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igraph / rigraph

igraph R package
https://r.igraph.org
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Installation failure on some CentOS systems, needs _GNU_SOURCE defined #560

Closed rLannes closed 1 year ago

rLannes commented 2 years ago

I got the following error trying to install Rigraph either using install.packages or remotes::instal_github.

I don't understand the error message, could you help me?

gcc -std=c99 -I"/ds/c7/R/4.04/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DPACKAGE_VERSION=\"1.3.4.9007\" -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/  -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -Wall -pedantic -fdiagnostics-color=always -c core/io/dl-parser.c -o core/io/dl-parser.o
   yy.tab.c:n function ‘yytnamerr
   yy.tab.c:1117:5:warning: plicit declaration of function ‘stpcpy[-Wimplicit-function-declaration]
   yy.tab.c:1117:36:error: valid operands to binary - (have ‘intand ‘char *
   yy.tab.c:1120:1:warning: reaches end of non-void function [-Wreturn-type]
   make: *** [core/io/dl-parser.o] Error 1
   ERROR: compilation failed for package ‘igraph’
─  removing ‘/tmp/Rtmp5pYjPI/Rinst9151599bae7/igraph’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'igraph' from GitHub:
  ! System command 'R' failed

If you are unsure, feel free to add your issue here - we will transfer it to
the main [igraph repo](https://github.com/igraph/igraph) if the root cause is
in the C core of igraph.

**Version information**
> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /ds/c7/R/4.04/lib64/R/lib/libRblas.so
LAPACK: /ds/c7/R/4.04/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] ps_1.7.1            prettyunits_1.1.1   withr_2.5.0         crayon_1.5.1       
 [5] rprojroot_2.0.3     R6_2.5.1            cli_3.3.0           curl_4.3.2         
 [9] rstudioapi_0.13     remotes_2.4.2       callr_3.7.1         tools_4.0.4        
[13] tinytex_0.40        xfun_0.31           compiler_4.0.4      processx_3.7.0     
[17] pkgbuild_1.3.1
szhorvat commented 2 years ago

Please post the complete output from install.packages("igraph") in a new session, which will help us pinpoint the problem.

There is likely an incompatibility with CentOS 7, which should be fixable if we understand what it is. That said, I strongly recommend against using extremely outdated systems such as CentOS 7. Note that this OS was released more than 8 years ago, and it is based on GCC 4.8, released well over 9 years ago. We cannot test igraph on such ancient systems.

rLannes commented 2 years ago

thank you for your answer, in the end I am unable to provides the full log as my sys admin installed it for me.

szhorvat commented 2 years ago

@rLannes Feel free to point your sysadmin to this issue. If they can provide the full output, it would be appreciated. This is almost certainly fixable, but we need to see the logs first.

zhpn1024 commented 1 year ago

I have the same issue:

