Hello, I have an issue on Mac OS ElCapitan ( just now upgraded to sierra) with Xcode 7 and gfortran 6.1 ( downloaded from https://gcc.gnu.org/wiki/GFortranBinaries. ). I'm developing an R package and wants to make it portable. The package was working fine until October 18th along with a Makevar file created under ~/.R. The Makevar file contains : F77 = gfortran FC = gfortran FLIBS = -L/usr/local/gfortran/lib (Please refer: http://stackoverflow.com/questions/40092423/r-package-with-fortran-source-code-how-to-make-makevars-file-under-pkgname-s/40127535#40127535 ). But now when I run R CMD CHECK on my system, its throws the following error: * installing *source* package ?EpiILM? ... ** libs gfortran-4.8 -fPIC -Wall -g -O2 -c Edata.f95 -o Edata.o make: gfortran-4.8: No such file or directory make: *** [Edata.o] Error 1 ERROR: compilation failed for package ?EpiILM? * removing ?/Users/Vineetha/Desktop/EpiILM.Rcheck/EpiILM? Basically, my Makevar file is not resolving the issue now. Any help would be appreciated. Thanks, Vineetha
R package
7 messages · Ken Beath, Kodalore Vijayan, Vineetha W, Keith O'Hara
The R binaries are built using gfortran v4.8.2; can you not build your package using that instead? Keith
On Oct 24, 2016, at 6:25 PM, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca> wrote: Hello, I have an issue on Mac OS ElCapitan ( just now upgraded to sierra) with Xcode 7 and gfortran 6.1 ( downloaded from https://gcc.gnu.org/wiki/GFortranBinaries. ). I'm developing an R package and wants to make it portable. The package was working fine until October 18th along with a Makevar file created under ~/.R. The Makevar file contains : F77 = gfortran FC = gfortran FLIBS = -L/usr/local/gfortran/lib (Please refer: http://stackoverflow.com/questions/40092423/r-package-with-fortran-source-code-how-to-make-makevars-file-under-pkgname-s/40127535#40127535 ). But now when I run R CMD CHECK on my system, its throws the following error: * installing *source* package ?EpiILM? ... ** libs gfortran-4.8 -fPIC -Wall -g -O2 -c Edata.f95 -o Edata.o make: gfortran-4.8: No such file or directory make: *** [Edata.o] Error 1 ERROR: compilation failed for package ?EpiILM? * removing ?/Users/Vineetha/Desktop/EpiILM.Rcheck/EpiILM? Basically, my Makevar file is not resolving the issue now. Any help would be appreciated. Thanks, Vineetha [[alternative HTML version deleted]]
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See full instructions at https://stat.ethz.ch/pipermail/r-sig-mac/2016-September/012056.html thanks to Bob Rudis. Ken
On 25 Oct. 2016, at 9:25 am, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca> wrote: Hello, I have an issue on Mac OS ElCapitan ( just now upgraded to sierra) with Xcode 7 and gfortran 6.1 ( downloaded from https://gcc.gnu.org/wiki/GFortranBinaries. ). I'm developing an R package and wants to make it portable. The package was working fine until October 18th along with a Makevar file created under ~/.R. The Makevar file contains : F77 = gfortran FC = gfortran FLIBS = -L/usr/local/gfortran/lib (Please refer: http://stackoverflow.com/questions/40092423/r-package-with-fortran-source-code-how-to-make-makevars-file-under-pkgname-s/40127535#40127535 ). But now when I run R CMD CHECK on my system, its throws the following error: * installing *source* package ?EpiILM? ... ** libs gfortran-4.8 -fPIC -Wall -g -O2 -c Edata.f95 -o Edata.o make: gfortran-4.8: No such file or directory make: *** [Edata.o] Error 1 ERROR: compilation failed for package ?EpiILM? * removing ?/Users/Vineetha/Desktop/EpiILM.Rcheck/EpiILM? Basically, my Makevar file is not resolving the issue now. Any help would be appreciated. Thanks, Vineetha [[alternative HTML version deleted]]
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Hi Ken, Its not working with Makevar anymore. I guess I have to degrade to gfortran4.8.2. Will try that. Thank you, Vineetha
On Mon, Oct 24, 2016 at 5:32 PM, Ken Beath <ken at kjbeath.com.au> wrote:
See full instructions at https://stat.ethz.ch/pipermail/r-sig-mac/2016- September/012056.html thanks to Bob Rudis. Ken
On 25 Oct. 2016, at 9:25 am, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca>
wrote:
Hello, I have an issue on Mac OS ElCapitan ( just now upgraded to sierra) with Xcode 7 and gfortran 6.1 ( downloaded from https://gcc.gnu.org/wiki/GFortranBinaries. ). I'm developing an R
package
and wants to make it portable. The package was working fine until October 18th along with a Makevar file created under ~/.R. The Makevar file contains : F77 = gfortran FC = gfortran FLIBS = -L/usr/local/gfortran/lib (Please refer: http://stackoverflow.com/questions/40092423/r-package-
with-fortran-source-code-how-to-make-makevars-file-under- pkgname-s/40127535#40127535
). But now when I run R CMD CHECK on my system, its throws the following error: * installing *source* package ?EpiILM? ... ** libs gfortran-4.8 -fPIC -Wall -g -O2 -c Edata.f95 -o Edata.o make: gfortran-4.8: No such file or directory make: *** [Edata.o] Error 1 ERROR: compilation failed for package ?EpiILM? * removing ?/Users/Vineetha/Desktop/EpiILM.Rcheck/EpiILM? Basically, my Makevar file is not resolving the issue now. Any help
would
be appreciated.
