Hello! I try to install Rmpi with install.packages(?Rmpi?), but it fails:> install.packages("Rmpi")Package which is only available in source form, and may need compilation of C/C++/Fortran: ?Rmpi? Do you want to attempt to install these from sources? (Yes/no/cancel) yes installing the source package ?Rmpi? trying URL 'https://cran.rstudio.com/src/contrib/Rmpi_0.6-7.tar.gz' Content type 'application/x-gzip' length 106869 bytes (104 KB) =================================================downloaded 104 KB * installing *source* package ?Rmpi? ... ** package ?Rmpi? successfully unpacked and MD5 sums checked checking for gcc... clang checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether clang accepts -g... yes checking for clang option to accept ISO C89... none needed checking for pkg-config... no checking how to run the C preprocessor... clang -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... rm: conftest.dSYM: is a directory rm: conftest.dSYM: is a directory yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking mpi.h usability... no checking mpi.h presence... no checking for mpi.h... no configure: error: "Cannot find mpi.h header file" ERROR: configuration failed for package ?Rmpi? * removing ?/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rmpi? Warning in install.packages : installation of package ?Rmpi? had non-zero exit status The downloaded source packages are in ?/private/var/folders/wd/5x8p9n_j1kx7sqqv2hk23vvm0000gs/T/RtmpKZ1waO/downloaded_packages? The systems is MacOS High Sierra 10.13.3. Thanks in advance! Best, Yufei
Hi! You need to have MPI in your path. Thanks, Erin On Fri, Jul 13, 2018 at 4:29 PM Yufei Zhao <yzhao17 at uoregon.edu> wrote:> Hello! > > I try to install Rmpi with install.packages(?Rmpi?), but it fails: > > > install.packages("Rmpi") > Package which is only available in source form, and may need compilation > of C/C++/Fortran: ?Rmpi? > Do you want to attempt to install these from sources? (Yes/no/cancel) yes > installing the source package ?Rmpi? > > trying URL 'https://cran.rstudio.com/src/contrib/Rmpi_0.6-7.tar.gz' > Content type 'application/x-gzip' length 106869 bytes (104 KB) > =================================================> downloaded 104 KB > > * installing *source* package ?Rmpi? ... > ** package ?Rmpi? successfully unpacked and MD5 sums checked > checking for gcc... clang > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether clang accepts -g... yes > checking for clang option to accept ISO C89... none needed > checking for pkg-config... no > checking how to run the C preprocessor... clang -E > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for ANSI C header files... rm: conftest.dSYM: is a directory > rm: conftest.dSYM: is a directory > yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking mpi.h usability... no > checking mpi.h presence... no > checking for mpi.h... no > configure: error: "Cannot find mpi.h header file" > ERROR: configuration failed for package ?Rmpi? > * removing > ?/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rmpi? > Warning in install.packages : > installation of package ?Rmpi? had non-zero exit status > > The downloaded source packages are in > > ?/private/var/folders/wd/5x8p9n_j1kx7sqqv2hk23vvm0000gs/T/RtmpKZ1waO/downloaded_packages? > > > The systems is MacOS High Sierra 10.13.3. > > Thanks in advance! > > Best, > Yufei > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Erin Hodgess Associate Professor Department of Mathematical and Statistics University of Houston - Downtown mailto: erinm.hodgess at gmail.com [[alternative HTML version deleted]]
I cannot specifically help, but you may wish to post this on the r-sig-mac list where there may be the expertise you need. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Fri, Jul 13, 2018 at 2:24 PM, Yufei Zhao <yzhao17 at uoregon.edu> wrote:> Hello! > > I try to install Rmpi with install.packages(?Rmpi?), but it fails: > > > install.packages("Rmpi") > Package which is only available in source form, and may need compilation > of C/C++/Fortran: ?Rmpi? > Do you want to attempt to install these from sources? (Yes/no/cancel) yes > installing the source package ?Rmpi? > > trying URL 'https://cran.rstudio.com/src/contrib/Rmpi_0.6-7.tar.gz' > Content type 'application/x-gzip' length 106869 bytes (104 KB) > =================================================> downloaded 104 KB > > * installing *source* package ?Rmpi? ... > ** package ?Rmpi? successfully unpacked and MD5 sums checked > checking for gcc... clang > checking whether the C compiler works... yes > checking for C compiler default output file name... a.out > checking for suffix of executables... > checking whether we are cross compiling... no > checking for suffix of object files... o > checking whether we are using the GNU C compiler... yes > checking whether clang accepts -g... yes > checking for clang option to accept ISO C89... none needed > checking for pkg-config... no > checking how to run the C preprocessor... clang -E > checking for grep that handles long lines and -e... /usr/bin/grep > checking for egrep... /usr/bin/grep -E > checking for ANSI C header files... rm: conftest.dSYM: is a directory > rm: conftest.dSYM: is a directory > yes > checking for sys/types.h... yes > checking for sys/stat.h... yes > checking for stdlib.h... yes > checking for string.h... yes > checking for memory.h... yes > checking for strings.h... yes > checking for inttypes.h... yes > checking for stdint.h... yes > checking for unistd.h... yes > checking mpi.h usability... no > checking mpi.h presence... no > checking for mpi.h... no > configure: error: "Cannot find mpi.h header file" > ERROR: configuration failed for package ?Rmpi? > * removing ?/Library/Frameworks/R.framework/Versions/3.5/ > Resources/library/Rmpi? > Warning in install.packages : > installation of package ?Rmpi? had non-zero exit status > > The downloaded source packages are in > ?/private/var/folders/wd/5x8p9n_j1kx7sqqv2hk23vvm0000gs/T/ > RtmpKZ1waO/downloaded_packages? > > > The systems is MacOS High Sierra 10.13.3. > > Thanks in advance! > > Best, > Yufei > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/ > posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]