'glpk.h' file not found on MacOS

joshua-zh commented 8 months ago

What happens?

When I installed rigraph from github, the error popped out. But I have installed glpk via Brew in the terminal.

In file included from vendor/cigraph/src/misc/feedback_arc_set.c:35: vendor/cigraph/src/internal/glpk_support.h:39:10: fatal error: 'glpk.h' file not found 39 | #include | ^~~~ 1 error generated. make: *** [vendor/cigraph/src/misc/feedback_arc_set.o] Error 1 ERROR: compilation failed for package ‘igraph’

removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/igraph’
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/igraph’ Warning message: In i.p(...) : installation of package ‘/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T//RtmpaOtbc1/file3f2e70c662ad/igraph_1.6.0.9006.tar.gz’ had non-zero exit status

To Reproduce

devtools::install_github("igraph/rigraph")

sessionInfo() R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.2

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Shanghai tzcode source: internal

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

loaded via a namespace (and not attached): [1] vctrs_0.6.5 cli_3.6.2 rlang_1.1.2.9000 stringi_1.8.3 processx_3.8.3 purrr_1.0.2
[7] pkgload_1.3.3 promises_1.2.1 shiny_1.8.0 xtable_1.8-4 glue_1.6.2 htmltools_0.5.7
[13] httpuv_1.6.13 pkgbuild_1.4.3.9000 ps_1.7.5 ellipsis_0.3.2 fastmap_1.1.1 lifecycle_1.0.4
[19] memoise_2.0.1 stringr_1.5.1 compiler_4.3.2 miniUI_0.1.1.1 sessioninfo_1.2.2 fs_1.6.3
[25] htmlwidgets_1.6.4 Rcpp_1.0.11 urlchecker_1.0.1 rstudioapi_0.15.0 later_1.3.2 digest_0.6.33
[31] R6_2.5.1 usethis_2.2.2 curl_5.2.0 callr_3.7.3 magrittr_2.0.3 tools_4.3.2
[37] mime_0.12 devtools_2.4.5 profvis_0.3.8 remotes_2.4.2.1 cachem_1.0.8 desc_1.4.3

krlmlr commented 8 months ago

Thanks. Can you please share the complete output of R CMD INSTALL . or devtools::install_github(), preferably formatted as code (with triple backticks ```) ?

joshua-zh commented 8 months ago

Thank you for your responding.

devtools::install_github("igraph/rigraph")
Downloading GitHub repo igraph/rigraph@HEAD
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T/RtmpWf22dv/remotesb55050b33daf/igraph-rigraph-a84e7e5/DESCRIPTION’ ...
─  preparing ‘igraph’: (435ms)
✔  checking DESCRIPTION meta-information
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts (613ms)
─  checking for empty or unneeded directories (342ms)
   Removed empty directory ‘igraph/.aviator’
─  building ‘igraph_1.6.0.9007.tar.gz’

