[R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit

[MAURICIO ZAMBRANO BIGIARINI]

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"When the pupil is ready, the master arrives."
(Zen proverb)
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Linux user #454569 -- Linux Mint user


On 20 July 2015 at 18:35, Dirk Eddelbuettel <edd at 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 at 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 $@
> edd at max:~$
>
> 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