[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>__>
>
>                               [[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>
>         <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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