Question: problem with using GSVA package
0
7.8 years ago by
Wendy Qiao360
Wendy Qiao360 wrote:
Hi all, I am trying to use the GSVA package, but I encounter the following problems. library(GSVA) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/GSVA/ libs/x86_64/GSVA.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library /GSVA/libs/x86_64/GSVA.so, 6): Symbol not found: _gsl_cdf_ugaussian_P Referenced from: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/GSVA/l ibs/x86_64/GSVA.so Expected in: dynamic lookup Error: package/namespace load failed for GSVA I tried to re-install the package and recompile all the packages, but it still gave the same error. Could anybody please help? Thank you so much! Wendy [[alternative HTML version deleted]]
gsva • 951 views
modified 7.8 years ago by Robert Castelo2.3k • written 7.8 years ago by Wendy Qiao360
Answer: problem with using GSVA package
0
7.8 years ago by
Robert Castelo2.3k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.3k wrote:
Hi Robert, Thank you very much for your reply. I tried your comments. Everything worked fine until "make install". This comment gives the following errors. Any suggestion is appreciated. Thank you very much. Making install in gsl make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'. Making install in utils make[2]: Nothing to be done for install-exec-am'. make[2]: Nothing to be done for install-data-am'. Making install in sys make[2]: Nothing to be done for install-exec-am'. test -z "/usr/local/include/gsl" || .././install-sh -c -d "/usr/local/include/gsl" mkdir: /usr/local/include: Permission denied mkdir: /usr/local/include: No such file or directory make[2]: *** [install-pkgincludeHEADERS] Error 1 make[1]: *** [install-am] Error 2 make: *** [install-recursive] Error 1 Wendy On 7 November 2011 07:32, Juan Roberto CASTELO VALDUEZA < robert.castelo@upf.edu> wrote: > hi Wendy, > > sorry about that, i forgot to say that you need to install in your > computer the so-called GNU Scientific Library from: > > http://www.gnu.org/s/gsl > > this is not part of R and should be installed separately. seeing your > output, i guess that you're working on an apple computer. in such a case > you can just try the following: > > 1. download the tarball in your Desktop > > http://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz > > 2. open the terminal window from Applications -> Utilities -> Terminal > > 3. write in the terminal window the following commands > > cd Desktop > cd gsl* > ./configure > make > make install > > if these commands are executed without errors, then you can go back to R > and should be able to install GSVA without problems. let me know if you > encounter any difficulty with this. > > cheers, > robert. > > ------------------------------ > From Wendy Qiao <wendy2.qiao@gmail.com> > Sent Mon 11/7/2011 12:51 PM > To bioconductor@r-project.org > Subject [BioC] problem with using GSVA package > > Hi all, > > I am trying to use the GSVA package, but I encounter the following problems. > > library(GSVA) > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/GSV A/libs/x86_64/GSVA.so': > > dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/libra ry/GSVA/libs/x86_64/GSVA.so, > 6): Symbol not found: _gsl_cdf_ugaussian_P > Referenced from: > /Library/Frameworks/R.framework/Versions/2.14/Resources/library/GSVA /libs/ > x86_64/GSVA.so > Expected in: dynamic lookup > > Error: package/namespace load failed for GSVA > > I tried to re-install the package and recompile all the packages, but it > still gave the same error. Could anybody please help? Thank you so much! > > Wendy > > [[alternative HTML version deleted]] > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing listBioconductor@r-project.orghttps://stat.ethz .ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
hi, i think i forgot again something. those steps try to make a "system-wide" installation by default trying to write to parts of the filesystem where one need's extra privileges to do it. please try, instead of make install write sudo make install then the system will ask for your password, enter your password and hopefully everything should go fine. let me know. cheers, robert. On Mon, 2011-11-07 at 07:56 -0500, Wendy Qiao wrote: > Hi Robert, > > > Thank you very much for your reply. I tried your comments. Everything > worked fine until "make install". This comment gives the following > errors. Any suggestion is appreciated. Thank you very much. > > > Making install in gsl > make[2]: Nothing to be done for install-exec-am'. > make[2]: Nothing to be done for install-data-am'. > Making install in utils > make[2]: Nothing to be done for install-exec-am'. > make[2]: Nothing to be done for install-data-am'. > Making install in sys > make[2]: Nothing to be done for install-exec-am'. > test -z "/usr/local/include/gsl" || .././install-sh -c -d > "/usr/local/include/gsl" > mkdir: /usr/local/include: Permission denied > mkdir: /usr/local/include: No such file or directory > make[2]: *** [install-pkgincludeHEADERS] Error 