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Angerer, Philipp

2017-Apr-19 10:42 UTC

[Rd] R 3.4 has broken C++11 support

Hi!

Well, my linux distribution has very recent versions
of everything, so a working C++11 compiler exists:

$ gcc --version | head -n1
gcc (GCC) 6.3.1 20170306

Could wrong ./configure options be at fault here? See:

https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=r-devel#n40

My sessionInfo():

$ R-devel --slave -e 'sessionInfo()' | head -n3
R Under development (unstable) (2017-04-18 r72542)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux

Thanks, Philipp
 

Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671

Angerer, Philipp

2017-Apr-19 11:17 UTC

head link

[Rd] R 3.4 has broken C++11 support

Hmm, doesn?t look like my R was configured incorrectly:



R is now configured for x86_64-pc-linux-gnu

  Source directory:          .
  Installation directory:    /opt/r-devel

  C compiler:                gcc  -march=x86-64 -mtune=generic -O2 -pipe
-fstack-protector-strong --param=ssp-buffer-size=4
  Fortran 77 compiler:       gfortran  -g -O2

  Default C++ compiler:      g++   -march=x86-64 -mtune=generic -O2 -pipe
-fstack-protector-strong --param=ssp-buffer-size=4
  C++98 compiler:            g++ -std=gnu++98 -march=x86-64 -mtune=generic -O2
-pipe -fstack-protector-strong --param=ssp-buffer-size=4
  C++11 compiler:            g++ -std=gnu++11 -march=x86-64 -mtune=generic -O2
-pipe -fstack-protector-strong --param=ssp-buffer-size=4
  C++14 compiler:            g++  -march=x86-64 -mtune=generic -O2 -pipe
-fstack-protector-strong --param=ssp-buffer-size=4
  C++17 compiler:              
  Fortran 90/95 compiler:    gfortran -g -O2
  Obj-C compiler:             

  Interfaces supported:      X11, tcltk
  External libraries:        readline, BLAS(generic), LAPACK(generic), curl
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:           shared R library, R profiling

  Capabilities skipped:      
  Options not enabled:       shared BLAS, memory profiling

  Recommended packages:      yes

----- Urspr?ngliche Mail -----
Von: "Angerer, Philipp" <philipp.angerer at
helmholtz-muenchen.de>
An: "Martyn Plummer" <plummerm at iarc.fr>
CC: "r-devel" <r-devel at r-project.org>
Gesendet: Mittwoch, 19. April 2017 12:42:33
Betreff: Re: [Rd] R 3.4 has broken C++11 support

Hi! 

Well, my linux distribution has very recent versions 
of everything, so a working C++11 compiler exists: 

$ gcc --version | head -n1 
gcc (GCC) 6.3.1 20170306 

Could wrong ./configure options be at fault here? See: 

https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=r-devel#n40 

My sessionInfo(): 

$ R-devel --slave -e 'sessionInfo()' | head -n3 
R Under development (unstable) (2017-04-18 r72542) 
Platform: x86_64-pc-linux-gnu (64-bit) 
Running under: Arch Linux 

Thanks, Philipp 

 

Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671

Martyn Plummer

2017-Apr-19 11:18 UTC

head link

[Rd] R 3.4 has broken C++11 support

On Wed, 2017-04-19 at 12:42 +0200, Angerer, Philipp
wrote:> Hi!
> 
> Well, my linux distribution has very recent versions
> of everything, so a working C++11 compiler exists:
> 
> $ gcc --version | head -n1
> gcc (GCC) 6.3.1 20170306
I am on Fedora 25 which also uses gcc 6.3.1. The default standard for
6.3.1 is C++14. The output from configure should contain these lines:

? Default C++ compiler:??????g++???
? C++98 compiler:????????????g++ -std=gnu++98?
? C++11 compiler:????????????g++ -std=gnu++11?
? C++14 compiler:????????????g++??
? C++17 compiler:??????????????

Please check.

