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02-19-2024 01:28 PM
Hi!
I am trying to install the igraph and networkD3 CRAN packages for use within a notebook. However, I am receiving the below installation error when attempting to do so.
Could someone please assist? Thank you!
* installing *source* package ‘igraph’ ...
** package ‘igraph’ successfully unpacked and MD5 sums checked
** using staged installation
libxml2 include directories: -I/usr/include/libxml2
libxml2 library link flags: -lxml2
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c simpleraytracer.cpp -o simpleraytracer.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rinterface_extra.c -o rinterface_extra.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rrandom.c -o rrandom.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rinterface.c -o rinterface.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpprinterface.cpp -o cpprinterface.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lazyeval.c -o lazyeval.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnaupd.f -o vendor/arpack/dnaupd.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dstatn.f -o vendor/arpack/dstatn.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsaupd.f -o vendor/arpack/dsaupd.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dvout.f -o vendor/arpack/dvout.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dstqrb.f -o vendor/arpack/dstqrb.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dlaqrb.f -o vendor/arpack/dlaqrb.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsaup2.f -o vendor/arpack/dsaup2.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dmout.f -o vendor/arpack/dmout.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dngets.f -o vendor/arpack/dngets.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dneupd.f -o vendor/arpack/dneupd.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsortc.f -o vendor/arpack/dsortc.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnaup2.f -o vendor/arpack/dnaup2.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dseigt.f -o vendor/arpack/dseigt.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dneigh.f -o vendor/arpack/dneigh.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dseupd.f -o vendor/arpack/dseupd.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsgets.f -o vendor/arpack/dsgets.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnapps.f -o vendor/arpack/dnapps.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsaitr.f -o vendor/arpack/dsaitr.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dstats.f -o vendor/arpack/dstats.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnconv.f -o vendor/arpack/dnconv.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/second.f -o vendor/arpack/second.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsesrt.f -o vendor/arpack/dsesrt.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsapps.f -o vendor/arpack/dsapps.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dgetv0.f -o vendor/arpack/dgetv0.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnaitr.f -o vendor/arpack/dnaitr.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsortr.f -o vendor/arpack/dsortr.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsconv.f -o vendor/arpack/dsconv.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/wrap.f -o vendor/arpack/wrap.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/ivout.f -o vendor/arpack/ivout.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/version.c -o vendor/cigraph/src/version.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/eigenvector.c -o vendor/cigraph/src/centrality/eigenvector.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/truss.cpp -o vendor/cigraph/src/centrality/truss.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack.cpp -o vendor/cigraph/src/centrality/prpack.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/pagerank.c -o vendor/cigraph/src/centrality/pagerank.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/closeness.c -o vendor/cigraph/src/centrality/closeness.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/hub_authority.c -o vendor/cigraph/src/centrality/hub_authority.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/coreness.c -o vendor/cigraph/src/centrality/coreness.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/centralization.c -o vendor/cigraph/src/centrality/centralization.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/betweenness.c -o vendor/cigraph/src/centrality/betweenness.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/centrality_other.c -o vendor/cigraph/src/centrality/centrality_other.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_utils.cpp -o vendor/cigraph/src/centrality/prpack/prpack_utils.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_base_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_base_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_result.cpp -o vendor/cigraph/src/centrality/prpack/prpack_result.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_solver.cpp -o vendor/cigraph/src/centrality/prpack/prpack_solver.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/glet.c -o vendor/cigraph/src/cliques/glet.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/maximal_cliques.c -o vendor/cigraph/src/cliques/maximal_cliques.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliquer_wrapper.c -o vendor/cigraph/src/cliques/cliquer_wrapper.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliques.c -o vendor/cigraph/src/cliques/cliques.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliquer/cliquer.c -o vendor/cigraph/src/cliques/cliquer/cliquer.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliquer/reorder.c -o vendor/cigraph/src/cliques/cliquer/reorder.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliquer/cliquer_graph.c -o vendor/cigraph/src/cliques/cliquer/cliquer_graph.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/community/voronoi.c -o vendor/cigraph/src/community/voronoi.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/community/optimal_modularity.c -o vendor/cigraph/src/community/optimal_modularity.o
In file included from vendor/cigraph/src/community/optimal_modularity.c:32:
vendor/cigraph/src/internal/glpk_support.h:39:10: fatal error: glpk.h: No such file or directory
39 | #include <glpk.h>
| ^~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:191: vendor/cigraph/src/community/optimal_modularity.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/igraph’
* installing *source* package ‘igraph’ ...
