Re: [Rd] Question about writing portable packages
Kevin Ushey: (12:10AM on Fri, Jun 07) I think the key word here is _other_ packages. It's entirely okay to call your package's own compiled code through the .Call interface (and the code you write may link to other packages; the obvious example being Rcpp code you write); however, it is not portable to use .Call to call compiled code from another package directly. This is because package authors are not required to maintain a consistent .Call interface to their compiled code; rather, they just have to make sure the direct user-facing R exported functions retain a stable interface over different versions (or, if changed, are done so with prior warning etc.) Also remember that, as long as you obey all of the licenses, you can simply copy the source code that needs to be compiled into your own package. You'll obviously need to track development of the other package (which you'll need to do anyway) but then you can be sure that the calls you want to use work. -- Gray Calhoun, Assistant Professor of Economics at Iowa State http://gray.clhn.co (web) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Compile error gfortran-4.6
Dears, I am writing a code in Fortran using OpenMP directives. When compiling the code in gfortran 4.4 does not occur any problem. When compiling the code in gfortran 4.6, an error message appears. In other compilers the error does not occur. A small example. ## Code in Fortran subroutine hello() implicit none integer :: nthreads, tid integer :: omp_get_num_threads, omp_get_thread_num integer :: omp_get_max_threads, omp_set_num_threads print *, 'Máximo de threads', omp_get_max_threads() !$omp parallel tid = omp_get_thread_num() print *, 'Hello World from thread = ', tid print *, 'Number of threads =', omp_get_thread_num() !$omp end parallel end subroutine hello ### Compiling and testing system(R CMD COMPILE hello.f90 FCFLAGS=-fopenmp) system(R CMD SHLIB hello.o) dyn.load(hello.so) .Fortran(hello) ### Error message /home/fmcron/Documentos/Fortran/OpenMP/exemplos/hello.so: undefined symbol: _gfortran_transfer_character_write Thanks Fábio Mathias Corrêa Universidade Estadual de Santa Cruz Departamento de Ciências Exatas e da Terra - DCET Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna CEP 45662-900. Ilhéus-Bahia Tel.: 73-3680-5076 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Compile error with gfortran-4.6
Dears, I am writing a code in Fortran using OpenMP directives. When compiling the code in gfortran 4.4 does not occur any problem. When compiling the code in gfortran 4.6, an error message appears. In other compilers the error does not occur. A small example. ## Code in Fortran subroutine hello() implicit none integer :: nthreads, tid integer :: omp_get_num_threads, omp_get_thread_num integer :: omp_get_max_threads, omp_set_num_threads print *, 'Máximo de threads', omp_get_max_threads() !$omp parallel tid = omp_get_thread_num() print *, 'Hello World from thread = ', tid print *, 'Number of threads =', omp_get_thread_num() !$omp end parallel end subroutine hello ### Compiling and testing system(R CMD COMPILE hello.f90 FCFLAGS=-fopenmp) system(R CMD SHLIB hello.o) dyn.load(hello.so) .Fortran(hello) ### Error message /home/fmcron/Documentos/Fortran/OpenMP/exemplos/hello.so: undefined symbol: _gfortran_transfer_character_write Thanks Fábio Mathias Corrêa Universidade Estadual de Santa Cruz Departamento de Ciências Exatas e da Terra - DCET Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna CEP 45662-900. Ilhéus-Bahia [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compile error with gfortran-4.6
This is not gfortran-help, but note that you are not doing this correctly. See 'Writing R Extensions' §1.2.1. The linking step needs a flag too. Beyond that, you failed to tell us your OS, and in fact there are no such versions of gfortran (4.6.0 != 4.6). The posting guide does ask you to be accurate in your version numbers (and not to send HTML). On 08/06/2013 14:43, Fabio Mathias Corrêa wrote: Dears, I am writing a code in Fortran using OpenMP directives. When compiling the code in gfortran 4.4 does not occur any problem. When compiling the code in gfortran 4.6, an error message appears. In other compilers the error does not occur. A small example. ## Code in Fortran You declare this to be Fortran 90. subroutine hello() implicit none integer :: nthreads, tid integer :: omp_get_num_threads, omp_get_thread_num integer :: omp_get_max_threads, omp_set_num_threads print *, 'Máximo de threads', omp_get_max_threads() !$omp parallel tid = omp_get_thread_num() print *, 'Hello World from thread = ', tid print *, 'Number of threads =', omp_get_thread_num() !$omp end parallel end subroutine hello ### Compiling and testing system(R CMD COMPILE hello.f90 FCFLAGS=-fopenmp) system(R CMD SHLIB hello.o) dyn.load(hello.so) .Fortran(hello) ### Error message /home/fmcron/Documentos/Fortran/OpenMP/exemplos/hello.so: undefined symbol: _gfortran_transfer_character_write Thanks Fábio Mathias Corrêa Universidade Estadual de Santa Cruz Departamento de Ciências Exatas e da Terra - DCET Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna CEP 45662-900. Ilhéus-Bahia [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Problem with gfortran-4.6