1 > make[1]: *** [install-am] Error 2 > make: *** [install-recursive] Error 1 > > > Wendy > > > > On 7 November 2011 07:32, Juan Roberto CASTELO VALDUEZA > <robert.castelo at="" upf.edu=""> wrote: > hi Wendy, > > sorry about that, i forgot to say that you need to install in > your computer the so-called GNU Scientific Library from: > > http://www.gnu.org/s/gsl > > this is not part of R and should be installed separately. > seeing your output, i guess that you're working on an apple > computer. in such a case you can just try the following: > > 1. download the tarball in your Desktop > > http://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz > > > 2. open the terminal window from Applications -> Utilities -> > Terminal > > 3. write in the terminal window the following commands > > cd Desktop > cd gsl* > ./configure > make > make install > > if these commands are executed without errors, then you can go > back to R and should be able to install GSVA without problems. > let me know if you encounter any difficulty with this. > > cheers, > robert. > > > ______________________________________________________________ > From Wendy Qiao <wendy2.qiao at="" gmail.com=""> > Sent Mon 11/7/2011 12:51 PM > To bioconductor at r-project.org > Subject [BioC] problem with using GSVA package > > > Hi all, I am trying to use the GSVA package, but I encounter > the following problems. library(GSVA) Error in dyn.load(file, > DLLpath = DLLpath, ...) : unable to load shared object > '/Library/Frameworks/R.framework/Versions/2.14/Resources/lib rary/GSVA/libs/x86_64/GSVA.so': dlopen(/Library/Frameworks/R.framework /Versions/2.14/Resources/library/GSVA/libs/x86_64/GSVA.so, 6): Symbol not found: _gsl_cdf_ugaussian_P Referenced from: /Library/Frameworks/R .framework/Versions/2.14/Resources/library/GSVA/libs/ > x86_64/GSVA.so > Expected in: dynamic lookup > > Error: package/namespace load failed for ?GSVA? > > I tried to re-install the package and recompile all the packages, but it > still gave the same error. Could anybody please help? Thank you so much! > > Wendy > > [[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 >
This package looks interesting, but when I tried installing GSVA ( V1.20) it failed with "Cannot find the GNU Scientific Library >= 1.6" I have gsl-1.14 installed and the bioc web pages states gsl>=1.12 David -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Robert Castelo Sent: Monday, November 07, 2011 9:03 AM To: Wendy Qiao Cc: bioconductor at r-project.org Subject: Re: [BioC] problem with using GSVA package hi, i think i forgot again something. those steps try to make a "system-wide" installation by default trying to write to parts of the filesystem where one need's extra privileges to do it. please try, instead of make install write sudo make install then the system will ask for your password, enter your password and hopefully everything should go fine. let me know. cheers, robert. On Mon, 2011-11-07 at 07:56 -0500, Wendy Qiao wrote: > Hi Robert, > > > Thank you very much for your reply. I tried your comments. Everything > worked fine until "make install". This comment gives the following > errors. Any suggestion is appreciated. Thank you very much. > > > Making install in gsl > make[2]: Nothing to be done for install-exec-am'. > make[2]: Nothing to be done for install-data-am'. > Making install in utils > make[2]: Nothing to be done for install-exec-am'. > make[2]: Nothing to be done for install-data-am'. > Making install in sys > make[2]: Nothing to be done for install-exec-am'. > test -z "/usr/local/include/gsl" || .././install-sh -c -d > "/usr/local/include/gsl" > mkdir: /usr/local/include: Permission denied > mkdir: /usr/local/include: No such file or directory > make[2]: *** [install-pkgincludeHEADERS] Error 1 > make[1]: *** [install-am] Error 2 > make: *** [install-recursive] Error 1 > > > Wendy > > > > On 7 November 2011 07:32, Juan Roberto CASTELO VALDUEZA > <robert.castelo at="" upf.edu=""> wrote: > hi Wendy, > > sorry about that, i forgot to say that you need to install in > your computer the so-called GNU Scientific Library from: > > http://www.gnu.org/s/gsl > > this is not part of R and should be installed separately. > seeing your output, i guess that you're working on an apple > computer. in such a case you can just try the following: > > 1. download the tarball in your Desktop > > http://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz > > > 2. open the terminal window from Applications -> Utilities -> > Terminal > > 3. write in the terminal window the following commands > > cd Desktop > cd gsl* > ./configure > make > make install > > if these commands are executed without errors, then you can go > back to R and should be able to install GSVA without problems. > let me know if you encounter any difficulty with this. > > cheers, > robert. > > > ______________________________________________________________ > From Wendy Qiao <wendy2.qiao at="" gmail.com=""> > Sent Mon 11/7/2011 12:51 PM > To bioconductor at