* installing *source* package ‘igraph’ ...
** using staged installation
libxml2 include directory: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
** libs
using C compiler: ‘Homebrew clang version 17.0.6’
using C++ compiler: ‘Homebrew clang version 17.0.6’
using SDK: ‘MacOSX14.2.sdk’
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.cpp -o init.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cpp11.cpp -o cpp11.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rinterface_extra.c -o rinterface_extra.o
rinterface_extra.c:417:56: warning: STR() is deprecated. Use igraph_strvector_get() instead. [-W#pragma-messages]
  417 |         SET_STRING_ELT(VECTOR_ELT(gal,i), 0, Rf_mkChar(STR(*strvec, 0)));
      |                                                        ^
vendor/cigraph/include/igraph_strvector.h:62:6: note: expanded from macro 'STR'
   62 |     (IGRAPH_PREPROCESSOR_WARNING("STR() is deprecated. Use igraph_strvector_get() instead.") \
      |      ^
vendor/cigraph/include/igraph_error.h:72:45: note: expanded from macro 'IGRAPH_PREPROCESSOR_WARNING'
   72 | #define IGRAPH_PREPROCESSOR_WARNING(reason) _Pragma(IGRAPH_I_STRINGIFY(GCC warning reason))
      |                                             ^
<scratch space>:27:6: note: expanded from here
   27 |  GCC warning "STR() is deprecated. Use igraph_strvector_get() instead."
      |      ^
rinterface_extra.c:3149:18: warning: 'igraph_incidence' is deprecated [-Wdeprecated-declarations]
 3149 |   IGRAPH_R_CHECK(igraph_incidence(&c_graph, &c_types, &c_incidence, c_directed, c_mode, c_multiple));
      |                  ^
vendor/cigraph/include/igraph_bipartite.h:92:15: note: 'igraph_incidence' has been explicitly marked deprecated here
   92 | IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_incidence(
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface_extra.c:3261:34: warning: incompatible pointer types passing 'int *' to parameter of type 'igraph_integer_t *' (aka 'long long *') [-Wincompatible-pointer-types]
 3261 |                           /*p=*/ INTEGER(p), /*i=*/ INTEGER(i),
      |                                  ^~~~~~~~~~
vendor/cigraph/include/igraph_sparsemat.h:276:59: note: passing argument to parameter 'p' here
  276 |                                         igraph_integer_t *p, igraph_integer_t *i, igraph_real_t *x, igraph_integer_t nz);
      |                                                           ^
rinterface_extra.c:3261:53: warning: incompatible pointer types passing 'int *' to parameter of type 'igraph_integer_t *' (aka 'long long *') [-Wincompatible-pointer-types]
 3261 |                           /*p=*/ INTEGER(p), /*i=*/ INTEGER(i),
      |                                                     ^~~~~~~~~~
vendor/cigraph/include/igraph_sparsemat.h:276:80: note: passing argument to parameter 'i' here
  276 |                                         igraph_integer_t *p, igraph_integer_t *i, igraph_real_t *x, igraph_integer_t nz);
      |                                                                                ^
rinterface_extra.c:4416:18: warning: 'igraph_lattice' is deprecated [-Wdeprecated-declarations]
 4416 |   IGRAPH_R_CHECK(igraph_lattice(&g, &dimvector, nei, directed, mutual, circular));
      |                  ^
vendor/cigraph/include/igraph_constructors.h:58:15: note: 'igraph_lattice' has been explicitly marked deprecated here
   58 | IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_lattice(igraph_t *graph, const igraph_vector_int_t *dimvector, igraph_integer_t nei,
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface_extra.c:5004:3: warning: 'igraph_erdos_renyi_game' is deprecated [-Wdeprecated-declarations]
 5004 |   igraph_erdos_renyi_game(&g, (igraph_erdos_renyi_t) type, n, porm, directed,
      |   ^
vendor/cigraph/include/igraph_games.h:222:15: note: 'igraph_erdos_renyi_game' has been explicitly marked deprecated here
  222 | IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_erdos_renyi_game(
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface_extra.c:6479:18: warning: 'igraph_read_graph_dimacs' is deprecated [-Wdeprecated-declarations]
 6479 |   IGRAPH_R_CHECK(igraph_read_graph_dimacs(&g, file, &problem, &label, &source, &target, &cap, directed));
      |                  ^
vendor/cigraph/include/igraph_foreign.h:53:15: note: 'igraph_read_graph_dimacs' has been explicitly marked deprecated here
   53 | IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_read_graph_dimacs(igraph_t *graph, FILE *instream,
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface_extra.c:6481:15: warning: STR() is deprecated. Use igraph_strvector_get() instead. [-W#pragma-messages]
 6481 |   if (!strcmp(STR(problem, 0), "max")) {
      |               ^
vendor/cigraph/include/igraph_strvector.h:62:6: note: expanded from macro 'STR'
   62 |     (IGRAPH_PREPROCESSOR_WARNING("STR() is deprecated. Use igraph_strvector_get() instead.") \
      |      ^
vendor/cigraph/include/igraph_error.h:72:45: note: expanded from macro 'IGRAPH_PREPROCESSOR_WARNING'
   72 | #define IGRAPH_PREPROCESSOR_WARNING(reason) _Pragma(IGRAPH_I_STRINGIFY(GCC warning reason))
      |                                             ^
<scratch space>:202:6: note: expanded from here
  202 |  GCC warning "STR() is deprecated. Use igraph_strvector_get() instead."
