lebensterben
commented
5 years ago @znmeb
I just installed this package in R and it was successful. My output seems to be identical except trivial differences in the order of lines.
> install.packages("influenceR")
Installing package into ‘/home/lucius/R/x86_64-generic-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://ftp.osuosl.org/pub/cran/src/contrib/influenceR_0.1.0.tar.gz'
Content type 'application/x-gzip' length 23498 bytes (22 KB)
==================================================
downloaded 22 KB
* installing *source* package ‘influenceR’ ...
** package ‘influenceR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,-z,now,-z,relro,-z,max-page-size=0x1000,-z,separate-code -Wno-error -ftree-vectorize -ftree-slp-vectorize -Wl,--enable-new-dtags -fcf-protection=return -m64 -march=westmere -mtune=haswell -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -fprofile-use -fprofile-dir=/var/tmp/pgo -fprofile-correction -fPIC -flto -c bridging.c -o bridging.o
bridging.c: In function ‘bridging._omp_fn.1’:
bridging.c:486:1: warning: ‘/var/tmp/pgo/#tmp#RtmpBPapaY#R.INSTALL414d6eb3f6f0#influenceR#src#bridging.gcda’ profile count data file not found [-Wmissing-profile]
486 | }
| ^
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,-z,now,-z,relro,-z,max-page-size=0x1000,-z,separate-code -Wno-error -ftree-vectorize -ftree-slp-vectorize -Wl,--enable-new-dtags -fcf-protection=return -m64 -march=westmere -mtune=haswell -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -fprofile-use -fprofile-dir=/var/tmp/pgo -fprofile-correction -fPIC -flto -c keyplayer-utils.c -o keyplayer-utils.o
keyplayer-utils.c: In function ‘BFS_parallel_frontier_expansion_with_distance’:
keyplayer-utils.c:496:1: warning: ‘/var/tmp/pgo/#tmp#RtmpBPapaY#R.INSTALL414d6eb3f6f0#influenceR#src#keyplayer-utils.gcda’ profile count data file not found [-Wmissing-profile]
496 | }
| ^
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,-z,now,-z,relro,-z,max-page-size=0x1000,-z,separate-code -Wno-error -ftree-vectorize -ftree-slp-vectorize -Wl,--enable-new-dtags -fcf-protection=return -m64 -march=westmere -mtune=haswell -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -fprofile-use -fprofile-dir=/var/tmp/pgo -fprofile-correction -fPIC -flto -c keyplayer.c -o keyplayer.o
keyplayer.c: In function ‘keyplayer_driver’:
keyplayer.c:33:8: warning: unused variable ‘allsets’ [-Wunused-variable]
33 | int *allsets;
| ^~~~~~~
keyplayer.c:32:11: warning: unused variable ‘fits’ [-Wunused-variable]
32 | double *fits;
| ^~~~
keyplayer.c:30:31: warning: unused variable ‘stop’ [-Wunused-variable]
30 | int np, rank, new_rank = 0, stop;
| ^~~~
keyplayer.c:30:17: warning: unused variable ‘new_rank’ [-Wunused-variable]
30 | int np, rank, new_rank = 0, stop;
| ^~~~~~~~
keyplayer.c:30:11: warning: unused variable ‘rank’ [-Wunused-variable]
30 | int np, rank, new_rank = 0, stop;
| ^~~~
keyplayer.c:30:7: warning: unused variable ‘np’ [-Wunused-variable]
30 | int np, rank, new_rank = 0, stop;
| ^~
keyplayer.c: In function ‘keyplayer_driver_omp._omp_fn.0’:
keyplayer.c:194:1: warning: ‘/var/tmp/pgo/#tmp#RtmpBPapaY#R.INSTALL414d6eb3f6f0#influenceR#src#keyplayer.gcda’ profile count data file not found [-Wmissing-profile]
194 | }
| ^
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,-z,now,-z,relro,-z,max-page-size=0x1000,-z,separate-code -Wno-error -ftree-vectorize -ftree-slp-vectorize -Wl,--enable-new-dtags -fcf-protection=return -m64 -march=westmere -mtune=haswell -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -fprofile-use -fprofile-dir=/var/tmp/pgo -fprofile-correction -fPIC -flto -c prefix_sums.c -o prefix_sums.o
prefix_sums.c: In function ‘prefix_sums’:
prefix_sums.c:63:1: warning: ‘/var/tmp/pgo/#tmp#RtmpBPapaY#R.INSTALL414d6eb3f6f0#influenceR#src#prefix_sums.gcda’ profile count data file not found [-Wmissing-profile]
63 | }
| ^
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,-z,now,-z,relro,-z,max-page-size=0x1000,-z,separate-code -Wno-error -ftree-vectorize -ftree-slp-vectorize -Wl,--enable-new-dtags -fcf-protection=return -m64 -march=westmere -mtune=haswell -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -fprofile-use -fprofile-dir=/var/tmp/pgo -fprofile-correction -fPIC -flto -c process_sparse.c -o process_sparse.o
process_sparse.c: In function ‘process_sparse_R’:
process_sparse.c:46:1: warning: ‘/var/tmp/pgo/#tmp#RtmpBPapaY#R.INSTALL414d6eb3f6f0#influenceR#src#process_sparse.gcda’ profile count data file not found [-Wmissing-profile]
46 | }
| ^
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,-z,now,-z,relro,-z,max-page-size=0x1000,-z,separate-code -Wno-error -ftree-vectorize -ftree-slp-vectorize -Wl,--enable-new-dtags -fcf-protection=return -m64 -march=westmere -mtune=haswell -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -fprofile-use -fprofile-dir=/var/tmp/pgo -fprofile-correction -fPIC -flto -c snap_wrapper.c -o snap_wrapper.o
snap_wrapper.c: In function ‘snap_keyplayer_R’:
snap_wrapper.c:194:7: warning: unused variable ‘r’ [-Wunused-variable]
194 | int r = read_graph_from_edgelist(&G, E, n, m);
| ^
snap_wrapper.c: In function ‘snap_bridging_R’:
snap_wrapper.c:223:7: warning: unused variable ‘r’ [-Wunused-variable]
223 | int r = read_graph_from_edgelist(&G, E, n, m);
| ^
snap_wrapper.c:219:5: warning: unused variable ‘mpi’ [-Wunused-variable]
219 | mpi = INTEGER(sMPI)[0]; // use mpi?
