ul.pt>>
> ; andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>
> <mailto: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>
> <mailto:email%3Aandreiaamaral at __fm.ul.pt
> <mailto:email%253Aandreiaamaral at fm.ul.pt>> ;
> andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>
> <mailto: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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