Thanks,
Vineetha
[[alternative HTML version deleted]]
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1 day later
Hello, I removed gfortran 6.1 and installed gfortran v4.8.2. Now i have another error: gfortran-4.8 -fPIC -Wall -g -O2 -c test.f95 -o test.o gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 gfortran-4.8 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o test.so test.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 ld: library not found for -ldylib1.o collect2: error: ld returned 1 exit status make: *** [test.so] Error 1 Any idea what this means or how I can solve? I have limited knowledge on these installations. Thanks, Vineetha On Tue, Oct 25, 2016 at 7:37 AM, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca
wrote:
Hi Ken, Its not working with Makevar anymore. I guess I have to degrade to gfortran4.8.2. Will try that. Thank you, Vineetha On Mon, Oct 24, 2016 at 5:32 PM, Ken Beath <ken at kjbeath.com.au> wrote:
See full instructions at https://stat.ethz.ch/pipermail /r-sig-mac/2016-September/012056.html thanks to Bob Rudis. Ken
On 25 Oct. 2016, at 9:25 am, Kodalore Vijayan, Vineetha W <
vwkv13 at mun.ca> wrote:
Hello, I have an issue on Mac OS ElCapitan ( just now upgraded to sierra) with Xcode 7 and gfortran 6.1 ( downloaded from https://gcc.gnu.org/wiki/GFortranBinaries. ). I'm developing an R
package
and wants to make it portable. The package was working fine until October 18th along with a Makevar
file
created under ~/.R. The Makevar file contains : F77 = gfortran FC = gfortran FLIBS = -L/usr/local/gfortran/lib (Please refer: http://stackoverflow.com/questions/40092423/r-package-with-
fortran-source-code-how-to-make-makevars-file-under-pkgna me-s/40127535#40127535
). But now when I run R CMD CHECK on my system, its throws the following error: * installing *source* package ?EpiILM? ... ** libs gfortran-4.8 -fPIC -Wall -g -O2 -c Edata.f95 -o Edata.o make: gfortran-4.8: No such file or directory make: *** [Edata.o] Error 1 ERROR: compilation failed for package ?EpiILM? * removing ?/Users/Vineetha/Desktop/EpiILM.Rcheck/EpiILM? Basically, my Makevar file is not resolving the issue now. Any help
would
be appreciated.
Thanks,
Vineetha
[[alternative HTML version deleted]]
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Can you check if the command line tools are installed by running: xcode-select --install in terminal. Keith
On Oct 26, 2016, at 5:28 PM, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca> wrote: Hello, I removed gfortran 6.1 and installed gfortran v4.8.2. Now i have another error: gfortran-4.8 -fPIC -Wall -g -O2 -c test.f95 -o test.o gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 gfortran-4.8 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o test.so test.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 ld: library not found for -ldylib1.o collect2: error: ld returned 1 exit status make: *** [test.so] Error 1 Any idea what this means or how I can solve? I have limited knowledge on these installations. Thanks, Vineetha On Tue, Oct 25, 2016 at 7:37 AM, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca
wrote:
Hi Ken, Its not working with Makevar anymore. I guess I have to degrade to gfortran4.8.2. Will try that. Thank you, Vineetha On Mon, Oct 24, 2016 at 5:32 PM, Ken Beath <ken at kjbeath.com.au> wrote:
See full instructions at https://stat.ethz.ch/pipermail /r-sig-mac/2016-September/012056.html thanks to Bob Rudis. Ken
On 25 Oct. 2016, at 9:25 am, Kodalore Vijayan, Vineetha W <
vwkv13 at mun.ca> wrote:
Hello, I have an issue on Mac OS ElCapitan ( just now upgraded to sierra) with Xcode 7 and gfortran 6.1 ( downloaded from https://gcc.gnu.org/wiki/GFortranBinaries. ). I'm developing an R
package
and wants to make it portable. The package was working fine until October 18th along with a Makevar
file
created under ~/.R. The Makevar file contains : F77 = gfortran FC = gfortran FLIBS = -L/usr/local/gfortran/lib (Please refer: http://stackoverflow.com/questions/40092423/r-package-with-
fortran-source-code-how-to-make-makevars-file-under-pkgna me-s/40127535#40127535
). But now when I run R CMD CHECK on my system, its throws the following error: * installing *source* package ?EpiILM? ... ** libs gfortran-4.8 -fPIC -Wall -g -O2 -c Edata.f95 -o Edata.o make: gfortran-4.8: No such file or directory make: *** [Edata.o] Error 1 ERROR: compilation failed for package ?EpiILM? * removing ?/Users/Vineetha/Desktop/EpiILM.Rcheck/EpiILM? Basically, my Makevar file is not resolving the issue now. Any help
would
be appreciated.