Martyn
> Could wrong ./configure options be at fault here? See:
> 
> https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=r-devel#n40
> 
> My sessionInfo():
> 
> $ R-devel --slave -e 'sessionInfo()' | head -n3
> R Under development (unstable) (2017-04-18 r72542)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Arch Linux
> 
> Thanks, Philipp
> ?
> 
> Helmholtz Zentrum Muenchen
> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
> Ingolstaedter Landstr. 1
> 85764 Neuherberg
> www.helmholtz-muenchen.de
> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr.
> Alfons Enhsen
> Registergericht: Amtsgericht Muenchen HRB 6466
> USt-IdNr: DE 129521671
>

Martyn Plummer

2017-Apr-19 11:21 UTC

head link

[Rd] R 3.4 has broken C++11 support

On Wed, 2017-04-19 at 13:17 +0200, Angerer, Philipp
wrote:> Hmm, doesn?t look like my R was configured incorrectly:
That looks fine. Can you please give a reproducible example of a
package that compiles correctly on R 3.3.3 but not with R 3.4.0 or R-
devel.

Martyn
> 
> 
> R is now configured for x86_64-pc-linux-gnu
> 
> ? Source directory:??????????.
> ? Installation directory:????/opt/r-devel
> 
> ? C compiler:????????????????gcc??-march=x86-64 -mtune=generic -O2 -pipe
-fstack-protector-strong --param=ssp-buffer-size=4
> ? Fortran 77 compiler:???????gfortran??-g -O2
> 
> ? Default C++ compiler:??????g++???-march=x86-64 -mtune=generic -O2 -pipe
-fstack-protector-strong --param=ssp-buffer-size=4
> ? C++98 compiler:????????????g++ -std=gnu++98 -march=x86-64 -mtune=generic
-O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4
> ? C++11 compiler:????????????g++ -std=gnu++11 -march=x86-64 -mtune=generic
-O2 -pipe -fstack-protector-strong --param=ssp-buffer-size=4
> ? C++14 compiler:????????????g++??-march=x86-64 -mtune=generic -O2 -pipe
-fstack-protector-strong --param=ssp-buffer-size=4
> ? C++17 compiler:??????????????
> ? Fortran 90/95 compiler:????gfortran -g -O2
> ? Obj-C compiler:?????????????
> 
> ? Interfaces supported:??????X11, tcltk
> ? External libraries:????????readline, BLAS(generic), LAPACK(generic), curl
> ? Additional capabilities:???PNG, JPEG, TIFF, NLS, cairo, ICU
> ? Options enabled:???????????shared R library, R profiling
> 
> ? Capabilities skipped:??????
> ? Options not enabled:???????shared BLAS, memory profiling
> 
> ? Recommended packages:??????yes
> 
> ----- Urspr?ngliche Mail -----
> Von: "Angerer, Philipp" <philipp.angerer at
helmholtz-muenchen.de>
> An: "Martyn Plummer" <plummerm at iarc.fr>
> CC: "r-devel" <r-devel at r-project.org>
> Gesendet: Mittwoch, 19. April 2017 12:42:33
> Betreff: Re: [Rd] R 3.4 has broken C++11 support
> 
> Hi!?
> 
> Well, my linux distribution has very recent versions?
> of everything, so a working C++11 compiler exists:?
> 
> $ gcc --version | head -n1?
> gcc (GCC) 6.3.1 20170306?
> 
> Could wrong ./configure options be at fault here? See:?
> 
> https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=r-devel#n40?
> 
> My sessionInfo():?
> 
> $ R-devel --slave -e 'sessionInfo()' | head -n3?
> R Under development (unstable) (2017-04-18 r72542)?
> Platform: x86_64-pc-linux-gnu (64-bit)?
> Running under: Arch Linux?
> 
> Thanks, Philipp?
> 
> ?
> 
> Helmholtz Zentrum Muenchen
> Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
> Ingolstaedter Landstr. 1
> 85764 Neuherberg
> www.helmholtz-muenchen.de
> Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
> Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr.
> Alfons Enhsen
> Registergericht: Amtsgericht Muenchen HRB 6466
> USt-IdNr: DE 129521671
>

