* installing *source* package ‘npRmpi’ ... ** this is package ‘npRmpi’ version ‘0.60-20’ ** package ‘npRmpi’ successfully unpacked and MD5 sums checked ** using staged installation setting mpi include path from RMPI_INCLUDE setting mpi lib path from RMPI_LIB_PATH checking for openpty in -lutil... yes checking for main in -lpthread... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘clang version 21.1.8’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/npRmpi/src' /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Rmpi.c -o Rmpi.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c RuniqueCombs.c -o RuniqueCombs.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c bspline.c -o bspline.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c conversion.c -o conversion.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c gsl_bspline.c -o gsl_bspline.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c hash.c -o hash.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c internal.c -o internal.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c jksum.c -o jksum.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c kernel.c -o kernel.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c kernelb.c -o kernelb.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c kernelcv.c -o kernelcv.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c kernele.c -o kernele.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c kernelw.c -o kernelw.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c mat_vec.c -o mat_vec.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c matrix.c -o matrix.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c np.c -o np.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c np_init.c -o np_init.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c nr.c -o nr.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c statmods.c -o statmods.o /usr/local/clang21/bin/clang -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -isystem /usr/local/clang21/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c tree.c -o tree.o /usr/local/clang21/bin/clang -std=gnu23 -shared -L/usr/local/clang/lib64 -L/usr/local/clang21/lib -L/usr/local/clang21/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o npRmpi.so Rmpi.o RuniqueCombs.o bspline.o conversion.o gsl_bspline.o hash.o internal.o jksum.o kernel.o kernelb.o kernelcv.o kernele.o kernelw.o mat_vec.o matrix.o np.o np_init.o nr.o statmods.o tree.o -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/npRmpi/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/npRmpi/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/npRmpi/src' installing to /data/gannet/ripley/R/packages/tests-clang/npRmpi.Rcheck/00LOCK-npRmpi/00new/npRmpi/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (npRmpi)