xps- not being able to load it
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@andreia-fonseca-3796
Last seen 7.9 years ago
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/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' 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 ' 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/download ed_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 ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]
xps xps • 2.3k views
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@steve-lianoglou-2771
Last seen 22 months ago
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Hi, The problem is that you do not have the required libraries installed on your system. If you look at the xps package page: http://www.bioconductor.org/packages/2.11/bioc/html/xps.html You will see that: (1) The "System Requirements" lists "root_..."; and (2) It tells you to read the README included in the package, which you can find here: http://www.bioconductor.org/packages/2.11/bioc/readmes/xps/README Where it says: """... the prior installation of ROOT is a prerequisite for the usage of this package. ROOT can be downloaded from http://root.cern.ch.""" Also, your error message points you to what the problem might be, for instance: On Mon, Mar 25, 2013 at 11:50 PM, Andreia Fonseca <andreia.fonseca at="" gmail.com=""> wrote: [snip] > 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/libra ry/xps/libs/i386/xps.so, > 6): Library not loaded: /usr/local/root/lib/root/libGui.so [/snip] You can see that the package expects `root` to be installed in /usr/local/ The instructions on how to install `root` there are in that README I linked to previously. HTH, -steve -- Steve Lianoglou Defender of The Thesis | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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cstrato ★ 3.9k
@cstrato-908
Last seen 6.2 years ago
Austria
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/libra ry/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/contri b/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/downlo aded_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 ; andreiaamaral at fc.ul.pt > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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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> 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="" 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 ; andreiaamaral@fc.ul.pt >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**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 ; andreiaamaral@fc.ul.pt [[alternative HTML version deleted]]
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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> 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> 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="" pack="" ages="" 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 ; andreiaamaral@fc.ul.pt >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.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 ; 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 [[alternative HTML version deleted]]
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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="">> 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="">> 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/__Resou rces/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/__Resour ces/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="" l="" eopard="" 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-//R tmpubosnY/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=""> ; > andreiaamaral at fc.ul.pt <mailto:andreiaamaral at="" fc.ul.pt=""> > > [[alternative HTML version deleted]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__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 at fm.ul.pt <mailto:email%3aandreiaamaral at="" fm.ul.pt=""> > ; 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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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 $make install I have tried the other way without setting the location but it did not work. then I tried ldconfig but it doesn't work, mac doesn't know this command. I also tried . bin/thisroot.sh but it still gives error in R I have found the file bashrc in /etc/bashrc but is read only and even making sudo I can not edit it. Is this the file or should I create another bashrc somewhere else? Thanks for the help. On Wed, Mar 27, 2013 at 1:37 PM, cstrato <cstrato@aon.at> wrote: > Dear Andreia, > > 1, Can you please tell me which file you did download from the ROOT > web-site or ftp-site? > > 2, Please tell me how and in which directory you have installed root, i.e. > which directory does contain the directory 'root'? > > 3, What do you mean with '. lib/thisroot.sh'? Please note that the command > mentioned in the README file is '. bin/thisroot.sh'. > > 4, I have installed root in directory '/Volumes/GigaDrive/ROOT', thus in > my .bashrc file I have added: > export ROOTSYS=/Volumes/GigaDrive/**ROOT/root > export PATH=$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="">>> >> 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>> 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="" 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%253aandr eiaamaral@fm.ul.pt="">> >> ; >> andreiaamaral@fc.ul.pt <mailto:andreiaamaral@fc.ul.pt**> >> >> [[alternative HTML version deleted]] >> >> ______________________________**___________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <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=""> >> > >> Search the archives: >> http://news.gmane.org/gmane.__** >> science.biology.informatics.__**conductor<http: news.gmane.org="" gma="" ne.__science.biology.informatics.__conductor=""> >> >> <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=""> >> > >> ; 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 [[alternative HTML version deleted]]
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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/____Resou rces/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/____Resour ces/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="" __l="" eopard="" contrib="" 2.15="" xps_1.18.__1.tgz=""> > > > <http: bioconductor.org="" __packages="" 2.11="" bioc="" bin="" macosx="" __l="" eopard="" contrib="" 2.15="" xps_1.18.__1.tgz=""> <http: bioconductor.org="" packages="" 2.11="" bioc="" bin="" macosx="" leopa="" rd="" 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-//R tmpubosnY/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]] > > ___________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-__project.org=""> <mailto:bioconductor at="" r-project.org="">> > https://stat.ethz.ch/mailman/____listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> > > > <https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">> > Search the archives: > http://news.gmane.org/gmane.____science.biology.informatics. ____conductor > <http: news.gmane.org="" gmane.__science.biology.informatics._="" _conductor=""> > > > <http: news.gmane.org="" gmane.