Build log ``` install.packages("igraph") --- Please select a CRAN mirror for use in this session --- trying URL 'https://cloud.r-project.org/src/contrib/igraph_1.5.0.1.tar.gz' Content type 'application/x-gzip' length 3314208 bytes (3.2 MB) ================================================== downloaded 3.2 MB * installing *source* package ‘igraph’ ... ** package ‘igraph’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... unsupported checking for gcc option to enable C99 features... none needed checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++11 accepts -g... yes checking for g++ -std=gnu++11 option to enable C++11 features... none needed checking whether the compiler supports GNU Fortran... yes checking whether gfortran accepts -g... yes checking for expm1... yes checking for fmin... yes checking for finite... yes checking for log2... yes checking for log1p... yes checking for rint... yes checking for rintf... yes checking for round... yes checking for stpcpy... yes checking for strcasecmp... yes checking for _stricmp... no checking for strdup... yes checking for isfinite... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/times.h... yes checking for net/if.h... yes checking for netinet/in.h... yes checking for net/if_dl.h... no checking for sys/sockio.h... no checking for sys/un.h... yes checking for sys/socket.h... yes checking for sys/ioctl.h... yes checking for sys/time.h... yes checking for sys/file.h... yes checking for struct sockaddr.sa_len... no checking for xml2-config... /usr/bin/xml2-config checking for xmlSAXUserParseFile in -lxml2... yes checking for libxml/parser.h... yes checking for __gmpz_add in -lgmp... yes checking for gmp.h... yes checking how to run the C++ preprocessor... g++ -std=gnu++11 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for glp_read_mps in -lglpk... no configure: creating ./config.status config.status: creating src/Makevars.tmp config.status: creating src/Makevars config.status: creating src/config.h *** Compiler settings used: CC=gcc LD= CFLAGS=-std=c99 CPPFLAGS=-I/usr/local/include CXX=g++ -std=gnu++11 CXXFLAGS=-g -O2 LDFLAGS=-L/usr/local/lib64 LIBS= ** libs gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/centrality/betweenness.c -o core/centrality/betweenness.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/centrality/centrality_other.c -o core/centrality/centrality_other.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/centrality/centralization.c -o core/centrality/centralization.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/centrality/closeness.c -o core/centrality/closeness.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/centrality/coreness.c -o core/centrality/coreness.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack.cpp -o core/centrality/prpack.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack/prpack_base_graph.cpp -o core/centrality/prpack/prpack_base_graph.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack/prpack_igraph_graph.cpp -o core/centrality/prpack/prpack_igraph_graph.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack/prpack_preprocessed_ge_graph.cpp -o core/centrality/prpack/prpack_preprocessed_ge_graph.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack/prpack_preprocessed_gs_graph.cpp -o core/centrality/prpack/prpack_preprocessed_gs_graph.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack/prpack_preprocessed_scc_graph.cpp -o core/centrality/prpack/prpack_preprocessed_scc_graph.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack/prpack_preprocessed_schur_graph.cpp -o core/centrality/prpack/prpack_preprocessed_schur_graph.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack/prpack_result.cpp -o core/centrality/prpack/prpack_result.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack/prpack_solver.cpp -o core/centrality/prpack/prpack_solver.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/centrality/prpack/prpack_utils.cpp -o core/centrality/prpack/prpack_utils.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/cliques/cliquer/cliquer.c -o core/cliques/cliquer/cliquer.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/cliques/cliquer/cliquer_graph.c -o core/cliques/cliquer/cliquer_graph.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/cliques/cliquer/reorder.c -o core/cliques/cliquer/reorder.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/cliques/cliquer_wrapper.c -o core/cliques/cliquer_wrapper.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/cliques/cliques.c -o core/cliques/cliques.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/cliques/glet.c -o core/cliques/glet.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/cliques/maximal_cliques.c -o core/cliques/maximal_cliques.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/community_misc.c -o core/community/community_misc.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/edge_betweenness.c -o core/community/edge_betweenness.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/fast_modularity.c -o core/community/fast_modularity.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/fluid.c -o core/community/fluid.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/infomap/infomap.cc -o core/community/infomap/infomap.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/infomap/infomap_FlowGraph.cc -o core/community/infomap/infomap_FlowGraph.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/infomap/infomap_Greedy.cc -o core/community/infomap/infomap_Greedy.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/infomap/infomap_Node.cc -o core/community/infomap/infomap_Node.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/label_propagation.c -o core/community/label_propagation.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/leading_eigenvector.c -o core/community/leading_eigenvector.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/leiden.c -o core/community/leiden.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/louvain.c -o core/community/louvain.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/modularity.c -o core/community/modularity.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/community/optimal_modularity.c -o core/community/optimal_modularity.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/spinglass/NetDataTypes.cpp -o core/community/spinglass/NetDataTypes.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/spinglass/NetRoutines.cpp -o core/community/spinglass/NetRoutines.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/spinglass/clustertool.cpp -o core/community/spinglass/clustertool.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/spinglass/pottsmodel_2.cpp -o core/community/spinglass/pottsmodel_2.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/walktrap/walktrap.cpp -o core/community/walktrap/walktrap.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/walktrap/walktrap_communities.cpp -o core/community/walktrap/walktrap_communities.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/walktrap/walktrap_graph.cpp -o core/community/walktrap/walktrap_graph.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/community/walktrap/walktrap_heap.cpp -o core/community/walktrap/walktrap_heap.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/connectivity/cohesive_blocks.c -o core/connectivity/cohesive_blocks.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/connectivity/components.c -o core/connectivity/components.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/connectivity/separators.c -o core/connectivity/separators.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/adjacency.c -o core/constructors/adjacency.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/atlas.c -o core/constructors/atlas.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/basic_constructors.c -o core/constructors/basic_constructors.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/de_bruijn.c -o core/constructors/de_bruijn.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/famous.c -o core/constructors/famous.o core/constructors/famous.c: In function ‘igraph_famous’: core/constructors/famous.c:429:10: warning: implicit declaration of function ‘strcasecmp’; did you mean ‘strncmp’? [-Wimplicit-function-declaration] if (!strcasecmp(name, "bull")) { ^~~~~~~~~~ strncmp gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/full.c -o core/constructors/full.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/kautz.c -o core/constructors/kautz.