Dear Christian,



thanks for the help I have followed your instructions and root is
installed, I can start root from any directory, however I am still not
being able to load xps on R, I am getting the same error (error message
below) how can I setup the the lib folder on
/usr/local/root/lib/root/libGui.so?

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'





On Wed, Mar 27, 2013 at 3:35 PM, cstrato <cstrato@aon.at> wrote:

> Dear Andreia,
>
> You have to create the .bashrc file in your home directory. It looks like
> this:
>
> # .bashrc
>
> # User specific aliases and functions
>
> #svn
> export PATH=$PATH:/usr/local/bin
>
> # ROOT settings
>
> export ROOTSYS=/Users/andreia/ROOT/**root
> export PATH=$ROOTSYS/bin:$PATH
> export LD_LIBRARY_PATH=$ROOTSYS/lib:$**LD_LIBRARY_PATH
>
> # Source global definitions
> if [ -f /etc/bashrc ]; then
>         . /etc/bashrc
> fi
>
>
> Best regards,
> Christian
>
>
>
> On 3/27/13 3:44 PM, Andreia Fonseca wrote:
>
>> Dear Christian,
>>
>> The version of Mac is 10.6.8 and the root is version 5.34.05. I just
>> have one more question before I start following your instructions. How
>> can I edit the file .bashrc? it is read only, and I have tried to edit
>> it using sudo and I couldn't too. Can you confirm me that this file is
>> the one I find in etc/?
>>
>> Thanks Andreia
>>
>> On Wed, Mar 27, 2013 at 2:31 PM, cstrato <cstrato@aon.at
>> <mailto:cstrato@aon.at>> wrote:
>>
>>     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<http://root.cern.ch/drupal/__content/production-version-534>
>>
>>         <http://root.cern.ch/drupal/**content/production-version-534<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
>>
>>         $make install
>>
>>         I have tried the other way without setting the location but it
>>         did not work.
>>
>>
>>         then I tried ldconfig but it doesn't work, mac doesn't know this
>>         command.
>>
>>         I also tried
>>
>>         . bin/thisroot.sh
>>
>>         but it still gives error in R
>>
>>
>>         I have found the file bashrc in /etc/bashrc but is read only and
>>         even making sudo I can not edit it. Is this the file or should I
>>         create another bashrc somewhere else?
>>         Thanks for the help.
>>
>>
>>
>>
>>         On Wed, Mar 27, 2013 at 1:37 PM, cstrato <cstrato@aon.at
>>         <mailto:cstrato@aon.at>
>>         <mailto:cstrato@aon.at <mailto:cstrato@aon.at>>> wrote:
>>
>>              Dear Andreia,
>>
>>              1, Can you please tell me which file you did download from
>>         the ROOT
>>              web-site or ftp-site?
>>
>>              2, Please tell me how and in which directory you have
>> installed
>>              root, i.e. which directory does contain the directory 'root'?
>>
>>              3, What do you mean with '. lib/thisroot.sh'? Please note
>>         that the
>>              command mentioned in the README file is '. bin/thisroot.sh'.
>>
>>              4, I have installed root in directory
>>         '/Volumes/GigaDrive/ROOT',
>>              thus in my .bashrc file I have added:
>>                  export ROOTSYS=/Volumes/GigaDrive/___**_ROOT/root
>>                  export PATH=$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@gmail.com
>>         <mailto:andreia.fonseca@gmail.**com <andreia.fonseca@gmail.com>>
>>         <mailto:andreia.fonseca@gmail.**__com
>>         <mailto:andreia.fonseca@gmail.**com <andreia.fonseca@gmail.com>>>
>>                  <mailto:andreia.fonseca@gmail.
>>         <mailto:andreia.fonseca@gmail.**>____com
>>
>>
>>                  <mailto:andreia.fonseca@gmail.**__com
>>         <mailto:andreia.fonseca@gmail.**com <andreia.fonseca@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@aon.at <mailto:cstrato@aon.at>
>>                  <mailto:cstrato@aon.at <mailto:cstrato@aon.at>>
>>                       <mailto:cstrato@aon.at <mailto:cstrato@aon.at>
>>         <mailto:cstrato@aon.at <mailto:cstrato@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>
>> >
>>
>>
>>         <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>
>> >>
>>
>>
>>
>>
>>         <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>
>> >
>>
>>         <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@fm.ul.pt
>>         <mailto:email%3Aandreiaamaral@**fm.ul.pt<email%253Aandreiaamaral@fm.ul.pt>
>> >
>>         <mailto:email%3Aandreiaamaral@**__fm.ul.pt
>>         <mailto:email%**253Aandreiaamaral@fm.ul.pt<email%25253Aandreiaamaral@fm.ul.pt>
>> >>
>>                               <mailto:email%3Aandreiaamaral@
>>         <mailto:email%**253Aandreiaamaral@ <email%25253Aandreiaamaral@>
