Re: [R-SIG-Mac] Fortran on MacOS Sierra

[Ken Beath]

lme4 and fastGHQuad

Ken

> On 30 Sep. 2016, at 10:46 pm, Bob Rudis  wrote:
> 
> Glad you're up and running!
> 
> ​If you have some specific examples I can try to reproduce (and report) as I 
> load the betas (I'm on beta 2 now).
> 
> -Bob
> 
> On Fri, Sep 30, 2016 at 8:26 AM, Ken Beath  wrote:
> Thanks, yes I sorted it out. I’d read the bit on Makevars but it just didn’t 
> seem what I wanted.
> 
> There are some problems with the 10.12.1 beta which affect built libraries 
> but at the moment I will just hope they go away.
> 
> Ken
> 
> > On 30 Sep. 2016, at 9:26 pm, Bob Rudis  wrote:
> >
> > 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 
> >  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  
> > wrote:
> > 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... 
> > 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,  rip...@stats.ox.ac.uk
> > Emeritus Professor of Applied Statistics, University of Oxford
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> 
> 
> 

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Re: [R-SIG-Mac] Fortran on MacOS Sierra

[Bob Rudis]

Glad you're up and running!

​If you have some specific examples I can try to reproduce (and report) as
I load the betas (I'm on beta 2 now).

-Bob

On Fri, Sep 30, 2016 at 8:26 AM, Ken Beath  wrote:

> Thanks, yes I sorted it out. I’d read the bit on Makevars but it just
> didn’t seem what I wanted.
>
> There are some problems with the 10.12.1 beta which affect built libraries
> but at the moment I will just hope they go away.
>
> Ken
>
> > On 30 Sep. 2016, at 9:26 pm, Bob Rudis  wrote:
> >
> > 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 <
> rip...@stats.ox.ac.uk> wrote:
> > 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... 
> > 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,  rip...@stats.ox.ac.uk
> > Emeritus Professor of Applied Statistics, University of Oxford
> >
> > ___
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
>

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Re: [R-SIG-Mac] Fortran on MacOS Sierra

[Ken Beath]

Thanks, yes I sorted it out. I’d read the bit on Makevars but it just didn’t 
seem what I wanted.

There are some problems with the 10.12.1 beta which affect built libraries but 
at the moment I will just hope they go away.

Ken

> On 30 Sep. 2016, at 9:26 pm, Bob Rudis  wrote:
> 
> 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 
>  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  
> wrote:
> 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... 
> 
> 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,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 

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Re: [R-SIG-Mac] Fortran on MacOS Sierra

[Bob Rudis]

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 
wrote:

> 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... 
>> 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,  rip...@stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
>
> ___
> R-SIG-Mac mailing list
> R-SIG-Mac@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

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Re: [R-SIG-Mac] Fortran on MacOS Sierra

[Prof Brian Ripley]

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... 
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,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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[R-SIG-Mac] Fortran on MacOS Sierra

[Ken Beath]

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... 

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?

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