r-project.org > Subject [BioC] problem with using GSVA package > > > Hi all, I am trying to use the GSVA package, but I encounter > the following problems. library(GSVA) Error in dyn.load(file, > DLLpath = DLLpath, ...) : unable to load shared object > '/Library/Frameworks/R.framework/Versions/2.14/Resources/lib rary/GSVA/libs/x86_64/GSVA.so': dlopen(/Library/Frameworks/R.framework /Versions/2.14/Resources/library/GSVA/libs/x86_64/GSVA.so, 6): Symbol not found: _gsl_cdf_ugaussian_P Referenced from: /Library/Frameworks/R .framework/Versions/2.14/Resources/library/GSVA/libs/ > x86_64/GSVA.so > Expected in: dynamic lookup > > Error: package/namespace load failed for ?GSVA? > > I tried to re-install the package and recompile all the packages, but it > still gave the same error. Could anybody please help? Thank you so much! > > Wendy > > [[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 > _______________________________________________ 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
hi David, you're right, i'm able to reproduce this error in my linux box, in the transition to the latest released something that escaped to my eye changed that created this problem. i'll try to find out and write back to you with the solution. in the meantime, please let me know whether you're on linux, windows or mac and whether you're on the latest R version 2.14. sorry for the inconvinience, robert. On Mon, 2011-11-07 at 11:52 -0500, Lapointe, David wrote: > This package looks interesting, but when I tried installing GSVA ( V1.20) it failed with > "Cannot find the GNU Scientific Library >= 1.6" > > I have gsl-1.14 installed and the bioc web pages states gsl>=1.12 > > David > > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Robert Castelo > Sent: Monday, November 07, 2011 9:03 AM > To: Wendy Qiao > Cc: bioconductor at r-project.org > Subject: Re: [BioC] problem with using GSVA package > > hi, i think i forgot again something. those steps try to make a > "system-wide" installation by default trying to write to parts of the > filesystem where one need's extra privileges to do it. > > please try, instead of > > make install > > write > > sudo make install > > then the system will ask for your password, enter your password and > hopefully everything should go fine. let me know. > > cheers, > robert. > > On Mon, 2011-11-07 at 07:56 -0500, Wendy Qiao wrote: > > Hi Robert, > > > > > > Thank you very much for your reply. I tried your comments. Everything > > worked fine until "make install". This comment gives the following > > errors. Any suggestion is appreciated. Thank you very much. > > > > > > Making install in gsl > > make[2]: Nothing to be done for install-exec-am'. > > make[2]: Nothing to be done for install-data-am'. > > Making install in utils > > make[2]: Nothing to be done for install-exec-am'. > > make[2]: Nothing to be done for install-data-am'. > > Making install in sys > > make[2]: Nothing to be done for install-exec-am'. > > test -z "/usr/local/include/gsl" || .././install-sh -c -d > > "/usr/local/include/gsl" > > mkdir: /usr/local/include: Permission denied > > mkdir: /usr/local/include: No such file or directory > > make[2]: *** [install-pkgincludeHEADERS] Error 1 > > make[1]: *** [install-am] Error 2 > > make: *** [install-recursive] Error 1 > > > > > > Wendy > > > > > > > > On 7 November 2011 07:32, Juan Roberto CASTELO VALDUEZA > > <robert.castelo at="" upf.edu=""> wrote: > > hi Wendy, > > > > sorry about that, i forgot to say that you need to install in > > your computer the so-called GNU Scientific Library from: > > > > http://www.gnu.org/s/gsl > > > > this is not part of R and should be installed separately. > > seeing your output, i guess that you're working on an apple > > computer. in such a case you can just try the following: > > > > 1. download the tarball in your Desktop > > > > http://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz > > > > > > 2. open the terminal window from Applications -> Utilities -> > > Terminal > > > > 3. write in the terminal window the following commands > > > > cd Desktop > > cd gsl* > > ./configure > > make > > make install > > > > if these commands are executed without errors, then you can go > > back to R and should be able to install GSVA without problems. > > let me know if you encounter any difficulty with this. > > > > cheers, > > robert. > > > > > > ______________________________________________________________ > > From Wendy Qiao <wendy2.qiao at="" gmail.com=""> > > Sent Mon 11/7/2011 12:51 PM > > To bioconductor at r-project.org > > Subject [BioC] problem with using GSVA package > > > > > > Hi all, I am trying to use the GSVA package, but I encounter > > the following problems. library(GSVA) Error in dyn.load(file, > > DLLpath = DLLpath, ...) : unable to load shared object > > '/Library/Frameworks/R.framework/Versions/2.14/Resources/l ibrary/GSVA/libs/x86_64/GSVA.so': dlopen(/Library/Frameworks/R.framewo rk/Versions/2.14/Resources/library/GSVA/libs/x86_64/GSVA.so, 6): Symbol not found: _gsl_cdf_ugaussian_P Referenced from: /Library/Frame works/R.framework/Versions/2.14/Resources/library/GSVA/libs/ > > x86_64/GSVA.so > > Expected in: dynamic lookup > > > > Error: package/namespace load failed for ?GSVA? > > > > I tried to re-install the package and recompile all the packages, but it > > still gave the same error. Could anybody please help? Thank you so much! > > > > Wendy > > > > [[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 > > > > _______________________________________________ > 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
