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July 25, 2013 20:14
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| g@G:~/Documents/pbd$ R CMD INSTALL Rmpi_PROF | |
| * installing to library ‘/home/g/R/x86_64-pc-linux-gnu-library/2.15’ | |
| * installing *source* package ‘Rmpi’ ... | |
| mv: cannot move `/home/g/R/x86_64-pc-linux-gnu-library/2.15/Rmpi' to `/home/g/R/x86_64-pc-linux-gnu-library/2.15/00LOCK-Rmpi_PROF/Rmpi': Permission denied | |
| checking for gcc... gcc -std=gnu99 | |
| 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 gcc -std=gnu99 accepts -g... yes | |
| checking for gcc -std=gnu99 option to accept ISO C89... none needed | |
| checking for mpirun... mpirun | |
| checking for mpiexec... mpiexec | |
| checking for orterun... orterun | |
| checking for sed... /bin/sed | |
| checking for mpicc... mpicc | |
| checking for ompi_info... ompi_info | |
| checking for mpich2version... mpich2version | |
| found sed, mpicc, and ompi_info ... | |
| gcc: error: unrecognized option '--showme:incdirs' | |
| >> TMP_INC_DIRS = | |
| gcc: error: unrecognized option '--showme:libdirs' | |
| >> TMP_LIB_DIRS = | |
| I am here /usr/lib/openmpi and it is OpenMPI | |
| Trying to find mpi.h ... | |
| Found in /usr/lib/openmpi/include | |
| Trying to find libmpi.so or libmpich.a ... | |
| Found libmpi in /usr/lib/openmpi/lib | |
| checking for orted... yes | |
| checking for openpty in -lutil... yes | |
| checking for main in -lpthread... yes | |
| configure: creating ./config.status | |
| config.status: creating src/Makevars | |
| Warning in file.copy(f, instdir, TRUE) : | |
| problem copying ./NAMESPACE to /home/g/R/x86_64-pc-linux-gnu-library/2.15/Rmpi/NAMESPACE: Permission denied | |
| Warning in file(file, ifelse(append, "a", "w")) : | |
| cannot open file '/home/g/R/x86_64-pc-linux-gnu-library/2.15/Rmpi/DESCRIPTION': Permission denied | |
| Error in file(file, ifelse(append, "a", "w")) : | |
| cannot open the connection | |
| ERROR: installing package DESCRIPTION failed for package ‘Rmpi’ | |
| * removing ‘/home/g/R/x86_64-pc-linux-gnu-library/2.15/Rmpi’ | |
| g@G:~/Documents/pbd$ sudo R CMD INSTALL Rmpi_PROF | |
| * installing to library ‘/home/g/R/x86_64-pc-linux-gnu-library/2.15’ | |
| * installing *source* package ‘Rmpi’ ... | |
| checking for gcc... gcc -std=gnu99 | |
| 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 gcc -std=gnu99 accepts -g... yes | |
| checking for gcc -std=gnu99 option to accept ISO C89... none needed | |
| checking for mpirun... mpirun | |
| checking for mpiexec... mpiexec | |
| checking for orterun... orterun | |
| checking for sed... /bin/sed | |
| checking for mpicc... mpicc | |
| checking for ompi_info... ompi_info | |
| checking for mpich2version... mpich2version | |
| found sed, mpicc, and ompi_info ... | |
| gcc: error: unrecognized option '--showme:incdirs' | |
| >> TMP_INC_DIRS = | |
| gcc: error: unrecognized option '--showme:libdirs' | |
| >> TMP_LIB_DIRS = | |
| I am here /usr/lib/openmpi and it is OpenMPI | |
| Trying to find mpi.h ... | |
| Found in /usr/lib/openmpi/include | |
| Trying to find libmpi.so or libmpich.a ... | |
| Found libmpi in /usr/lib/openmpi/lib | |
| checking for orted... yes | |
| checking for openpty in -lutil... yes | |
| checking for main in -lpthread... yes | |
| configure: creating ./config.status | |
| config.status: creating src/Makevars | |
| ** libs | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/lib/openmpi/include -DMPI2 -DOPENMPI -fpic -O3 -pipe -g -c RegQuery.c -o RegQuery.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/lib/openmpi/include -DMPI2 -DOPENMPI -fpic -O3 -pipe -g -c Rmpi.c -o Rmpi.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/lib/openmpi/include -DMPI2 -DOPENMPI -fpic -O3 -pipe -g -c conversion.c -o conversion.o | |
| gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/lib/openmpi/include -DMPI2 -DOPENMPI -fpic -O3 -pipe -g -c internal.c -o internal.o | |
| gcc -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib/openmpi/lib -lmpi -lutil -lpthread -L/usr/lib/R/lib -lR | |
| installing to /home/g/R/x86_64-pc-linux-gnu-library/2.15/Rmpi/libs | |
| ** R | |
| ** demo | |
| ** inst | |
| ** preparing package for lazy loading | |
| ** help | |
| *** installing help indices | |
| ** building package indices | |
| ** testing if installed package can be loaded | |
| * DONE (Rmpi) |
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gcc -std=gnu99 -shared -L/usr/local/lib -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/home/snoweye/work-my/local/ompi/lib -lmpi -lutil -lpthread