Hello, I am trying to install the igraph package onto the HPC, but am encountering some issues. Interestingly, the installation was a success in R/4.0.4 but failed in R/4.2.1. Would greatly appreciate any help!
Below is all the code and output:
install.packages(“igraph”)
Installing package into ‘/home/mjzhang/R_libs/4.2.1’
(as ‘lib’ is unspecified)
trying URL ‘https://mirror-hk.koddos.net/CRAN/src/contrib/igraph_2.0.2.tar.gz’
Content type ‘application/x-gzip’ length 4965448 bytes (4.7 MB)
==================================================
downloaded 4.7 MB
- installing source package ‘igraph’ …
** package ‘igraph’ successfully unpacked and MD5 sums checked
** using staged installation
libxml2 include directories: -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include
libxml2 library link flags: -L/share1/anaconda/3.8/lib -lxml2 -L/share1/anaconda/3.8/lib -lz -L/share1/anaconda/3.8/lib -llzma -L/share1/anaconda/3.8/lib -L/share1/anaconda/3.8/lib -licui18n -licuuc -licudata -lm -ldl
** libs
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c simpleraytracer.cpp -o simpleraytracer.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rinterface_extra.c -o rinterface_extra.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rrandom.c -o rrandom.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c rinterface.c -o rinterface.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cpp11.cpp -o cpp11.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c cpprinterface.cpp -o cpprinterface.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c lazyeval.c -o lazyeval.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c init.cpp -o init.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dnaupd.f -o vendor/arpack/dnaupd.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dstatn.f -o vendor/arpack/dstatn.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dsaupd.f -o vendor/arpack/dsaupd.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dvout.f -o vendor/arpack/dvout.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dstqrb.f -o vendor/arpack/dstqrb.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dlaqrb.f -o vendor/arpack/dlaqrb.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dsaup2.f -o vendor/arpack/dsaup2.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dmout.f -o vendor/arpack/dmout.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dngets.f -o vendor/arpack/dngets.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dneupd.f -o vendor/arpack/dneupd.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dsortc.f -o vendor/arpack/dsortc.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dnaup2.f -o vendor/arpack/dnaup2.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dseigt.f -o vendor/arpack/dseigt.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dneigh.f -o vendor/arpack/dneigh.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dseupd.f -o vendor/arpack/dseupd.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dsgets.f -o vendor/arpack/dsgets.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dnapps.f -o vendor/arpack/dnapps.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dsaitr.f -o vendor/arpack/dsaitr.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dstats.f -o vendor/arpack/dstats.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dnconv.f -o vendor/arpack/dnconv.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/second.f -o vendor/arpack/second.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dsesrt.f -o vendor/arpack/dsesrt.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dsapps.f -o vendor/arpack/dsapps.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dgetv0.f -o vendor/arpack/dgetv0.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dnaitr.f -o vendor/arpack/dnaitr.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dsortr.f -o vendor/arpack/dsortr.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/dsconv.f -o vendor/arpack/dsconv.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/wrap.f -o vendor/arpack/wrap.o
gfortran -fno-optimize-sibling-calls -fvisibility=hidden -fpic -g -O2 -c vendor/arpack/ivout.f -o vendor/arpack/ivout.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/version.c -o vendor/cigraph/src/version.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/eigenvector.c -o vendor/cigraph/src/centrality/eigenvector.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/truss.cpp -o vendor/cigraph/src/centrality/truss.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack.cpp -o vendor/cigraph/src/centrality/prpack.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/pagerank.c -o vendor/cigraph/src/centrality/pagerank.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/closeness.c -o vendor/cigraph/src/centrality/closeness.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/hub_authority.c -o vendor/cigraph/src/centrality/hub_authority.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/coreness.c -o vendor/cigraph/src/centrality/coreness.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/centralization.c -o vendor/cigraph/src/centrality/centralization.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/betweenness.c -o vendor/cigraph/src/centrality/betweenness.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/centrality_other.c -o vendor/cigraph/src/centrality/centrality_other.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack/prpack_utils.cpp -o vendor/cigraph/src/centrality/prpack/prpack_utils.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack/prpack_base_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_base_graph.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack/prpack_result.cpp -o vendor/cigraph/src/centrality/prpack/prpack_result.o
/share1/gcc/10.2.0/bin/g++ -std=gnu++14 -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/centrality/prpack/prpack_solver.cpp -o vendor/cigraph/src/centrality/prpack/prpack_solver.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/cliques/glet.c -o vendor/cigraph/src/cliques/glet.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/cliques/maximal_cliques.c -o vendor/cigraph/src/cliques/maximal_cliques.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/cliques/cliquer_wrapper.c -o vendor/cigraph/src/cliques/cliquer_wrapper.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/cliques/cliques.c -o vendor/cigraph/src/cliques/cliques.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/cliques/cliquer/cliquer.c -o vendor/cigraph/src/cliques/cliquer/cliquer.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/cliques/cliquer/reorder.c -o vendor/cigraph/src/cliques/cliquer/reorder.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/cliques/cliquer/cliquer_graph.c -o vendor/cigraph/src/cliques/cliquer/cliquer_graph.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c vendor/cigraph/src/community/voronoi.c -o vendor/cigraph/src/community/voronoi.o
/share1/gcc/10.2.0/bin/gcc -I"/share1/R/4.2.1/lib64/R/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/share1/anaconda/3.8/include/libxml2 -I/share1/anaconda/3.8/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I’/share1/R/4.2.1/lib64/R/library/cpp11/include’ -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -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: *** [/share1/R/4.2.1/lib64/R/etc/Makeconf:168: vendor/cigraph/src/community/optimal_modularity.o] Error 1
ERROR: compilation failed for package ‘igraph’ - removing ‘/home/mjzhang/R_libs/4.2.1/igraph’
The downloaded source packages are in
‘/tmp/RtmplhrkoS/downloaded_packages’
Warning message:
In install.packages(“igraph”) :
installation of package ‘igraph’ had non-zero exit status