Hi Robert, I am on Linux (Fedora 14) and gsl is installed as a RPM. I have updated to R 2.14. Other packages installed fine. David -----Original Message----- From: Robert Castelo [mailto:robert.castelo@upf.edu] Sent: Monday, November 07, 2011 12:24 PM To: Lapointe, David Cc: bioconductor at r-project.org Subject: RE: [BioC] problem with using GSVA package hi David, you're right, i'm able to reproduce this error in my linux box, in the transition to the latest released something that escaped to my eye changed that created this problem. i'll try to find out and write back to you with the solution. in the meantime, please let me know whether you're on linux, windows or mac and whether you're on the latest R version 2.14. sorry for the inconvinience, robert. On Mon, 2011-11-07 at 11:52 -0500, Lapointe, David wrote: > This package looks interesting, but when I tried installing GSVA ( V1.20) it failed with > "Cannot find the GNU Scientific Library >= 1.6" > > I have gsl-1.14 installed and the bioc web pages states gsl>=1.12 > > David > > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Robert Castelo > Sent: Monday, November 07, 2011 9:03 AM > To: Wendy Qiao > Cc: bioconductor at r-project.org > Subject: Re: [BioC] problem with using GSVA package > > hi, i think i forgot again something. those steps try to make a > "system-wide" installation by default trying to write to parts of the > filesystem where one need's extra privileges to do it. > > please try, instead of > > make install > > write > > sudo make install > > then the system will ask for your password, enter your password and > hopefully everything should go fine. let me know. > > cheers, > robert. > > On Mon, 2011-11-07 at 07:56 -0500, Wendy Qiao wrote: > > Hi Robert, > > > > > > Thank you very much for your reply. I tried your comments. Everything > > worked fine until "make install". This comment gives the following > > errors. Any suggestion is appreciated. Thank you very much. > > > > > > Making install in gsl > > make[2]: Nothing to be done for install-exec-am'. > > make[2]: Nothing to be done for install-data-am'. > > Making install in utils > > make[2]: Nothing to be done for install-exec-am'. > > make[2]: Nothing to be done for install-data-am'. > > Making install in sys > > make[2]: Nothing to be done for install-exec-am'. > > test -z "/usr/local/include/gsl" || .././install-sh -c -d > > "/usr/local/include/gsl" > > mkdir: /usr/local/include: Permission denied > > mkdir: /usr/local/include: No such file or directory > > make[2]: *** [install-pkgincludeHEADERS] Error 1 > > make[1]: *** [install-am] Error 2 > > make: *** [install-recursive] Error 1 > > > > > > Wendy > > > > > > > > On 7 November 2011 07:32, Juan Roberto CASTELO VALDUEZA > > <robert.castelo at="" upf.edu=""> wrote: > > hi Wendy, > > > > sorry about that, i forgot to say that you need to install in > > your computer the so-called GNU Scientific Library from: > > > > http://www.gnu.org/s/gsl > > > > this is not part of R and should be installed separately. > > seeing your output, i guess that you're working on an apple > > computer. in such a case you can just try the following: > > > > 1. download the tarball in your Desktop > > > > http://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz > > > > > > 2. open the terminal window from Applications -> Utilities -> > > Terminal > > > > 3. write in the terminal window the following commands > > > > cd Desktop > > cd gsl* > > ./configure > > make > > make install > > > > if these commands are executed without errors, then you can go > > back to R and should be able to install GSVA without problems. > > let me know if you encounter any difficulty with this. > > > > cheers, > > robert. > > > > > > ______________________________________________________________ > > From Wendy Qiao <wendy2.qiao at="" gmail.com=""> > > Sent Mon 11/7/2011 12:51 PM > > To bioconductor at r-project.org > > Subject [BioC] problem with using GSVA package > > > > > > Hi all, I am trying to use the GSVA package, but I encounter > > the following problems. library(GSVA) Error in dyn.load(file, > > DLLpath = DLLpath, ...) : unable to load shared object > > '/Library/Frameworks/R.framework/Versions/2.14/Resources/l ibrary/GSVA/libs/x86_64/GSVA.so': dlopen(/Library/Frameworks/R.framewo rk/Versions/2.14/Resources/library/GSVA/libs/x86_64/GSVA.so, 6): Symbol not found: _gsl_cdf_ugaussian_P Referenced from: /Library/Frame works/R.framework/Versions/2.14/Resources/library/GSVA/libs/ > > x86_64/GSVA.so > > Expected in: dynamic lookup > > > > Error: package/namespace load failed for ?GSVA? > > > > I tried to re-install the package and recompile all the packages, but it > > still gave the same error. Could anybody please help? Thank you so much! > > > > Wendy > > > > [[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 > > > > _______________________________________________ > 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