** package ‘igraph’ successfully unpacked and MD5 sums checked
** using staged installation
libxml2 include directories: -I/usr/include/libxml2
libxml2 library link flags: -lxml2
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c simpleraytracer.cpp -o simpleraytracer.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rinterface_extra.c -o rinterface_extra.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rrandom.c -o rrandom.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rinterface.c -o rinterface.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpprinterface.cpp -o cpprinterface.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lazyeval.c -o lazyeval.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnaupd.f -o vendor/arpack/dnaupd.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dstatn.f -o vendor/arpack/dstatn.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsaupd.f -o vendor/arpack/dsaupd.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dvout.f -o vendor/arpack/dvout.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dstqrb.f -o vendor/arpack/dstqrb.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dlaqrb.f -o vendor/arpack/dlaqrb.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsaup2.f -o vendor/arpack/dsaup2.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dmout.f -o vendor/arpack/dmout.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dngets.f -o vendor/arpack/dngets.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dneupd.f -o vendor/arpack/dneupd.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsortc.f -o vendor/arpack/dsortc.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnaup2.f -o vendor/arpack/dnaup2.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dseigt.f -o vendor/arpack/dseigt.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dneigh.f -o vendor/arpack/dneigh.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dseupd.f -o vendor/arpack/dseupd.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsgets.f -o vendor/arpack/dsgets.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnapps.f -o vendor/arpack/dnapps.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsaitr.f -o vendor/arpack/dsaitr.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dstats.f -o vendor/arpack/dstats.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnconv.f -o vendor/arpack/dnconv.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/second.f -o vendor/arpack/second.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsesrt.f -o vendor/arpack/dsesrt.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsapps.f -o vendor/arpack/dsapps.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dgetv0.f -o vendor/arpack/dgetv0.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dnaitr.f -o vendor/arpack/dnaitr.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsortr.f -o vendor/arpack/dsortr.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/dsconv.f -o vendor/arpack/dsconv.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/wrap.f -o vendor/arpack/wrap.o
gfortran -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -c vendor/arpack/ivout.f -o vendor/arpack/ivout.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/version.c -o vendor/cigraph/src/version.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/eigenvector.c -o vendor/cigraph/src/centrality/eigenvector.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/truss.cpp -o vendor/cigraph/src/centrality/truss.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack.cpp -o vendor/cigraph/src/centrality/prpack.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/pagerank.c -o vendor/cigraph/src/centrality/pagerank.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/closeness.c -o vendor/cigraph/src/centrality/closeness.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/hub_authority.c -o vendor/cigraph/src/centrality/hub_authority.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/coreness.c -o vendor/cigraph/src/centrality/coreness.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/centralization.c -o vendor/cigraph/src/centrality/centralization.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/betweenness.c -o vendor/cigraph/src/centrality/betweenness.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/centrality_other.c -o vendor/cigraph/src/centrality/centrality_other.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_utils.cpp -o vendor/cigraph/src/centrality/prpack/prpack_utils.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_base_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_base_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_result.cpp -o vendor/cigraph/src/centrality/prpack/prpack_result.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/centrality/prpack/prpack_solver.cpp -o vendor/cigraph/src/centrality/prpack/prpack_solver.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/glet.c -o vendor/cigraph/src/cliques/glet.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/maximal_cliques.c -o vendor/cigraph/src/cliques/maximal_cliques.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliquer_wrapper.c -o vendor/cigraph/src/cliques/cliquer_wrapper.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliques.c -o vendor/cigraph/src/cliques/cliques.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliquer/cliquer.c -o vendor/cigraph/src/cliques/cliquer/cliquer.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliquer/reorder.c -o vendor/cigraph/src/cliques/cliquer/reorder.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/cliques/cliquer/cliquer_graph.c -o vendor/cigraph/src/cliques/cliquer/cliquer_graph.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/community/voronoi.c -o vendor/cigraph/src/community/voronoi.o