Thanks,
Vineetha
[[alternative HTML version deleted]]
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yes, its installed now. And now R CMD CHECK gives me the following warnings. * installing *source* package ?pkgname? ... ** libs gfortran-4.8 -fPIC -Wall -g -O2 -c epidata.f95 -o epidata.o gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 gfortran-4.8 -fPIC -Wall -g -O2 -c epilike.f95 -o epilike.o gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 gfortran-4.8 -fPIC -Wall -g -O2 -c epimc.f95 -o epimc.o gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 gfortran-4.8 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o pkgname.so epidata.o epilike.o epimc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 ld: warning: object file (epidata.o) was built for newer OSX version (10.12) than being linked (10.4) ld: warning: object file (epilike.o) was built for newer OSX version (10.12) than being linked (10.4) ld: warning: object file (epimc.o) was built for newer OSX version (10.12) than being linked (10.4) installing to /Users/Vineetha/Desktop/pkgname.Rcheck/pkgname/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (pkgname) -Vineetha
On Wed, Oct 26, 2016 at 3:38 PM, Keith O'Hara <keith.ohara at nyu.edu> wrote:
Can you check if the command line tools are installed by running: xcode-select --install in terminal. Keith
On Oct 26, 2016, at 5:28 PM, Kodalore Vijayan, Vineetha W <vwkv13 at mun.ca>
wrote:
Hello, I removed gfortran 6.1 and installed gfortran v4.8.2. Now i have another error: gfortran-4.8 -fPIC -Wall -g -O2 -c test.f95 -o test.o gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 gfortran-4.8 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o
test.so
test.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation gfortran-4.8: warning: couldn?t understand kern.osversion ?16.0.0 ld: library not found for -ldylib1.o collect2: error: ld returned 1 exit status make: *** [test.so] Error 1 Any idea what this means or how I can solve? I have limited knowledge on these installations. Thanks, Vineetha On Tue, Oct 25, 2016 at 7:37 AM, Kodalore Vijayan, Vineetha W <
vwkv13 at mun.ca
wrote:
Hi Ken, Its not working with Makevar anymore. I guess I have to degrade to gfortran4.8.2. Will try that. Thank you, Vineetha On Mon, Oct 24, 2016 at 5:32 PM, Ken Beath <ken at kjbeath.com.au> wrote:
See full instructions at https://stat.ethz.ch/pipermail /r-sig-mac/2016-September/012056.html thanks to Bob Rudis. Ken
On 25 Oct. 2016, at 9:25 am, Kodalore Vijayan, Vineetha W <
vwkv13 at mun.ca> wrote:
Hello, I have an issue on Mac OS ElCapitan ( just now upgraded to sierra)
with
Xcode 7 and gfortran 6.1 ( downloaded from https://gcc.gnu.org/wiki/GFortranBinaries. ). I'm developing an R
package
and wants to make it portable. The package was working fine until October 18th along with a Makevar
file
created under ~/.R. The Makevar file contains : F77 = gfortran FC = gfortran FLIBS = -L/usr/local/gfortran/lib (Please refer: http://stackoverflow.com/questions/40092423/r-package-with-
fortran-source-code-how-to-make-makevars-file-under-pkgna me-s/40127535#40127535
). But now when I run R CMD CHECK on my system, its throws the following error: * installing *source* package ?EpiILM? ... ** libs gfortran-4.8 -fPIC -Wall -g -O2 -c Edata.f95 -o Edata.o make: gfortran-4.8: No such file or directory make: *** [Edata.o] Error 1 ERROR: compilation failed for package ?EpiILM? * removing ?/Users/Vineetha/Desktop/EpiILM.Rcheck/EpiILM? Basically, my Makevar file is not resolving the issue now. Any help
would
be appreciated.
Thanks,
Vineetha
[[alternative HTML version deleted]]
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