>> >____fm.ul.**pt <http://fm.ul.pt> <http://fm.ul.pt>
>>                  <mailto:email%__**253Aandreiaamaral@fm.ul.pt<email%25__253Aandreiaamaral@fm.ul.pt>
>>         <mailto:email%**25253Aandreiaamaral@fm.ul.pt<email%2525253Aandreiaamaral@fm.ul.pt>
>> >>**> ;
>>
>>         andreiaamaral@fc.ul.pt <mailto:andreiaamaral@fc.ul.pt**>
>>         <mailto:andreiaamaral@fc.ul.pt <mailto:andreiaamaral@fc.ul.pt**
>> >__>
>>                  <mailto:andreiaamaral@fc.ul.pt
>>         <mailto:andreiaamaral@fc.ul.pt**> <mailto:andreiaamaral@fc.ul.pt
>>         <mailto:andreiaamaral@fc.ul.pt**>__>__>
>>
>>                                        [[alternative HTML version
>> deleted]]
>>
>>
>>           ______________________________**_______________________
>>
>>
>>                               Bioconductor mailing list
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>> >
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>>         <mailto:Bioconductor@r-**project.org <Bioconductor@r-project.org>
>> >>
>>                  <mailto:Bioconductor@r-____**project.org<Bioconductor@r-____project.org>
>>         <mailto:Bioconductor@r-__**project.org<Bioconductor@r-__project.org>
>> >
>>                  <mailto:Bioconductor@r-__**project.org<Bioconductor@r-__project.org>
>>         <mailto:Bioconductor@r-**project.org <Bioconductor@r-project.org>
>> >>>
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>> >>
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>> >
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>> >>>
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>> informatics.____conductor<http://news.gmane.org/gmane.____science.biology.informatics.____conductor>
>> >
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>> >>
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>> >
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>> 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@fm.ul.pt <mailto:email%3Aandreiaamaral@**
>> fm.ul.pt <email%253Aandreiaamaral@fm.ul.pt>>
>>                  <mailto:email%3Aandreiaamaral@**__fm.ul.pt
>>         <mailto:email%**253Aandreiaamaral@fm.ul.pt<email%25253Aandreiaamaral@fm.ul.pt>
>> >>
>>                  <mailto:email%3Aandreiaamaral@
>>         <mailto:email%**253Aandreiaamaral@ <email%25253Aandreiaamaral@>
>> >____fm.ul.**pt <http://fm.ul.pt> <http://fm.ul.pt>
>>                  <mailto:email%__**253Aandreiaamaral@fm.ul.pt<email%25__253Aandreiaamaral@fm.ul.pt>
>>         <mailto:email%**25253Aandreiaamaral@fm.ul.pt<email%2525253Aandreiaamaral@fm.ul.pt>
>> >>**>
>>                       ; andreiaamaral@fc.ul.pt
>>
>>         <mailto:andreiaamaral@fc.ul.pt**> <mailto:andreiaamaral@fc.ul.pt
>>         <mailto:andreiaamaral@fc.ul.pt**>__>
>>                  <mailto:andreiaamaral@fc.ul.pt
>>         <mailto:andreiaamaral@fc.ul.pt**> <mailto:andreiaamaral@fc.ul.pt
>>         <mailto:andreiaamaral@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@fm.ul.pt <mailto:email%3Aandreiaamaral@**
>> fm.ul.pt <email%253Aandreiaamaral@fm.ul.pt>>
>>                  <mailto:email%3Aandreiaamaral@**__fm.ul.pt
>>         <mailto:email%**253Aandreiaamaral@fm.ul.pt<email%25253Aandreiaamaral@fm.ul.pt>
>> >>
>>                  <mailto:email%3Aandreiaamaral@
>>         <mailto:email%**253Aandreiaamaral@ <email%25253Aandreiaamaral@>
>> >____fm.ul.**pt <http://fm.ul.pt> <http://fm.ul.pt>
>>                  <mailto:email%__**253Aandreiaamaral@fm.ul.pt<email%25__253Aandreiaamaral@fm.ul.pt>
>>         <mailto:email%**25253Aandreiaamaral@fm.ul.pt<email%2525253Aandreiaamaral@fm.ul.pt>
>> >>**> ;
>>
>>         andreiaamaral@fc.ul.pt <mailto:andreiaamaral@fc.ul.pt**>
>>         <mailto:andreiaamaral@fc.ul.pt <mailto:andreiaamaral@fc.ul.pt**
>> >__>
>>                  <mailto:andreiaamaral@fc.ul.pt
>>         <mailto:andreiaamaral@fc.ul.pt**> <mailto:andreiaamaral@fc.ul.pt
>>         <mailto:andreiaamaral@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@fm.ul.pt
>>         <mailto:email%3Aandreiaamaral@**fm.ul.pt<email%253Aandreiaamaral@fm.ul.pt>
>> >
>>         <mailto:email%3Aandreiaamaral@**__fm.ul.pt
>>         <mailto:email%**253Aandreiaamaral@fm.ul.pt<email%25253Aandreiaamaral@fm.ul.pt>>>
>> ;
>>         andreiaamaral@fc.ul.pt <mailto:andreiaamaral@fc.ul.pt**>
>>         <mailto:andreiaamaral@fc.ul.pt <mailto:andreiaamaral@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@fm.ul.pt <mailto:email%3Aandreiaamaral@**fm.ul.pt<email%253Aandreiaamaral@fm.ul.pt>>
>> ;
>> andreiaamaral@fc.ul.pt <mailto:andreiaamaral@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@fm.ul.pt ; andreiaamaral@fc.ul.pt

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