| ^~~
snap_wrapper.c:253:1: warning: ‘/var/tmp/pgo/#tmp#RtmpBPapaY#R.INSTALL414d6eb3f6f0#influenceR#src#snap_wrapper.gcda’ profile count data file not found [-Wmissing-profile]
253 | }
| ^
gcc -I"/usr/lib64/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,-z,now,-z,relro,-z,max-page-size=0x1000,-z,separate-code -Wno-error -ftree-vectorize -ftree-slp-vectorize -Wl,--enable-new-dtags -fcf-protection=return -m64 -march=westmere -mtune=haswell -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -fprofile-use -fprofile-dir=/var/tmp/pgo -fprofile-correction -fPIC -flto -c vertex_betweenness_centrality.c -o vertex_betweenness_centrality.o
vertex_betweenness_centrality.c: In function ‘vertex_betweenness_centrality_parBFS’:
vertex_betweenness_centrality.c:81:14: warning: variable ‘stream’ set but not used [-Wunused-but-set-variable]
81 | int* stream;
| ^~~~~~
vertex_betweenness_centrality.c:66:9: warning: unused variable ‘seed’ [-Wunused-variable]
66 | int seed = 2387;
| ^~~~
vertex_betweenness_centrality.c: In function ‘vertex_betweenness_centrality_simple’:
vertex_betweenness_centrality.c:549:13: warning: unused variable ‘myLock’ [-Wunused-variable]
549 | int myLock;
| ^~~~~~
vertex_betweenness_centrality.c:543:14: warning: variable ‘stream’ set but not used [-Wunused-but-set-variable]
543 | int* stream;
| ^~~~~~
vertex_betweenness_centrality.c:519:9: warning: unused variable ‘seed’ [-Wunused-variable]
519 | int seed = 2387;
| ^~~~
vertex_betweenness_centrality.c:514:10: warning: unused variable ‘chunkSize’ [-Wunused-variable]
514 | long chunkSize;
| ^~~~~~~~~
vertex_betweenness_centrality.c: In function ‘vertex_betweenness_centrality_simple._omp_fn.0’:
vertex_betweenness_centrality.c:868:1: warning: ‘/var/tmp/pgo/#tmp#RtmpBPapaY#R.INSTALL414d6eb3f6f0#influenceR#src#vertex_betweenness_centrality.gcda’ profile count data file not found [-Wmissing-profile]
868 | }
| ^
gcc -g -shared -O2 -g -feliminate-unused-debug-types -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=32 -Wformat -Wformat-security -Wl,-z,now,-z,relro,-z,max-page-size=0x1000,-z,separate-code -Wno-error -ftree-vectorize -ftree-slp-vectorize -Wl,--enable-new-dtags -fcf-protection=return -m64 -march=westmere -mtune=haswell -fasynchronous-unwind-tables -fno-omit-frame-pointer -Wp,-D_REENTRANT -O3 -falign-functions=32 -fno-semantic-interposition -flto=12 -fprofile-use -fprofile-dir=/var/tmp/pgo -fprofile-correction -fPIC -flto -fpic -L/usr/lib64/R/lib -L/usr/local/lib64 -o influenceR.so bridging.o keyplayer-utils.o keyplayer.o prefix_sums.o process_sparse.o snap_wrapper.o vertex_betweenness_centrality.o -fopenmp -L/usr/lib64/R/lib -lR
installing to /home/lucius/R/x86_64-generic-linux-gnu-library/3.6/00LOCK-influenceR/00new/influenceR/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (influenceR)
The downloaded source packages are in
‘/tmp/Rtmp4nRQkU/downloaded_packages’
fenrus75
znmeb
It can't find
lto-wrapper- this has something to do with gcc link-time optimization.Here's what's installed: