[BioC] xps- not being able to load it

cstrato cstrato at aon.at
Mon Apr 1 12:26:06 CEST 2013


Dear Andreia,

In which directory did you install ROOT?
How did you set ROOTSYS in your .bashrc?

It seems that you have still installed ROOT also in /usr/local/. If this 
is the case then you need to delete /usr/local/root (or at least rename 
the root folder)

BTW, if it is easier for you then you can download a ROOT binary for 
Snow Leopard from:
ftp://root.cern.ch/root/root_v5.34.05.macosx106-x86_64-gcc-4.2.tar.gz
This is the version which the Bioconductor maintainers have installed on 
the Snow Leopard server for the upcoming release of BioC 2.12 on this 
Thursday (April 4).

Best regards,
Christian


On 4/1/13 11:24 AM, Andreia Fonseca wrote:
> 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 at aon.at
> <mailto:cstrato at 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 at aon.at
>         <mailto:cstrato at aon.at>
>         <mailto:cstrato at aon.at <mailto:cstrato at 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
>
>                  $make install
>
>                  I have tried the other way without setting the location
>         but it
>                  did not work.
>
>
>                  then I tried ldconfig but it doesn't work, mac doesn't
>         know this
>                  command.
>
>                  I also tried
>
>                  . bin/thisroot.sh
>
>                  but it still gives error in R
>
>
>                  I have found the file bashrc in /etc/bashrc but is read
>         only and
>                  even making sudo I can not edit it. Is this the file or
>         should I
>                  create another bashrc somewhere else?
>                  Thanks for the help.
>
>
>
>
>                  On Wed, Mar 27, 2013 at 1:37 PM, cstrato
>         <cstrato at aon.at <mailto:cstrato at aon.at>
>                  <mailto:cstrato at aon.at <mailto:cstrato at aon.at>>
>                  <mailto:cstrato at aon.at <mailto:cstrato at aon.at>
>         <mailto:cstrato at aon.at <mailto:cstrato at aon.at>>>> wrote:
>
>                       Dear Andreia,
>
>                       1, Can you please tell me which file you did
>         download from
>                  the ROOT
>                       web-site or ftp-site?
>
>                       2, Please tell me how and in which directory you
>         have installed
>                       root, i.e. which directory does contain the
>         directory 'root'?
>
>                       3, What do you mean with '. lib/thisroot.sh'?
>         Please note
>                  that the
>                       command mentioned in the README file is '.
>         bin/thisroot.sh'.
>
>                       4, I have installed root in directory
>                  '/Volumes/GigaDrive/ROOT',
>                       thus in my .bashrc file I have added:
>                           export ROOTSYS=/Volumes/GigaDrive/______ROOT/root
>                           export PATH=$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>>
>                  <mailto:andreia.fonseca at gmail.
>         <mailto:andreia.fonseca at gmail.>____com
>                  <mailto:andreia.fonseca at gmail.__com
>         <mailto:andreia.fonseca at gmail.com>>>
>                           <mailto:andreia.fonseca at gmail
>         <mailto:andreia.fonseca at gmail>.
>                  <mailto:andreia.fonseca at gmail
>         <mailto:andreia.fonseca at gmail>.__>____com
>
>
>                           <mailto:andreia.fonseca at gmail.
>         <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>>
>                           <mailto:cstrato at aon.at <mailto:cstrato at aon.at>
>         <mailto:cstrato at aon.at <mailto:cstrato at aon.at>>>
>                                <mailto:cstrato at aon.at
>         <mailto:cstrato at aon.at> <mailto:cstrato at aon.at
>         <mailto:cstrato at aon.at>>
>                  <mailto: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>>
>
>
>
>         <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 at fm.ul.pt <mailto:email%3Aandreiaamaral at fm.ul.pt>
>                  <mailto:email%3Aandreiaamaral at __fm.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>
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>                  <mailto:andreiaamaral at fc.ul.pt
>         <mailto:andreiaamaral at fc.ul.pt>__>
>         <mailto:andreiaamaral at fc.ul.pt <mailto:andreiaamaral at fc.ul.pt>
>                  <mailto:andreiaamaral at fc.ul.pt
>         <mailto:andreiaamaral at fc.ul.pt>__>__>
>                           <mailto:andreiaamaral at fc.ul.pt
>         <mailto:andreiaamaral at fc.ul.pt>
>                  <mailto:andreiaamaral at fc.ul.pt
>         <mailto:andreiaamaral at fc.ul.pt>__>
>         <mailto: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>>
>                           <mailto:email%3Aandreiaamaral@
>         <mailto:email%253Aandreiaamaral@>____fm.ul.pt <http://fm.ul.pt>
>                  <mailto:email%__253Aandreiaamaral at fm.ul.pt
>         <mailto:email%25253Aandreiaamaral at fm.ul.pt>>>
>                           <mailto:email%3Aandreiaamaral@
>         <mailto:email%253Aandreiaamaral@>
>                  <mailto:email%__253Aandreiaamaral@
>         <mailto:email%25253Aandreiaamaral@>>____fm.ul.__pt
>         <http://fm.ul.pt> <http://fm.ul.pt>
>                           <mailto:email%____253Aandreiaamaral at fm.ul.pt
>         <mailto:email%25__253Aandreiaamaral at fm.ul.pt>
>                  <mailto:email%__25253Aandreiaamaral at fm.ul.pt
>         <mailto:email%2525253Aandreiaamaral 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>__>
>                  <mailto:andreiaamaral at fc.ul.pt
>         <mailto:andreiaamaral at fc.ul.pt> <mailto:andreiaamaral at fc.ul.pt
>         <mailto:andreiaamaral at fc.ul.pt>__>__>
>                           <mailto:andreiaamaral at fc.ul.pt
>         <mailto:andreiaamaral at fc.ul.pt>
>                  <mailto:andreiaamaral at fc.ul.pt
>         <mailto:andreiaamaral at fc.ul.pt>__>
>         <mailto: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>>
>                  <mailto:email%3Aandreiaamaral@
>         <mailto:email%253Aandreiaamaral@>____fm.ul.pt <http://fm.ul.pt>
>                  <mailto:email%__253Aandreiaamaral at fm.ul.pt
>         <mailto:email%25253Aandreiaamaral 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>__>
>                  <mailto: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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