hi again, could you give me the result of typing gsl-config --version in your terminal window?? thanks, robert. On Mon, 2011-11-07 at 12:35 -0500, Lapointe, David wrote: > Hi Robert, > > I am on Linux (Fedora 14) and gsl is installed as a RPM. I have updated to R 2.14. Other packages installed fine. > > David > > -----Original Message----- > From: Robert Castelo [mailto:robert.castelo at upf.edu] > Sent: Monday, November 07, 2011 12:24 PM > To: Lapointe, David > Cc: bioconductor at r-project.org > Subject: RE: [BioC] problem with using GSVA package > > hi David, > > you're right, i'm able to reproduce this error in my linux box, in the > transition to the latest released something that escaped to my eye > changed that created this problem. i'll try to find out and write back > to you with the solution. in the meantime, please let me know whether > you're on linux, windows or mac and whether you're on the latest R > version 2.14. > > sorry for the inconvinience, > robert. > > On Mon, 2011-11-07 at 11:52 -0500, Lapointe, David wrote: > > This package looks interesting, but when I tried installing GSVA ( V1.20) it failed with > > "Cannot find the GNU Scientific Library >= 1.6" > > > > I have gsl-1.14 installed and the bioc web pages states gsl>=1.12 > > > > David > > > > -----Original Message----- > > From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Robert Castelo > > Sent: Monday, November 07, 2011 9:03 AM > > To: Wendy Qiao > > Cc: bioconductor at r-project.org > > Subject: Re: [BioC] problem with using GSVA package > > > > hi, i think i forgot again something. those steps try to make a > > "system-wide" installation by default trying to write to parts of the > > filesystem where one need's extra privileges to do it. > > > > please try, instead of > > > > make install > > > > write > > > > sudo make install > > > > then the system will ask for your password, enter your password and > > hopefully everything should go fine. let me know. > > > > cheers, > > robert. > > > > On Mon, 2011-11-07 at 07:56 -0500, Wendy Qiao wrote: > > > Hi Robert, > > > > > > > > > Thank you very much for your reply. I tried your comments. Everything > > > worked fine until "make install". This comment gives the following > > > errors. Any suggestion is appreciated. Thank you very much. > > > > > > > > > Making install in gsl > > > make[2]: Nothing to be done for install-exec-am'. > > > make[2]: Nothing to be done for install-data-am'. > > > Making install in utils > > > make[2]: Nothing to be done for install-exec-am'. > > > make[2]: Nothing to be done for install-data-am'. > > > Making install in sys > > > make[2]: Nothing to be done for install-exec-am'. > > > test -z "/usr/local/include/gsl" || .././install-sh -c -d > > > "/usr/local/include/gsl" > > > mkdir: /usr/local/include: Permission denied > > > mkdir: /usr/local/include: No such file or directory > > > make[2]: *** [install-pkgincludeHEADERS] Error 1 > > > make[1]: *** [install-am] Error 2 > > > make: *** [install-recursive] Error 1 > > > > > > > > > Wendy > > > > > > > > > > > > On 7 November 2011 07:32, Juan Roberto CASTELO VALDUEZA > > > <robert.castelo at="" upf.edu=""> wrote: > > > hi Wendy, > > > > > > sorry about that, i forgot to say that you need to install in > > > your computer the so-called GNU Scientific Library from: > > > > > > http://www.gnu.org/s/gsl > > > > > > this is not part of R and should be installed separately. > > > seeing your output, i guess that you're working on an apple > > > computer. in such a case you can just try the following: > > > > > > 1. download the tarball in your Desktop > > > > > > http://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz > > > > > > > > > 2. open the terminal window from Applications -> Utilities -> > > > Terminal > > > > > > 3. write in the terminal window the following commands > > > > > > cd Desktop > > > cd gsl* > > > ./configure > > > make > > > make install > > > > > > if these commands are executed without errors, then you can go > > > back to R and should be able to install GSVA without problems. > > > let me know if you encounter any difficulty with this. > > > > > > cheers, > > > robert. > > > > > > > > > ______________________________________________________________ > > > From Wendy Qiao <wendy2.qiao at="" gmail.com=""> > > > Sent Mon 11/7/2011 12:51 PM > > > To bioconductor at r-project.org > > > Subject [BioC] problem with using GSVA package > > > > > > > > > Hi all, I am trying to use the GSVA package, but I encounter > > > the following problems. library(GSVA) Error in