Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
On 21 Jul 2015, at 08:12 , Johannes Ranke jra...@uni-bremen.de wrote: Could you guys move to r-devel? This has nothing to do with _package_ development. OK, the details of how to configure a build are maybe a bit too far off... But in general, testing with a recent development build is an important part of submitting packages to CRAN, so it seems to me that this list may serve to collect information on how this can be done? In a word: No. So is getting R installed in the first place, running it on a Mac, sorting out library dependencies, etc. All of these things have their own mailing lists, full of people that know about stuff. We do not want to duplicate their content here, possibly with lesser competence. Plus, it clogs up the archives of _this_ list. -pd -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
On 20 July 2015 at 18:05, MAURICIO ZAMBRANO BIGIARINI wrote: | Dear list, | | I'm trying to set up the development version of R (R-devel ) for | testing some packages before submitting them to CRAN. I'm using Linux | Mint 17.1 64-bit, which is an Ubuntu-based distro. | | I followed the advice of Dirk on | https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001935.html | | | Everything seems to run fine until .configure: | | R is now configured for x86_64-unknown-linux-gnu | | Source directory: . | Installation directory:/usr/local/lib/R-devel | | C compiler:ccache gcc -std=gnu99 -g -O2 | Fortran 77 compiler: gfortran -g -O2 | | C++ compiler: ccache g++ -g -O2 | C++11 compiler:ccache g++ -std=c++11 -g -O2 | 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: no Looks good but ... | | | However, when running make, I got an error saying: | | /usr/bin/ld: ../appl/dchdc.o: relocation R_X86_64_32 against | `.rodata' can not be used when making a shared object; recompile with | -fPIC | | | I would highly appreciate any advice on how to solve this issue (or | what should I recompile with -fPIC and how). ... naybe your R was built without shared library support? The binaries resulting from my configuration (ie the Debian or Ubuntu packages obtained either from the distro themselves or the CRAN mirrors) have 'pic' set: edd@max:~$ grep -i pic /etc/R/Makeconf CPICFLAGS = -fpic CXXPICFLAGS = -fpic CXX1XPICFLAGS = -fpic DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS) FCPICFLAGS = -fpic FPICFLAGS = -fpic SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) ## We want to ensure libR is picked up from $(R_HOME)/lib ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS) ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS) ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS) ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS) ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS) $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ edd@max:~$ Here /etc/R/Makefonf is just a convenient link to $(R_HOME)/etc/Makeconf. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
= When the pupil is ready, the master arrives. (Zen proverb) = Linux user #454569 -- Linux Mint user On 20 July 2015 at 18:35, Dirk Eddelbuettel e...@debian.org wrote: On 20 July 2015 at 18:05, MAURICIO ZAMBRANO BIGIARINI wrote: | Dear list, | | I'm trying to set up the development version of R (R-devel ) for | testing some packages before submitting them to CRAN. I'm using Linux | Mint 17.1 64-bit, which is an Ubuntu-based distro. | | I followed the advice of Dirk on | https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001935.html | | | Everything seems to run fine until .configure: | | R is now configured for x86_64-unknown-linux-gnu | | Source directory: . | Installation directory:/usr/local/lib/R-devel | | C compiler:ccache gcc -std=gnu99 -g -O2 | Fortran 77 compiler: gfortran -g -O2 | | C++ compiler: ccache g++ -g -O2 | C++11 compiler:ccache g++ -std=c++11 -g -O2 | 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: no Looks good but ... | | | However, when running make, I got an error saying: | | /usr/bin/ld: ../appl/dchdc.o: relocation R_X86_64_32 against | `.rodata' can not be used when making a shared object; recompile with | -fPIC | | | I would highly appreciate any advice on how to solve this issue (or | what should I recompile with -fPIC and how). ... naybe your R was built without shared library support? The binaries resulting from my configuration (ie the Debian or Ubuntu packages obtained either from the distro themselves or the CRAN mirrors) have 'pic' set: edd@max:~$ grep -i pic /etc/R/Makeconf CPICFLAGS = -fpic CXXPICFLAGS = -fpic CXX1XPICFLAGS = -fpic DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS) FCPICFLAGS = -fpic FPICFLAGS = -fpic SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) ## We want to ensure libR is picked up from $(R_HOME)/lib ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS) ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS) ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS) ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS) ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS) $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ edd@max:~$ Here /etc/R/Makefonf is just a convenient link to $(R_HOME)/etc/Makeconf. Dirk Thank you very much Dirk, but I forgot to mention that this is my very first time trying to set up R-devel. In my ~/SVN/R-devel/trunk/Makeconf file I currently don't have the first two lines you mentioned: CPICFLAGS = -fpic CXXPICFLAGS = -fpic and instead of SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) I have DYLIB_LDFLAGS = -shared -fopenmp# $(DYLIBS_LTO) how can I be sure that I I enabled the shared library support ? Mauricio __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
On 20 July 2015 at 18:56, MAURICIO ZAMBRANO BIGIARINI wrote: | how can I be sure that I I enabled the shared library support ? edd@max:~/svn/r-devel$ ./configure --help | grep enable-R-sh --enable-R-shlibbuild the shared/dynamic library 'libR' [no] edd@max:~/svn/r-devel$ Make sure you set --enable-R-shlib. It is in the script which you linked to in your previous email. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
On 20 July 2015 at 20:29, peter dalgaard pda...@gmail.com wrote: Oi! Could you guys move to r-devel? This has nothing to do with _package_ development. Thanks for the advice. I was not sure about the list I should have submitted this message, but looking at http://www.r-project.org/mail.html: R-package-devel is to get help about package development in R,... If you are having problems developing a package or passing R CMD check, this is the place to ask! R-devel: This list is intended for questions and discussion about code development in R. ... The list is also for proposals of new functionality for R, and pre-testing of new versions. It is meant particularly for those who maintain an active position in the development of R. and as my original intend was to passing R CMD check--as-cran using the development version of R, I chose r-package-devel. I'll create a shorten version of this message in r-devel (not sure if this is the right way of moving a message from one mailing list to another). Mauricio -Peter D On 21 Jul 2015, at 00:49 , MAURICIO ZAMBRANO BIGIARINI mauricio.zambr...@ufrontera.cl wrote: -- Forwarded message -- From: Dirk Eddelbuettel e...@debian.org Date: 20 July 2015 at 19:21 Subject: Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit To: MAURICIO ZAMBRANO BIGIARINI mauricio.zambr...@ufrontera.cl Cc: Dirk Eddelbuettel e...@debian.org, r-package-devel@r-project.org On 20 July 2015 at 18:56, MAURICIO ZAMBRANO BIGIARINI wrote: | how can I be sure that I I enabled the shared library support ? edd@max:~/svn/r-devel$ ./configure --help | grep enable-R-sh --enable-R-shlibbuild the shared/dynamic library 'libR' [no] edd@max:~/svn/r-devel$ Make sure you set --enable-R-shlib. It is in the script which you linked to in your previous email. I thought I did it already when running configure: ./configure --prefix=/usr/local/lib/R-devel --enable-R-shlib --with-blas --with-lapack --with-readline --without-recommended-packages I just tried to run again your script (mentioned in my previous e-mail) from scratch and I'm still getting an error: R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/usr/local/lib/R-devel C compiler:ccache gcc -ggdb -pipe -std=gnu99 -Wall -pedantic Fortran 77 compiler: ccache gfortran -g -O2 C++ compiler: ccache g++ -ggdb -pipe -Wall -pedantic C++11 compiler:ccache g++ -std=c++11 -ggdb -pipe -Wall -pedantic Fortran 90/95 compiler:ccache 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: no make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' make[1]: Nothing to be done for `front-matter'. make[1]: Nothing to be done for `html-non-svn'. make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' SVN-REVISION is unchanged make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/m4' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/m4' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/tools' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/tools' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/html' make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/html' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/etc' make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/etc' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/share' make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/share' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' creating src/scripts/R.fe make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/include' config.status: creating src/include/config.h config.status: src/include/config.h is unchanged Rmath.h is unchanged make[3]: Entering