gcc -I"/usr/share/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/cpp11/include' -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vendor/cigraph/src/community/optimal_modularity.c -o vendor/cigraph/src/community/optimal_modularity.o
In file included from vendor/cigraph/src/community/optimal_modularity.c:32:
vendor/cigraph/src/internal/glpk_support.h:39:10: fatal error: glpk.h: No such file or directory
39 | #include <glpk.h>
| ^~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:191: vendor/cigraph/src/community/optimal_modularity.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/igraph’
ERROR: dependency ‘igraph’ is not available for package ‘networkD3’
* removing ‘/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c/networkD3’
Installing package into ‘/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/igraph_2.0.2.tar.gz'
Content type 'application/x-gzip' length 4965448 bytes (4.7 MB)
==================================================
downloaded 4.7 MB
Warning in utils::install.packages(package, ...) :
installation of package ‘igraph’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmppqDoPI/downloaded_packages’
Warning in p_install(package, character.only = TRUE, ...) :
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘igraph’
Warning in pacman::p_load(char = x, character.only = T) :
Failed to install/load:
igraph
Installing package into ‘/local_disk0/.ephemeral_nfs/envs/rEnv-1a9d05b3-cd4c-41b1-a6f3-ff1f535b673c’
(as ‘lib’ is unspecified)
also installing the dependency ‘igraph’
trying URL 'https://cloud.r-project.org/src/contrib/igraph_2.0.2.tar.gz'
Content type 'application/x-gzip' length 4965448 bytes (4.7 MB)
==================================================
downloaded 4.7 MB
trying URL 'https://cloud.r-project.org/src/contrib/networkD3_0.4.tar.gz'
Content type 'application/x-gzip' length 128302 bytes (125 KB)
==================================================
downloaded 125 KB
Warning in utils::install.packages(package, ...) :
installation of package ‘igraph’ had non-zero exit status
Warning in utils::install.packages(package, ...) :
installation of package ‘networkD3’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmppqDoPI/downloaded_packages’
Warning in p_install(package, character.only = TRUE, ...) :
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘networkD3’
Warning in pacman::p_load(char = x, character.only = T) :
Failed to install/load:
networkD3
[[1]]
igraph
FALSE
[[2]]
networkD3
FALSE
1 ACCEPTED SOLUTION
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03-07-2024 10:49 AM
Hi! I just figured this out myself. I'm not sure why this is suddenly occurring, since igraph has always loaded fine for me in databricks but didn't this week. I found that the following solution worked.
In your notebook before installing your R libraries, make a %sh chunk (just type that at the top) so the code looks like this:
```
%sh
sudo apt-get update
sudo apt-get -y install libglpk-dev
```
This should work. I found the solution here: https://github.com/igraph/rigraph/issues/490#issuecomment-966890059
SUPERSEDED BY THE TROUBLESHOOTING PAGE I am trying to install igraph from CRAN with install.packages("igraph"), and I get an error like this: In file included from feedback_arc_set.c:31: igraph_glpk_support.h:36:10: fatal error: glpk.h: ...
3 REPLIES 3
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02-19-2024 10:41 PM
Hi @thethirtyfour,
-
Binary Installation:
- First, try installing the package from binary (precompiled) rather than building it from source. In R, run the following command:
install.packages("igraph", type = "binary") - This should avoid compilation issues and use the precompiled version of the package.
- First, try installing the package from binary (precompiled) rather than building it from source. In R, run the following command:
-
NetworkD3:
- For the
networkD3package, ensure you have the most recent version of RStudio (version 0.99 or higher). When using this version, graphs will appear in the Viewer Pane. - You can use the
igraph_to_networkD3function to convert igraph graphs to lists compatible with netwo...
- For the
Give these steps a try, and let me know if you encounter any further issues. 🌟
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03-07-2024 06:54 AM
Hi Kaniz, type = "binary" is not supported in Databricks:
with an error message:
Error in utils install.packages(pkgs, ...) : type 'binary' is not supported on this platform
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03-07-2024 10:49 AM
Hi! I just figured this out myself. I'm not sure why this is suddenly occurring, since igraph has always loaded fine for me in databricks but didn't this week. I found that the following solution worked.
In your notebook before installing your R libraries, make a %sh chunk (just type that at the top) so the code looks like this:
```
%sh
sudo apt-get update
sudo apt-get -y install libglpk-dev
```
This should work. I found the solution here: https://github.com/igraph/rigraph/issues/490#issuecomment-966890059
SUPERSEDED BY THE TROUBLESHOOTING PAGE I am trying to install igraph from CRAN with install.packages("igraph"), and I get an error like this: In file included from feedback_arc_set.c:31: igraph_glpk_support.h:36:10: fatal error: glpk.h: ...
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