Dears, I am writing a code in Fortran using OpenMP directives. When compiling the code in gfortran 4.4 does not occur any problem. When compiling the code in gfortran 4.6, an error message appears. In other compilers the error does not occur. A small example. ## Code in Fortran subroutine hello() implicit none integer :: nthreads, tid integer :: omp_get_num_threads, omp_get_thread_num integer :: omp_get_max_threads, omp_set_num_threads print *, 'Máximo de threads', omp_get_max_threads() !$omp parallel tid = omp_get_thread_num() print *, 'Hello World from thread = ', tid print *, 'Number of threads =', omp_get_thread_num() !$omp end parallel end subroutine hello ### Compiling and testing system(R CMD COMPILE hello.f90 FCFLAGS=-fopenmp) system(R CMD SHLIB hello.o) dyn.load(hello.so) .Fortran(hello) ### Error message /home/fmcron/Documentos/Fortran/OpenMP/exemplos/hello.so: undefined symbol: _gfortran_transfer_character_write Thanks Fábio Mathias Corrêa Universidade Estadual de Santa Cruz Departamento de Ciências Exatas e da Terra - DCET Campus Soane Nazaré de Andrade, km 16 Rodovia Ilhéus-Itabuna CEP 45662-900. Ilhéus-Bahia Tel.: 73-3680-5076 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD INSTALL and file permission settings
Summary: The directory /usr/local/lib/R/site-library can be used for site-wide multi-user installations of R. This is even the default on Debian and Ubuntu (following a suggestion by Kurt and Fritz a decade ago over beers -- what could be better). However, R enforces wrong permissions on directories and files there (removing group-write) which effectively defeats this purpose, and breaks multiuser installation: if Tom, Dick and Harry are members of group 'r-users', each one can install in the directory, but neither can _upgrade_ a package installed by one of the others. I would like to correct this. Details: For a while now, R CMD INSTALL dispatches installation work to the R function tools:::.install_packages() from the file tools/install.R. The function does a lot of hardcoded 'chmod' with constant arguments: edd@max:~/svn/r-devel/src/library/tools/R$ grep Sys.chmod install.R if (!WINDOWS) Sys.chmod(file.path(dest, files), 755) Sys.chmod(file.path(instdir, f), 644) Sys.chmod(Sys.glob(file.path(instdir, data, *)), 644) Sys.chmod(Sys.glob(file.path(instdir, demo, *)), 644) Sys.chmod(Sys.glob(file.path(instdir, exec, *)), 755) Sys.chmod(i2_files[execs], 755) edd@max:~/svn/r-devel/src/library/tools/R$ Moreover, it also calls a C function for cleanup cleanup: edd@max:~/svn/r-devel/src/library/tools/R$ grep .Call(dir install.R .Call(dirchmod, instdir) .Call(dirchmod, ss) .Call(dirchmod, ss) ## tree, since the later .Call(dirchmod) call will edd@max:~/svn/r-devel/src/library/tools/R$ which also uses unconditional 644 / 755 mode_t mask = S_IRUSR | S_IRGRP | S_IROTH | S_IWUSR, /* 0644 */ dirmask = mask | S_IXUSR | S_IXGRP | S_IXOTH; /* 0755 */ Proposal: Add a new option() [with a to-be-determined name] which, if enabled, turns on group-write modes for files and directories, ie 664 and 775. One way would be to set two character vars at the beginning of _install_packages and to pass a flag to the dirchmod call as so that 'S_IWGRP' (the 00020 write by group permission) can be set. I would be happy to write such a patch (including documentation updates) if someone from R Core can signal willigness to look at it. Thanks, Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD INSTALL and file permission settings
Hi all, Dirk Eddelbuettel e...@debian.org writes: Summary: The directory /usr/local/lib/R/site-library can be used for site-wide multi-user installations of R. This is even the default on Debian and Ubuntu (following a suggestion by Kurt and Fritz a decade ago over beers -- what could be better). However, R enforces wrong permissions on directories and files there (removing group-write) which effectively defeats this purpose, and breaks multiuser installation: if Tom, Dick and Harry are members of group 'r-users', each one can install in the directory, but neither can _upgrade_ a package installed by one of the others. I would like to correct this. This is just a message from a user who would greatly appreciate such a change. We have written a script based on inotify to correct that group writing permissions which we would gladly dismiss again. Best, Andreas __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