dyn.load(file, > > > DLLpath = DLLpath, ...) : unable to load shared object > > > '/Library/Frameworks/R.framework/Versions/2.14/Resources /library/GSVA/libs/x86_64/GSVA.so': dlopen(/Library/Frameworks/R.frame work/Versions/2.14/Resources/library/GSVA/libs/x86_64/GSVA.so, 6): Symbol not found: _gsl_cdf_ugaussian_P Referenced from: /Library/Frame works/R.framework/Versions/2.14/Resources/library/GSVA/libs/ > > > x86_64/GSVA.so > > > Expected in: dynamic lookup > > > > > > Error: package/namespace load failed for ?GSVA? > > > > > > I tried to re-install the package and recompile all the packages, but it > > > still gave the same error. Could anybody please help? Thank you so much! > > > > > > Wendy > > > > > > [[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 > > > > > > > _______________________________________________ > > 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 > >
Answer: problem with using GSVA package
0
7.8 years ago by
Robert Castelo2.3k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.3k wrote:
hi, ok, it makes sense because i noticed that as long as gsl-config was not available in my PATH variable i could reproduce your error, but as long as i put it in the PATH variable, just as if i had a system-wide installation of GSL, then GSVA was installing even if the supposedly required version was 1.6 (strange too). please make sure that you installation of GSL is such that either gsl-config falls into one of the paths in your PATH environment variable, and it should work, alternatively add the path where gsl-config is to your PATH environment variable. i'll fix in the meantime the 1.6 requirement which in fact does not seem to be causing the real problem, at least on my side. please let me know if you succeed, robert. On Mon, 2011-11-07 at 12:56 -0500, Lapointe, David wrote: > No gsl-config. Strange. > > -----Original Message----- > From: Robert Castelo [mailto:robert.castelo at upf.edu] > Sent: Monday, November 07, 2011 12:50 PM > To: Lapointe, David > Cc: bioconductor at r-project.org > Subject: RE: [BioC] problem with using GSVA package > > hi again, > > could you give me the result of typing > > gsl-config --version > > in your terminal window?? > > thanks, > robert. > > On Mon, 2011-11-07 at 12:35 -0500, Lapointe, David wrote: > > Hi Robert, > > > > I am on Linux (Fedora 14) and gsl is installed as a RPM. I have updated to R 2.14. Other packages installed fine. > > > > David > > > > -----Original Message----- > > From: Robert Castelo [mailto:robert.castelo at upf.edu] > > Sent: Monday, November 07, 2011 12:24 PM > > To: Lapointe, David > > Cc: bioconductor at r-project.org > > Subject: RE: [BioC] problem with using GSVA package > > > > hi David, > > > > you're right, i'm able to reproduce this error in my linux box, in the > > transition to the latest released something that escaped to my eye > > changed that created this problem. i'll try to find out and write back > > to you with the solution. in the meantime, please let me know whether > > you're on linux, windows or mac and whether you're on the latest R > > version 2.14. > > > > sorry for the inconvinience, > > robert. > > > > On Mon, 2011-11-07 at 11:52 -0500, Lapointe, David wrote: > > > This package looks interesting, but when I tried installing GSVA ( V1.20) it failed with > > > "Cannot find the GNU Scientific Library >= 1.6" > > > > > > I have gsl-1.14 installed and the bioc web pages states gsl>=1.12 > > > > > > David > > > > > > -----Original Message----- > > > From: bioconductor-bounces at r-project.org [mailto :bioconductor-bounces at r-project.org] On Behalf Of Robert Castelo > > > Sent: Monday, November 07, 2011 9:03 AM > > > To: Wendy Qiao > > > Cc: bioconductor at r-project.org > > > Subject: Re: [BioC] problem with using GSVA package > > > > > > hi, i think i forgot again something. those steps try to make a > > > "system-wide" installation by default trying to write to parts of the > > > filesystem where one need's extra privileges to do it. > > > > > > please try, instead of > > > > > > make install > > > > > > write > > > > > > sudo make install > > > > > > then the system will ask for your password, enter your password and > > > hopefully everything should go fine. let me know. > > > > > > cheers, > > > robert. > > > > > > On Mon, 2011-11-07 at 07:56 -0500, Wendy Qiao wrote: > > > > Hi Robert, > > > > > > > > > > > > Thank you very much for your reply. I tried your comments. Everything > > > > worked fine until "make install". This comment gives the following > > > > errors. Any suggestion is appreciated. Thank you very much. > > > > > > > > > > > > Making install in gsl > > > > make[2]: Nothing to be done for install-exec-am'. > > > > make[2]: Nothing to be done for install-data-am'. > > > > Making install in utils > > > > make[2]: Nothing to be done for install-exec-am'. > > > > make[2]: Nothing to be done for install-data-am'. > > > > Making install in sys > > > > make[2]: Nothing to be done for install-exec-am'. > > > > test -z "/usr/local/include/gsl" || .././install-sh -c -d > > > > "/usr/local/include/gsl" > > > > mkdir: /usr/local/include: Permission denied > > > > mkdir: /usr/local/include: No such file or directory > > > > make[2]: *** [install-pkgincludeHEADERS] Error 1 > > > > make[1]: *** [install-am] Error 2 > > > > make: *** [install-recursive] Error 1 > > > > > > > > > > > > Wendy > > > > > > > > > > > > > > > > On 7 November 2011 07:32, Juan Roberto CASTELO VALDUEZA > > > > <robert.castelo at="" upf.edu=""> wrote: > > > > hi Wendy, > > > > > > > > sorry about that, i forgot to say that you need to install in > > > > your computer the so-called GNU Scientific Library from: > > > > > > > > http://www.gnu.org/s/gsl > > > > > > > > this is not part of R and should be installed separately. > > > > seeing your output, i guess that you're working on an apple > > > > computer. in such a case you can just try the following: > > > > > > > > 1. download the tarball in your Desktop > > > > > > > > http://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz > > > > > > > > > > > > 2. open the terminal window from Applications -> Utilities -> > > > > Terminal > > > > > > > > 3. write in the terminal window the following commands > > > > > > > > cd Desktop > > > > cd gsl* > > > > ./configure > > > > make > > > > make install > > > > > > > > if these commands are executed without errors, then you can go > > > > back to R and should be able to install GSVA without problems. > > > > let me know if you encounter any difficulty with this. > > > > > > > > cheers, > > > > robert. > > > > > > > > > > > > ______________________________________________________________ > > > > From Wendy Qiao <wendy2.qiao at="" gmail.com=""> > > > > Sent Mon 11/7/2011 12:51 PM > > > > To bioconductor at r-project.org > > > > Subject [BioC] problem with using GSVA package > > > > > > > > > > > > Hi all, I am trying to use the GSVA package, but I encounter > > > > the following problems. library(GSVA) Error in dyn.load(file, > > > > DLLpath = DLLpath, ...) : unable to load shared object > > > > '/Library/Frameworks/R.framework/Versions/2.14/Resourc es/library/GSVA/libs/x86_64/GSVA.so': dlopen(/Library/Frameworks/R.fra mework/Versions/2.14/Resources/library/GSVA/libs/x86_64/GSVA.so, 6): Symbol not found: _gsl_cdf_ugaussian_P Referenced from: /Library/Frame works/R.framework/Versions/2.14/Resources/library/GSVA/libs/ > > > > x86_64/GSVA.so > > > > Expected in: dynamic lookup > > > > > > > > Error: package/namespace load failed for ?GSVA? > > > > > > > > I tried to re-install the package and recompile all the packages, but it > > > > still gave the same error. Could anybody please help? Thank you so much! > > > > > > > > Wendy > > > > > > > > [[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 > > > > > > > > > > _______________________________________________ > > > 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 > > > > > >
I needed to install gsl-devel. Now it loads. Thanks -----Original Message----- From: Robert Castelo [mailto:robert.castelo@upf.edu] Sent: Monday, November 07, 2011 1:12 PM To: Lapointe, David Cc: bioconductor at r-project.org Subject: RE: [BioC] problem with using GSVA package hi, ok, it makes sense because i noticed that as long as gsl-config was not available in my PATH variable i could reproduce your error, but as long as i put it in the PATH variable, just as if i had a system-wide installation of GSL, then GSVA was installing even if the supposedly required version was 1.6 (strange too). please make sure that you installation of GSL is such that either gsl-config falls into one of the paths in your PATH environment variable, and it should work, alternatively add the path where gsl-config is to your PATH environment variable. i'll fix in the meantime the 1.6 requirement which in fact does not seem to be causing the real problem, at least on my side. please let me know if you succeed, robert. On Mon, 2011-11-07 at 12:56 -0500, Lapointe, David wrote: > No gsl-config. Strange. > > -----Original Message----- > From: Robert Castelo [mailto:robert.castelo at upf.edu] > Sent: Monday, November 07, 2011 12:50 PM > To: Lapointe, David > Cc: bioconductor at r-project.org > Subject: RE: [BioC] problem with using GSVA package > > hi again, > > could you give me the result of typing > > gsl-config --version > > in your terminal window?? > > thanks, > robert. > > On Mon, 2011-11-07 at 12:35 -0500, Lapointe, David wrote: > > Hi Robert, > > > > I am on Linux (Fedora 14) and gsl is installed as a RPM. I have updated to R 2.14. Other packages installed fine. > > > > David > > > > -----Original Message----- > > From: Robert Castelo [mailto:robert.castelo at upf.edu] > > Sent: Monday, November 07, 2011 12:24 PM > > To: Lapointe, David > > Cc: bioconductor at r-project.org > > Subject: RE: [BioC] problem with using GSVA package > > > > hi David, > > > > you're right, i'm able to reproduce this error in my linux box, in the > > transition to the latest released something that escaped to my eye > > changed that created this