Entering edit mode
Andreia Fonseca
▴
810
@andreia-fonseca-3796
Last seen 7.9 years ago
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/l
ibs/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/li
bs/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: bioconduct="" or.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.o="" rg="" ____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.o="" rg="" ____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.o="" rg="" ____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="" packa="" ges="" 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%253aandreiaa maral@fm.ul.pt="">
>> >
>> <mailto:email%3aandreiaamaral@**__fm.ul.pt>> <mailto:email%**253aandreiaamaral@fm.ul.pt<email%25253aandr eiaamaral@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%2525253a andreiaamaral@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]]
>>
>>
>> ______________________________**_______________________
>>
>>
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>> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org="">
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>> <mailto:bioconductor@r-**project.org <bioconductor@r-project.org="">
>> >>>
>> https://stat.ethz.ch/mailman/_**_____listinfo/bioconductor<
https://stat.ethz.ch/mailman/______listinfo/bioconductor>
>> <https: stat.ethz.ch="" mailman="" **____listinfo="" bioconductor<h="" ttps:="" stat.ethz.ch="" mailman="" ____listinfo="" bioconductor="">
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>> >>
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>> <https: stat.ethz.ch="" mailman="" **="">> ____listinfo/bioconductor<https: stat.ethz.ch="" mailman="" ____listinfo="" bioconductor="">
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>> >
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>> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https="" :="" stat.ethz.ch="" mailman="" listinfo="" bioconductor="">
>> >>>
>> Search the archives:
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>> <http: news.gmane.org="" gmane._**___science.biology.**="">> informatics.____conductor<http: news.gmane.org="" gmane.____science.b="" iology.informatics.____conductor="">
>> >
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>> >>
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>> >
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>>
<http: news.gmane.org="" gmane.**science.biology.informatics.**="">> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor="">
>> >>>
>>
>>
>>
>>
>> --
>>
>>
>>
------------------------------**____--------------------------**
>> --__--__----------------------**----__----__---
>>
>>
>> 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%25253aandr eiaamaral@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%2525253a andreiaamaral@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%25253aandr eiaamaral@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%2525253a andreiaamaral@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%253aandreiaa maral@fm.ul.pt="">
>> >
>> <mailto:email%3aandreiaamaral@**__fm.ul.pt>> <mailto:email%**253aandreiaamaral@fm.ul.pt<email%25253aandr eiaamaral@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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