Re: [R-SIG-Mac] LogicReg package problems
On Mon, Jan 16, 2012 at 2:57 AM, BEES INC bees@gmail.com wrote: Hey there I am having a bit of trouble getting this working, I had to do a bit of fiddling with makefiles to get it to find the right gfortran, but it builds links without error, however the install gives the following error: You have used some special (?) gfortran at compile time (based on the above, but I am not sure). This may not work with R that has been compiled with another gfortran and it might also not work at run time. We really need more information about exactly what you have done. Kasper Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Full install is as follows: $ R CMD INSTALL --no-multiarch LogicReg_1.4.11.tar.gz * installing to library ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library’ * installing *source* package ‘LogicReg’ ... ** package ‘LogicReg’ successfully unpacked and MD5 sums checked ** Creating default NAMESPACE file ** libs *** arch - i386 gfortran -fPIC -g -O2 -c My_own_scoring.f -o My_own_scoring.o gfortran -fPIC -g -O2 -c external.f -o external.o gfortran -fPIC -g -O2 -c slogic.f -o slogic.o gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c swrite.c -o swrite.o gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/gfortran/lib/gcc/i686-apple-darwin9/4.6.2 -o LogicReg.so My_own_scoring.o external.o slogic.o swrite.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386 ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg’ $ Any ideas? Thanks ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] LogicReg package problems
I do not believe gfortran comes with OS X, so I installed the latest version. R was picking up a version that had been installed with octave, which is why I needed to make some changes as I did not want to link R libs with something packaged with octave (because if i update or remove octave all my R libs will break). I don't think that is a material part of the issue, and doing some digging I see it is not just my machine: http://cran.r-project.org/web/checks/check_results_LogicReg.html http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/LogicReg-00install.html Which shows the same error. Can you build the package OK? Thanks On Tue, Jan 17, 2012 at 1:16 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Mon, Jan 16, 2012 at 2:57 AM, BEES INC bees@gmail.com wrote: Hey there I am having a bit of trouble getting this working, I had to do a bit of fiddling with makefiles to get it to find the right gfortran, but it builds links without error, however the install gives the following error: You have used some special (?) gfortran at compile time (based on the above, but I am not sure). This may not work with R that has been compiled with another gfortran and it might also not work at run time. We really need more information about exactly what you have done. Kasper Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Full install is as follows: $ R CMD INSTALL --no-multiarch LogicReg_1.4.11.tar.gz * installing to library ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library’ * installing *source* package ‘LogicReg’ ... ** package ‘LogicReg’ successfully unpacked and MD5 sums checked ** Creating default NAMESPACE file ** libs *** arch - i386 gfortran -fPIC -g -O2 -c My_own_scoring.f -o My_own_scoring.o gfortran -fPIC -g -O2 -c external.f -o external.o gfortran -fPIC -g -O2 -c slogic.f -o slogic.o gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c swrite.c -o swrite.o gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/gfortran/lib/gcc/i686-apple-darwin9/4.6.2 -o LogicReg.so My_own_scoring.o external.o slogic.o swrite.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386 ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg’ $ Any ideas? Thanks ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] LogicReg package problems
I should add, it is the same version of gfortran that R is expecting, just installed in a different location On Tue, Jan 17, 2012 at 1:25 AM, BEES INC bees@gmail.com wrote: I do not believe gfortran comes with OS X, so I installed the latest version. R was picking up a version that had been installed with octave, which is why I needed to make some changes as I did not want to link R libs with something packaged with octave (because if i update or remove octave all my R libs will break). I don't think that is a material part of the issue, and doing some digging I see it is not just my machine: http://cran.r-project.org/web/checks/check_results_LogicReg.html http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/LogicReg-00install.html Which shows the same error. Can you build the package OK? Thanks On Tue, Jan 17, 2012 at 1:16 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Mon, Jan 16, 2012 at 2:57 AM, BEES INC bees@gmail.com wrote: Hey there I am having a bit of trouble getting this working, I had to do a bit of fiddling with makefiles to get it to find the right gfortran, but it builds links without error, however the install gives the following error: You have used some special (?) gfortran at compile time (based on the above, but I am not sure). This may not work with R that has been compiled with another gfortran and it might also not work at run time. We really need more information about exactly what you have done. Kasper Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Full install is as follows: $ R CMD INSTALL --no-multiarch LogicReg_1.4.11.tar.gz * installing to library ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library’ * installing *source* package ‘LogicReg’ ... ** package ‘LogicReg’ successfully unpacked and MD5 sums checked ** Creating default NAMESPACE file ** libs *** arch - i386 gfortran -fPIC -g -O2 -c My_own_scoring.f -o My_own_scoring.o gfortran -fPIC -g -O2 -c external.f -o external.o gfortran -fPIC -g -O2 -c slogic.f -o slogic.o gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c swrite.c -o swrite.o gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/gfortran/lib/gcc/i686-apple-darwin9/4.6.2 -o LogicReg.so My_own_scoring.o external.o slogic.o swrite.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386 ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg’ $ Any ideas? Thanks ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] LogicReg package problems
Ok, I was wondering if you were picking up the same gfortran at run and compile time. I see the error on the cran building machine, so it is probably an issue at the package level. I suggest emailing the two authors about it. I know for sure Ingo is using a Mac as a laptop, so perhaps he has something insightful to say about this. Kasper On Mon, Jan 16, 2012 at 9:31 AM, BEES INC bees@gmail.com wrote: I should add, it is the same version of gfortran that R is expecting, just installed in a different location On Tue, Jan 17, 2012 at 1:25 AM, BEES INC bees@gmail.com wrote: I do not believe gfortran comes with OS X, so I installed the latest version. R was picking up a version that had been installed with octave, which is why I needed to make some changes as I did not want to link R libs with something packaged with octave (because if i update or remove octave all my R libs will break). I don't think that is a material part of the issue, and doing some digging I see it is not just my machine: http://cran.r-project.org/web/checks/check_results_LogicReg.html http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/LogicReg-00install.html Which shows the same error. Can you build the package OK? Thanks On Tue, Jan 17, 2012 at 1:16 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Mon, Jan 16, 2012 at 2:57 AM, BEES INC bees@gmail.com wrote: Hey there I am having a bit of trouble getting this working, I had to do a bit of fiddling with makefiles to get it to find the right gfortran, but it builds links without error, however the install gives the following error: You have used some special (?) gfortran at compile time (based on the above, but I am not sure). This may not work with R that has been compiled with another gfortran and it might also not work at run time. We really need more information about exactly what you have done. Kasper Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Full install is as follows: $ R CMD INSTALL --no-multiarch LogicReg_1.4.11.tar.gz * installing to library ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library’ * installing *source* package ‘LogicReg’ ... ** package ‘LogicReg’ successfully unpacked and MD5 sums checked ** Creating default NAMESPACE file ** libs *** arch - i386 gfortran -fPIC -g -O2 -c My_own_scoring.f -o My_own_scoring.o gfortran -fPIC -g -O2 -c external.f -o external.o gfortran -fPIC -g -O2 -c slogic.f -o slogic.o gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c swrite.c -o swrite.o gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/gfortran/lib/gcc/i686-apple-darwin9/4.6.2 -o LogicReg.so My_own_scoring.o external.o slogic.o swrite.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386 ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg’ $ Any ideas? Thanks ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] LogicReg package problems
What precise OS and which architecture is this (see the posting guide)? AFAIK LogicReg will install on x86_64 on a Mac (nowadays the default for most people) but not the 32-bit architectures. It predefines some very large arrays: try reducing LGCn1MAX (twice) in slogic.f . It then works for me (I tried 1). And if this works for you, please report to the package maintainer. On 16/01/2012 14:31, BEES INC wrote: I should add, it is the same version of gfortran that R is expecting, just installed in a different location On Tue, Jan 17, 2012 at 1:25 AM, BEES INCbees@gmail.com wrote: I do not believe gfortran comes with OS X, so I installed the latest version. R was picking up a version that had been installed with octave, which is why I needed to make some changes as I did not want to link R libs with something packaged with octave (because if i update or remove octave all my R libs will break). I don't think that is a material part of the issue, and doing some digging I see it is not just my machine: http://cran.r-project.org/web/checks/check_results_LogicReg.html http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/LogicReg-00install.html Which shows the same error. Can you build the package OK? Thanks On Tue, Jan 17, 2012 at 1:16 AM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: On Mon, Jan 16, 2012 at 2:57 AM, BEES INCbees@gmail.com wrote: Hey there I am having a bit of trouble getting this working, I had to do a bit of fiddling with makefiles to get it to find the right gfortran, but it builds links without error, however the install gives the following error: You have used some special (?) gfortran at compile time (based on the above, but I am not sure). This may not work with R that has been compiled with another gfortran and it might also not work at run time. We really need more information about exactly what you have done. Kasper Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Full install is as follows: $ R CMD INSTALL --no-multiarch LogicReg_1.4.11.tar.gz * installing to library ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library’ * installing *source* package ‘LogicReg’ ... ** package ‘LogicReg’ successfully unpacked and MD5 sums checked ** Creating default NAMESPACE file ** libs *** arch - i386 gfortran -fPIC -g -O2 -c My_own_scoring.f -o My_own_scoring.o gfortran -fPIC -g -O2 -c external.f -o external.o gfortran -fPIC -g -O2 -c slogic.f -o slogic.o gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include-fPIC -g -O2 -c swrite.c -o swrite.o gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/gfortran/lib/gcc/i686-apple-darwin9/4.6.2 -o LogicReg.so My_own_scoring.o external.o slogic.o swrite.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386 ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg’ $ Any ideas? Thanks ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing
[R-SIG-Mac] LogicReg package problems
Hey there I am having a bit of trouble getting this working, I had to do a bit of fiddling with makefiles to get it to find the right gfortran, but it builds links without error, however the install gives the following error: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Full install is as follows: $ R CMD INSTALL --no-multiarch LogicReg_1.4.11.tar.gz * installing to library ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library’ * installing *source* package ‘LogicReg’ ... ** package ‘LogicReg’ successfully unpacked and MD5 sums checked ** Creating default NAMESPACE file ** libs *** arch - i386 gfortran -fPIC -g -O2 -c My_own_scoring.f -o My_own_scoring.o gfortran -fPIC -g -O2 -c external.f -o external.o gfortran -fPIC -g -O2 -c slogic.f -o slogic.o gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include-fPIC -g -O2 -c swrite.c -o swrite.o gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/gfortran/lib/gcc/i686-apple-darwin9/4.6.2 -o LogicReg.so My_own_scoring.o external.o slogic.o swrite.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386 ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so': dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so, 6): no suitable image found. Did find: /Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg/libs/i386/LogicReg.so: out of address space Error: loading failed Execution halted ERROR: loading failed * removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/LogicReg’ $ Any ideas? Thanks ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