problem. i'll try to find out and write back > > to you with the solution. in the meantime, please let me know whether > > you're on linux, windows or mac and whether you're on the latest R > > version 2.14. > > > > sorry for the inconvinience, > > robert. > > > > On Mon, 2011-11-07 at 11:52 -0500, Lapointe, David wrote: > > > This package looks interesting, but when I tried installing GSVA ( V1.20) it failed with > > > "Cannot find the GNU Scientific Library >= 1.6" > > > > > > I have gsl-1.14 installed and the bioc web pages states gsl>=1.12 > > > > > > David > > > > > > -----Original Message----- > > > From: bioconductor-bounces at r-project.org [mailto :bioconductor-bounces at r-project.org] On Behalf Of Robert Castelo > > > Sent: Monday, November 07, 2011 9:03 AM > > > To: Wendy Qiao > > > Cc: bioconductor at r-project.org > > > Subject: Re: [BioC] problem with using GSVA package > > > > > > hi, i think i forgot again something. those steps try to make a > > > "system-wide" installation by default trying to write to parts of the > > > filesystem where one need's extra privileges to do it. > > > > > > please try, instead of > > > > > > make install > > > > > > write > > > > > > sudo make install > > > > > > then the system will ask for your password, enter your password and > > > hopefully everything should go fine. let me know. > > > > > > cheers, > > > robert. > > > > > > On Mon, 2011-11-07 at 07:56 -0500, Wendy Qiao wrote: > > > > Hi Robert, > > > > > > > > > > > > Thank you very much for your reply. I tried your comments. Everything > > > > worked fine until "make install". This comment gives the following > > > > errors. Any suggestion is appreciated. Thank you very much. > > > > > > > > > > > > Making install in gsl > > > > make[2]: Nothing to be done for install-exec-am'. > > > > make[2]: Nothing to be done for install-data-am'. > > > > Making install in utils > > > > make[2]: Nothing to be done for install-exec-am'. > > > > make[2]: Nothing to be done for install-data-am'. > > > > Making install in sys > > > > make[2]: Nothing to be done for install-exec-am'. > > > > test -z "/usr/local/include/gsl" || .././install-sh -c -d > > > > "/usr/local/include/gsl" > > > > mkdir: /usr/local/include: Permission denied > > > > mkdir: /usr/local/include: No such file or directory > > > > make[2]: *** [install-pkgincludeHEADERS] Error 1 > > > > make[1]: *** [install-am] Error 2 > > > > make: *** [install-recursive] Error 1 > > > > > > > > > > > > Wendy > > > > > > > > > > > > > > > > On 7 November 2011 07:32, Juan Roberto CASTELO VALDUEZA > > > > <robert.castelo at="" upf.edu=""> wrote: > > > > hi Wendy, > > > > > > > > sorry about that, i forgot to say that you need to install in > > > > your computer the so-called GNU Scientific Library from: > > > > > > > > http://www.gnu.org/s/gsl > > > > > > > > this is not part of R and should be installed separately. > > > > seeing your output, i guess that you're working on an apple > > > > computer. in such a case you can just try the following: > > > > > > > > 1. download the tarball in your Desktop > > > > > > > > http://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz > > > > > > > > > > > > 2. open the terminal window from Applications -> Utilities -> > > > > Terminal > > > > > > > > 3. write in the terminal window the following commands > > > > > > > > cd Desktop > > > > cd gsl* > > > > ./configure > > > > make > > > > make install > > > > > > > > if these commands are executed without errors, then you can go > > > > back to R and should be able to install GSVA without problems. > > > > let me know if you encounter any difficulty with this. > > > > > > > > cheers, > > > > robert. > > > > > > > > > > > > ______________________________________________________________ > > > > From Wendy Qiao <wendy2.qiao at="" gmail.com=""> > > > > Sent Mon 11/7/2011 12:51 PM > > > > To bioconductor at r-project.org > > > > Subject [BioC] problem with using GSVA package > > > > > > > > > > > > Hi all, I am trying to use the GSVA package, but I encounter > > > > the following problems. library(GSVA) Error in dyn.load(file, > > > > DLLpath = DLLpath, ...) : unable to load shared object > > > > '/Library/Frameworks/R.framework/Versions/2.14/Resourc es/library/GSVA/libs/x86_64/GSVA.so': dlopen(/Library/Frameworks/R.fra mework/Versions/2.14/Resources/library/GSVA/libs/x86_64/GSVA.so, 6): Symbol not found: _gsl_cdf_ugaussian_P Referenced from: /Library/Frame works/R.framework/Versions/2.14/Resources/library/GSVA/libs/ > > > > x86_64/GSVA.so > > > > Expected in: dynamic lookup > > > > > > > > Error: package/namespace load failed for ?GSVA? > > > > > > > > I tried to re-install the package and recompile all the packages, but it > > > > still gave the same error. Could anybody please help? Thank you so much! > > > > > > > > Wendy > > > > > > > > [[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 > > > > > > > > > > _______________________________________________ > > > 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 > > > > > >