[R-SIG-Mac] Fortran on MacOS Sierra

Bob Rudis bob at rud.is
Fri Sep 30 13:26:02 CEST 2016

Coudert's packages are unsigned which seems like a significant oversight
and a CRAN manual entry recommending installing unsigned binaries does not
sit well with me and may not work in the next macOS release.

Ken: to avoid you having to dig you need to download <
http://coudert.name/software/gfortran-6.1-ElCapitan.dmg> and install it,
overriding the security warning (ugh).

You then need to add this to your ~/.R/Makevars (or to the site one)

F77 = /usr/local/gfortran/bin/gfortran
FC = /usr/local/gfortran/bin/gfortran
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0
-L/usr/local/gfortran/lib -lgfortran -lquadmath -lm

You'll still get the massive amount of warnings (they aren't harmful) but
the pkg will compile/install from source.

On Fri, Sep 30, 2016 at 5:04 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk>

> This seems to be Sierra, which has 'tidied up' system libraries.
> The recommendation for El Capitan at http://coudert.name/software.html
> also works correctly on Sierra. (See the manual, preferably before posting.)
> There are good reasons why the posting guide asks for 'at a minimum' the
> output of sessionInfo() ....
> On 30/09/2016 09:31, Ken Beath wrote:
>> I tried to build frailtypack from source using R 3.3.1 and it failed with
>> the following message (after a ridiculous amount of warnings)
>> 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
>> frailtypack.so Adonnees.o AparamMultive.o Aparameters.o aGhermite.o
>> aaOptim.o aaOptimres.o aaUseFunction.o aaUseFunctionG.o aamarq98o.o
>> additive.o afuncpasres.o ahrmsym.o aresidusMartingale.o atestWald.o
>> distance.o epoce.o epoce_log.o epoce_long.o frailtypack.o funcpaG_tps.o
>> funcpaGcpm.o funcpaGcpm_intcens.o funcpaGcpm_log.o funcpaGsplines.o
>> funcpaGsplines_intcens.o funcpaGsplines_log.o funcpaGweib.o
>> funcpaGweib_intcens.o funcpaGweib_log.o funcpaMultivCpm.o
>> funcpaMultivSplines.o funcpaMultivWeib.o funcpaacpm.o funcpaasplines.o
>> funcpaaweib.o funcpaj_tps.o funcpajcpm.o funcpajcpm_log.o funcpajgeneral.o
>> funcpajlongisplines.o funcpajlongiweib.o funcpajsplines.o
>> funcpajsplines_fam.o funcpajsplines_intcens.o funcpajsplines_log.o
>> funcpajweib.o funcpajweib_fam.o funcpajweib_intcens.o funcpajweib_log.o
>> f... <truncated>
>> 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: *** [frailtypack.so] Error 1
>> ERROR: compilation failed for package ‘frailtypack’
>> I was going to attempt the build with gfortran 4.2 but haven’t been able
>> to revert back from 4.8
>> So does it happen with 4.2 and if not, how can I revert back?
>> If not is this an R problem or the package?
> --
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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