Dirk Eddelbuettel

2017-Apr-19 11:22 UTC

head link

[Rd] R 3.4 has broken C++11 support

On 19 April 2017 at 12:42, Angerer, Philipp via R-devel wrote:
| Well, my linux distribution has very recent versions
| of everything, so a working C++11 compiler exists:
| 
| $ gcc --version | head -n1
| gcc (GCC) 6.3.1 20170306
| 
| Could wrong ./configure options be at fault here? See:
| 
| https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=r-devel#n40
| 
| My sessionInfo():
| 
| $ R-devel --slave -e 'sessionInfo()' | head -n3
| R Under development (unstable) (2017-04-18 r72542)
| Platform: x86_64-pc-linux-gnu (64-bit)
| Running under: Arch Linux

Maybe you can share with us how you configure the build of R-devel?  I tend
to locally build every week or so and I have the following on Ubuntu 16.10:

  CXX = ccache g++ 
  CXXCPP = $(CXX) -E
  CXXFLAGS = -ggdb -pipe -Wall -pedantic $(LTO)
  CXXPICFLAGS = -fpic
  CXX98 = ccache g++
  CXX98FLAGS = -ggdb -pipe -Wall -pedantic
  CXX98PICFLAGS = -fpic
  CXX98STD = -std=gnu++98
  CXX11 = ccache g++
  CXX11FLAGS = -ggdb -pipe -Wall -pedantic
  CXX11PICFLAGS = -fpic
  CXX11STD = -std=gnu++11
  CXX14 = ccache g++
  CXX14FLAGS = -ggdb -pipe -Wall -pedantic
  CXX14PICFLAGS = -fpic
  CXX14STD = 
  CXX17 = 
  CXX17FLAGS = 
  CXX17PICFLAGS = 
  CXX17STD = 

I call configure in build shell script (which has not changed in years) with 

  R_PAPERSIZE=letter				\
  R_BATCHSAVE="--no-save --no-restore" 		\
  R_BROWSER=xdg-open				\
  PAGER=/usr/bin/pager				\
  PERL=/usr/bin/perl				\
  R_UNZIPCMD=/usr/bin/unzip			\
  R_ZIPCMD=/usr/bin/zip				\
  R_PRINTCMD=/usr/bin/lpr			\
  LIBnn=lib					\
  AWK=/usr/bin/awk                              \
  CC="ccache gcc"				\
  CFLAGS="-ggdb -pipe -std=gnu99 -Wall -pedantic" \
  CXX="ccache g++"				\
  CXXFLAGS="-ggdb -pipe -Wall -pedantic" 	\
  FC="ccache gfortran"	 	  		\
  F77="ccache gfortran"				\
  MAKE="make -j4"				\
  ./configure 					\
      --prefix=/usr/local/lib/R-devel 		\
      --enable-R-shlib 				\
      --without-blas 				\
      --without-lapack 				\
      --without-recommended-packages

Works here ...

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

Angerer, Philipp

2017-Apr-19 14:32 UTC

head link

[Rd] R 3.4 has broken C++11 support

Hi Dirk and Martyn,
> That looks fine. Can you please give a reproducible example of a package
> that compiles correctly on R 3.3.3 but not with R 3.4.0 or R-devel.
here you go, it?s pretty much the simplest package possible that needs C++11:

https://github.com/flying-sheep/cxx11test
> Maybe you can share with us how you configure the build of R-devel?
Sure, in the mail you quoted, I already linked exactly that:

https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=r-devel#n40
> ./configure --prefix=/opt/r-devel \
>	--libdir=/opt/r-devel/lib \
>	--sysconfdir=/etc/R-devel \
>	--datarootdir=/opt/r-devel/share \
>	  rsharedir=/opt/r-devel/share/R/ \
>	  rincludedir=/opt/r-devel/include/R/ \
>	  rdocdir=/opt/r-devel/share/doc/R/ \
>	--with-x \
>	--enable-R-shlib \
>	--with-lapack \
>	--with-blas \
>	F77=gfortran \
>	LIBnn=lib

Thanks and cheers,
Philipp
 

Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
www.helmholtz-muenchen.de
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671

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