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/lcf.c -o core/constructors/lcf.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/linegraph.c -o core/constructors/linegraph.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/prufer.c -o core/constructors/prufer.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/constructors/regular.c -o core/constructors/regular.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/array.c -o core/core/array.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/buckets.c -o core/core/buckets.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/cutheap.c -o core/core/cutheap.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/dqueue.c -o core/core/dqueue.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/error.c -o core/core/error.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/estack.c -o core/core/estack.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/fixed_vectorlist.c -o core/core/fixed_vectorlist.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/grid.c -o core/core/grid.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/heap.c -o core/core/heap.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/indheap.c -o core/core/indheap.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/interruption.c -o core/core/interruption.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/marked_queue.c -o core/core/marked_queue.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/matrix.c -o core/core/matrix.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/memory.c -o core/core/memory.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/printing.c -o core/core/printing.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/progress.c -o core/core/progress.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/psumtree.c -o core/core/psumtree.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/set.c -o core/core/set.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/sparsemat.c -o core/core/sparsemat.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/spmatrix.c -o core/core/spmatrix.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/stack.c -o core/core/stack.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/statusbar.c -o core/core/statusbar.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/strvector.c -o core/core/strvector.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/trie.c -o core/core/trie.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/vector.c -o core/core/vector.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/core/vector_ptr.c -o core/core/vector_ptr.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/flow/flow.c -o core/flow/flow.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/flow/st-cuts.c -o core/flow/st-cuts.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/barabasi.c -o core/games/barabasi.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/callaway_traits.c -o core/games/callaway_traits.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/citations.c -o core/games/citations.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/correlated.c -o core/games/correlated.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/degree_sequence.c -o core/games/degree_sequence.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/games/degree_sequence_vl/gengraph_box_list.cpp -o core/games/degree_sequence_vl/gengraph_box_list.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/games/degree_sequence_vl/gengraph_degree_sequence.cpp -o core/games/degree_sequence_vl/gengraph_degree_sequence.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/games/degree_sequence_vl/gengraph_graph_molloy_hash.cpp -o core/games/degree_sequence_vl/gengraph_graph_molloy_hash.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.cpp -o core/games/degree_sequence_vl/gengraph_graph_molloy_optimized.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/games/degree_sequence_vl/gengraph_mr-connected.cpp -o core/games/degree_sequence_vl/gengraph_mr-connected.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/games/degree_sequence_vl/gengraph_powerlaw.cpp -o core/games/degree_sequence_vl/gengraph_powerlaw.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/games/degree_sequence_vl/gengraph_random.cpp -o core/games/degree_sequence_vl/gengraph_random.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/dotproduct.c -o core/games/dotproduct.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/erdos_renyi.c -o core/games/erdos_renyi.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/establishment.c -o core/games/establishment.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/forestfire.c -o core/games/forestfire.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/grg.c -o core/games/grg.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/growing_random.c -o core/games/growing_random.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/islands.c -o core/games/islands.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/k_regular.c -o core/games/k_regular.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/preference.c -o core/games/preference.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/recent_degree.c -o core/games/recent_degree.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/sbm.c -o core/games/sbm.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/static_fitness.c -o core/games/static_fitness.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/tree.c -o core/games/tree.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/games/watts_strogatz.c -o core/games/watts_strogatz.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/graph/adjlist.c -o core/graph/adjlist.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/graph/attributes.c -o core/graph/attributes.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/graph/basic_query.c -o core/graph/basic_query.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/graph/cattributes.c -o core/graph/cattributes.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/graph/iterators.c -o core/graph/iterators.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/graph/type_indexededgelist.c -o core/graph/type_indexededgelist.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/graph/visitors.c -o core/graph/visitors.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/hrg/hrg.cc -o core/hrg/hrg.o g++ -std=gnu++11 -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c core/hrg/hrg_types.cc -o core/hrg/hrg_types.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/internal/glpk_support.c -o core/internal/glpk_support.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/internal/hacks.c -o core/internal/hacks.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/internal/lsap.c -o core/internal/lsap.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/internal/qsort.c -o core/internal/qsort.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/internal/qsort_r.c -o core/internal/qsort_r.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/internal/zeroin.c -o core/internal/zeroin.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/io/dimacs.c -o core/io/dimacs.o gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/io/dl-lexer.c -o core/io/dl-lexer.o src/core/io/dl-lexer.c: In function ‘igraph_dl_yy_init_buffer’: src/core/io/dl-lexer.c:1878:48: warning: implicit declaration of function ‘fileno’; did you mean ‘mblen’? [-Wimplicit-function-declaration] gcc -I"/usr/local/lib64/R/include" -DNDEBUG -DUSING_R -I. -Icore -Iinclude -Ivendor -I/usr/include/libxml2 -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DPRPACK_IGRAPH_SUPPORT -DIGRAPH_THREAD_LOCAL=/**/ -I'/usr/local/lib64/R/library/cpp11/include' -I/usr/local/include -fvisibility=hidden -fpic -std=c99 -c core/io/dl-parser.c -o core/io/dl-parser.o yy.tab.c: In function ‘yytnamerr’: yy.tab.c:1125:20: warning: implicit declaration of function ‘stpcpy’; did you mean ‘strcpy’? [-Wimplicit-function-declaration] yy.tab.c:1187:12: note: in expansion of macro ‘yystpcpy’ yy.tab.c:1187:36: error: invalid operands to binary - (have ‘int’ and ‘char *’) make: *** [core/io/dl-parser.o] Error 1 ERROR: compilation failed for package ‘igraph’ * removing ‘/usr/local/lib64/R/library/igraph’ The downloaded source packages are in ‘/tmp/Rtmph7LGxw/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages("igraph") : installation of package ‘igraph’ had non-zero exit status > ```
szhorvat commented 1 year ago

