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=libThanks 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
On Wed, 2017-04-19 at 16:32 +0200, Angerer, Philipp wrote:> 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/cxx11testThis works for me (See below). Make sure you are not overwriting some key variables in a personal Makevars file or a site-wide Makevars.site file. [plummerm at D-160182 temp]$ ~/R-devel/r-devel/build/bin/R CMD INSTALL cxx11test_1.0.tar.gz? * installing to library ?/home/plummerm/R-devel/r-devel/build/library? * installing *source* package ?cxx11test? ... ** libs g++ -std=gnu++11 -I/home/plummerm/R-devel/r-devel/build/include -DNDEBUG??-I"/home/plummerm/R-devel/r-devel/build/library/Rcpp/include" -I/usr/local/include???-fpic??-g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I/home/plummerm/R-devel/r-devel/build/include -DNDEBUG??-I"/home/plummerm/R-devel/r-devel/build/library/Rcpp/include" -I/usr/local/include???-fpic??-g -O2 -c test.cpp -o test.o g++ -std=gnu++11 -shared -L/usr/local/lib64 -o cxx11test.so RcppExports.o test.o installing to /home/plummerm/R-devel/r-devel/build/library/cxx11test/libs ** R ** preparing package for lazy loading ** help No man pages found in package???cxx11test?? *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (cxx11test) Martyn> > 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 >
FWIW works for me too, with or without my ~/.R/Makevars edd at max:~/git$ git clone https://github.com/flying-sheep/cxx11test Cloning into 'cxx11test'... remote: Counting objects: 13, done. remote: Compressing objects: 100% (10/10), done. remote: Total 13 (delta 0), reused 13 (delta 0), pack-reused 0 Unpacking objects: 100% (13/13), done. Checking connectivity... done. edd at max:~/git$ cd cxx11test/ edd at max:~/git/cxx11test(master)$ RD CMD INSTALL . * installing to library ?/usr/local/lib/R/site-library? * installing *source* package ?cxx11test? ... ** libs ccache g++ -std=gnu++11 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include -fpic -ggdb -pipe -Wall -pedantic -c RcppExports.cpp -o RcppExports.o ccache g++ -std=gnu++11 -I/usr/local/lib/R-devel/lib/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include -fpic -ggdb -pipe -Wall -pedantic -c test.cpp -o test.o ccache g++ -std=gnu++11 -shared -L/usr/local/lib/R-devel/lib/R/lib -L/usr/local/lib -o cxx11test.so RcppExports.o test.o -L/usr/local/lib/R-devel/lib/R/lib -lR installing to /usr/local/lib/R/site-library/cxx11test/libs ** R ** preparing package for lazy loading ** help No man pages found in package ?cxx11test? *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (cxx11test) edd at max:~/git/cxx11test(master)$ Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Hi Philipp,
Fellow Archlinux user here. I think the problem is with the r-devel
PKGBUILD file, rather than anything wrong in R itself. The PKGBUILD
file does this:
ln -s /etc/R/${i} ${i}
when it should do
ln -s /etc/R-devel/${i} ${i}
You can fix your installed version with
cd /opt/r-devel/lib/R/etc/
sudo rm ./*
sudo ln -s /etc/R-devel/javaconf
sudo ln -s /etc/R-devel/ldpaths
sudo ln -s /etc/R-devel/Makeconf
sudo ln -s /etc/R-devel/Renviron
sudo ln -s /etc/R-devel/repositories
Or (better) fix the PKGBUILD and makepkg/pacman -U
Best,
Ista
On Wed, Apr 19, 2017 at 10:32 AM, Angerer, Philipp via R-devel
<r-devel at r-project.org> wrote:> 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
indeed. Makeconf isn?t in the right spot, so the correct vars aren?t set.
thank you all and sorry for the noise!
Von: "Ista Zahn" <istazahn at gmail.com>
An: "Angerer, Philipp" <philipp.angerer at
helmholtz-muenchen.de>
CC: "Dirk Eddelbuettel" <edd at debian.org>, "Martyn
Plummer" <plummerm at iarc.fr>, "r-devel" <r-devel at
r-project.org>
Gesendet: Mittwoch, 19. April 2017 19:10:20
Betreff: Re: [Rd] R 3.4 has broken C++11 support
Hi Philipp,
Fellow Archlinux user here. I think the problem is with the r-devel
PKGBUILD file, rather than anything wrong in R itself. The PKGBUILD
file does this:
ln -s /etc/R/${i} ${i}
when it should do
ln -s /etc/R-devel/${i} ${i}
You can fix your installed version with
cd /opt/r-devel/lib/R/etc/
sudo rm ./*
sudo ln -s /etc/R-devel/javaconf
sudo ln -s /etc/R-devel/ldpaths
sudo ln -s /etc/R-devel/Makeconf
sudo ln -s /etc/R-devel/Renviron
sudo ln -s /etc/R-devel/repositories
Or (better) fix the PKGBUILD and makepkg/pacman -U
Best,
Ista
On Wed, Apr 19, 2017 at 10:32 AM, Angerer, Philipp via R-devel
<r-devel at r-project.org> wrote: > 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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
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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