__science.biology.informatics.__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 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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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> 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=""> >> >> 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 >> >> $make install >> >> I have tried the other way without setting the location but it did not >> work. >> >> >> then I tried ldconfig but it doesn't work, mac doesn't know this command. >> >> I also tried >> >> . bin/thisroot.sh >> >> but it still gives error in R >> >> >> I have found the file bashrc in /etc/bashrc but is read only and even >> making sudo I can not edit it. Is this the file or should I create another >> bashrc somewhere else? >> Thanks for the help. >> >> >> >> >> On Wed, Mar 27, 2013 at 1:37 PM, cstrato <cstrato@aon.at>> <mailto:cstrato@aon.at>> wrote: >> >> Dear Andreia, >> >> 1, Can you please tell me which file you did download from the ROOT >> web-site or ftp-site? >> >> 2, Please tell me how and in which directory you have installed >> root, i.e. which directory does contain the directory 'root'? >> >> 3, What do you mean with '. lib/thisroot.sh'? Please note that the >> command mentioned in the README file is '. bin/thisroot.sh'. >> >> 4, I have installed root in directory '/Volumes/GigaDrive/ROOT', >> thus in my .bashrc file I have added: >> export ROOTSYS=/Volumes/GigaDrive/__**ROOT/root >> export PATH=$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="">>>> >> 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="">>> 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.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%253aandreiaamaral@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**="">> >__> >> >> [[alternative HTML version deleted]] >> >> ______________________________** >> _____________________ >> >> Bioconductor mailing list >> 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=""> >> >> >> https://stat.ethz.ch/mailman/_**___listinfo/bioconductor<ht tps:="" stat.ethz.ch="" mailman="" ____listinfo="" bioconductor=""> >> <https: stat.ethz.ch="" mailman="" **__listinfo="" bioconductor<htt="" ps:="" stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> > >> >> >> >> <https: stat.ethz.ch="" mailman="" **__listinfo="" bioconductor<htt="" ps:="" stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https="" :="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> >> >> Search the archives: >> http://news.gmane.org/gmane.__**__science.biology.informatics.** >> ____conductor<http: news.gmane.org="" gmane.____science.biology.infor="" matics.____conductor=""> >> <http: news.gmane.org="" gmane._**_science.biology.informatics._**="">> _conductor<http: news.gmane.org="" gmane.__science.biology.informatic="" s.__conductor=""> >> > >> >> >> >> <http: news.gmane.org="" gmane._**_science.biology.informatics._**="">> _conductor<http: news.gmane.org="" gmane.__science.biology.informatic="" s.__conductor=""> >> <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%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%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 [[alternative HTML version deleted]]
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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="">> 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=""> > > 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 > > $make install > > I have tried the other way without setting the location but it > did not work. > > > then I tried ldconfig but it doesn't work, mac doesn't know this > command. > > I also tried > > . bin/thisroot.sh > > but it still gives error in R > > > I have found the file bashrc in /etc/bashrc but is read only and > even making sudo I can not edit it. Is this the file or should I > create another bashrc somewhere else? > Thanks for the help. > > > > > On Wed, Mar 27, 2013 at 1:37 PM, cstrato <cstrato at="" aon.at=""> <mailto:cstrato at="" aon.at=""> > <mailto:cstrato at="" aon.at="" <mailto:cstrato="" at="" aon.at="">>> wrote: > > Dear Andreia, > > 1, Can you please tell me which file you did download from > the ROOT > web-site or ftp-site? > > 2, Please tell me how and in which directory you have installed > root, i.e. which directory does contain the directory 'root'? > > 3, What do you mean with '. lib/thisroot.sh'? Please note > that the > command mentioned in the README file is '. bin/thisroot.sh'. > > 4, I have installed root in directory > '/Volumes/GigaDrive/ROOT', > thus in my .bashrc file I have added: > export ROOTSYS=/Volumes/GigaDrive/____ROOT/root > export PATH=$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="">>>> 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="">>>> 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/______R esources/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/______Re sources/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="" __l="" eopard="" 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="" __l="" eopard="" contrib="" 2.15="" xps_1.18.__1.tgz=""> > > <http: bioconductor.org="" __packages="" 2.11="" bioc="" bin="" macosx="" __l="" eopard="" contrib="" 2.15="" xps_1.18.__1.tgz=""> <http: bioconductor.org="" packages="" 2.11="" bioc="" bin="" macosx="" leopa="" rd="" 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="">> > <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="">__>__> > > [[alternative HTML version deleted]] > > > _____________________________________________________ > > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-__project.org=""> <mailto:bioconductor at="" r-project.org="">> > <mailto:bioconductor at="" r-____project.org=""> <mailto:bioconductor at="" r-__project.org=""> > <mailto:bioconductor at="" r-__project.org=""> <mailto:bioconductor at="" r-project.org="">>> > https://stat.ethz.ch/mailman/______listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" ____listinfo="" bioconductor=""> > <https: stat.ethz.ch="" mailman="" ____listinfo="" bioconductor=""> <https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor="">> > > > > <https: stat.ethz.ch="" mailman="" ____listinfo="" bioconductor=""> <https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> > <https: stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">>> > Search the archives: > http://news.gmane.org/gmane.______science.biology.informatic s.______conductor > <http: news.gmane.org="" gmane.____science.biology.informatics="" .____conductor=""> > > <http: news.gmane.org="" gmane.____science.biology.informatics="" .____conductor=""> <http: news.gmane.org="" gmane.__science.biology.informatics._="" _conductor="">> > > > > > <http: news.gmane.org="" gmane.____science.biology.informatics="" .____conductor=""> <http: news.gmane.org="" gmane.__science.biology.informatics._="" _conductor=""> > > <http: news.gmane.org="" gmane.__science.biology.informatics.__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 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="">> > <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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