Please indicate your operating system and it version, as well as the GCC version you have (gcc --version). Also post the output of executing sessionInfo() in R.

zhpn1024 commented 1 year ago 
> sessionInfo()

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /usr/local/lib64/R/lib/libRblas.so
LAPACK: /usr/local/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3    tcltk_4.0.3
gcc --version
gcc (GCC) 8.4.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
uname -a
Linux T01 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

cat /proc/version
Linux version 3.10.0-1160.el7.x86_64 (mockbuild@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) ) #1 SMP Mon Oct 19 16:18:59 UTC 2020

cat /etc/redhat-release
CentOS Linux release 7.9.2009 (Core)
szhorvat commented 1 year ago

The headers on your system do not seem to include POSIX-standard functions such as strcasecmp, fileno or stpcpy, even though igraph does define _GNU_SOURCE.

I am not sure why this is. I wonder if you get any errors when you compile this C program:

// test.c

#include <string.h>

int main(void) {
    char *a = "abc", *b = "def";
    stpcpy(a,b);
    return 0;
}

Do you get any errors when you compile in the following ways?

gcc test.c
gcc -D_GNU_SOURCE=1 test.c
gcc -D_POSIX_C_SOURCE=200809L test.c

To look into this properly, we'll need access to a CentOS 7 system, which will take time.

I should note that CentOS has been discontinued. CentOS 8 is already unsupported, and CentOS 7 (which is nearly 10 years old!) will lose all support in less than a year. https://endoflife.date/centos I suggest you do not use this extremely outdated operating system.

zhpn1024 commented 1 year ago

All the gcc commands ran with no error, but running the output file has the error: Segmentation fault (core dumped)

ntamas commented 1 year ago

Looking into this in a Docker container with CentOS 7, FYI.

ntamas commented 1 year ago

I cannot reproduce this problem in a clean CentOS 7 Docker container with R 4.0.3, installed from an official RPM package from cdn.rstudio.com (since CentOS 7 originally comes with R 3.6.0). install.packages("igraph") works just fine in this environment.

Output of sessionInfo():

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.0.3 tools_4.0.3

GCC version (standard, from CentOS 7):

[root@4daed352a77c /]# gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)

Other relevant info:

[root@4daed352a77c /]# uname -a
Linux 4daed352a77c 5.10.124-linuxkit #1 SMP PREEMPT Thu Jun 30 08:18:26 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
[root@4daed352a77c /]# cat /proc/version
Linux version 5.10.124-linuxkit (root@buildkitsandbox) (gcc (Alpine 10.2.1_pre1) 10.2.1 20201203, GNU ld (GNU Binutils) 2.35.2) #1 SMP PREEMPT Thu Jun 30 08:18:26 UTC 2022
[root@4daed352a77c /]# cat /etc/redhat-release
CentOS Linux release 7.9.2009 (Core)
zhpn1024 commented 1 year ago

It seems the main difference is the gcc version 4.8.5 vs 8.4.0

szhorvat commented 1 year ago

I tried with GCC 8.3.1 installed from official CentOS repositories like so: https://unix.stackexchange.com/a/508769/309566 I still cannot reproduce the issue. There is something special about your setup that prevents POSIX functions from being visible to the compiler.

At this point we have to stop putting effort into this, considering that:

You might try the following:

Create ~/.R/Makevars if it does not exist yet, and add the following to it:

CPPFLAGS += -D_GNU_SOURCE=1
zhpn1024 commented 1 year ago

The CPPFLAGS works. Thank you!

szhorvat commented 1 year ago

Thanks for the feedback about that. We'll apply this fix to the next version then. Can you add that compiler option, @krlmlr ?

github-actions[bot] commented 2 months ago

This old thread has been automatically locked. If you think you have found something related to this, please open a new issue and link to this old issue if necessary.