      |      ^
rinterface_extra.c:6494:22: warning: STR() is deprecated. Use igraph_strvector_get() instead. [-W#pragma-messages]
 6494 |   } else if (!strcmp(STR(problem, 0), "edge")) {
      |                      ^
vendor/cigraph/include/igraph_strvector.h:62:6: note: expanded from macro 'STR'
   62 |     (IGRAPH_PREPROCESSOR_WARNING("STR() is deprecated. Use igraph_strvector_get() instead.") \
      |      ^
vendor/cigraph/include/igraph_error.h:72:45: note: expanded from macro 'IGRAPH_PREPROCESSOR_WARNING'
   72 | #define IGRAPH_PREPROCESSOR_WARNING(reason) _Pragma(IGRAPH_I_STRINGIFY(GCC warning reason))
      |                                             ^
<scratch space>:205:6: note: expanded from here
  205 |  GCC warning "STR() is deprecated. Use igraph_strvector_get() instead."
      |      ^
rinterface_extra.c:6537:18: warning: 'igraph_write_graph_dimacs' is deprecated [-Wdeprecated-declarations]
 6537 |   IGRAPH_R_CHECK(igraph_write_graph_dimacs(&g, stream, source, target, &cap));
      |                  ^
vendor/cigraph/include/igraph_foreign.h:89:15: note: 'igraph_write_graph_dimacs' has been explicitly marked deprecated here
   89 | IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_write_graph_dimacs(const igraph_t *graph, FILE *outstream,
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface_extra.c:8327:18: warning: 'igraph_laplacian' is deprecated [-Wdeprecated-declarations]
 8327 |   IGRAPH_R_CHECK(igraph_laplacian(&c_graph, (c_sparse ? 0 : &c_res), (c_sparse ? &c_sparseres : 0), c_normalized, (Rf_isNull(weights) ? 0 : &c_weights)));
      |                  ^
vendor/cigraph/include/igraph_structural.h:164:15: note: 'igraph_laplacian' has been explicitly marked deprecated here
  164 | IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_laplacian(
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
11 warnings generated.
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cpprinterface.cpp -o cpprinterface.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c lazyeval.c -o lazyeval.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rinterface.c -o rinterface.o
rinterface.c:3853:18: warning: 'igraph_hub_score' is deprecated [-Wdeprecated-declarations]
 3853 |   IGRAPH_R_CHECK(igraph_hub_score(&c_graph, &c_vector, &c_value, c_scale, (Rf_isNull(weights) ? 0 : &c_weights), &c_options));
      |                  ^
vendor/cigraph/include/igraph_centrality.h:193:1: note: 'igraph_hub_score' has been explicitly marked deprecated here
  193 | IGRAPH_DEPRECATED IGRAPH_EXPORT igraph_error_t igraph_hub_score(const igraph_t *graph, igraph_vector_t *vector,
      | ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface.c:3902:18: warning: 'igraph_authority_score' is deprecated [-Wdeprecated-declarations]
 3902 |   IGRAPH_R_CHECK(igraph_authority_score(&c_graph, &c_vector, &c_value, c_scale, (Rf_isNull(weights) ? 0 : &c_weights), &c_options));
      |                  ^
vendor/cigraph/include/igraph_centrality.h:197:1: note: 'igraph_authority_score' has been explicitly marked deprecated here
  197 | IGRAPH_DEPRECATED IGRAPH_EXPORT igraph_error_t igraph_authority_score(const igraph_t *graph, igraph_vector_t *vector,
      | ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface.c:5300:18: warning: 'igraph_random_edge_walk' is deprecated [-Wdeprecated-declarations]
 5300 |   IGRAPH_R_CHECK(igraph_random_edge_walk(&c_graph, (Rf_isNull(weights) ? 0 : &c_weights), &c_edgewalk, c_start, c_mode, c_steps, c_stuck));
      |                  ^
vendor/cigraph/include/igraph_paths.h:354:15: note: 'igraph_random_edge_walk' has been explicitly marked deprecated here
  354 | IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_random_edge_walk(const igraph_t *graph,
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface.c:5927:18: warning: 'igraph_bipartite_game' is deprecated [-Wdeprecated-declarations]
 5927 |   IGRAPH_R_CHECK(igraph_bipartite_game(&c_graph, &c_types, c_type, c_n1, c_n2, c_p, c_m, c_directed, c_mode));
      |                  ^
vendor/cigraph/include/igraph_bipartite.h:102:15: note: 'igraph_bipartite_game' has been explicitly marked deprecated here
  102 | IGRAPH_EXPORT IGRAPH_DEPRECATED  igraph_error_t igraph_bipartite_game(
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface.c:6354:84: warning: variable 'c_outfile' is uninitialized when used here [-Wuninitialized]
 6354 |   IGRAPH_R_CHECK(igraph_maximal_cliques_subset(&c_graph, &c_subset, &c_res, &c_no, c_outfile, c_min_size, c_max_size));
      |                                                                                    ^~~~~~~~~
./rinterface.h:40:35: note: expanded from macro 'IGRAPH_R_CHECK'
   40 |         igraph_error_type_t __c = func; \
      |                                   ^~~~
rinterface.c:6336:18: note: initialize the variable 'c_outfile' to silence this warning
 6336 |   FILE* c_outfile;
      |                  ^
      |                   = NULL
rinterface.c:8316:58: warning: variable 'c_instream' is uninitialized when used here [-Wuninitialized]
 8316 |   IGRAPH_R_CHECK(igraph_read_graph_dimacs_flow(&c_graph, c_instream, &c_problem, &c_label, &c_source, &c_target, &c_capacity, c_directed));
      |                                                          ^~~~~~~~~~
./rinterface.h:40:35: note: expanded from macro 'IGRAPH_R_CHECK'
   40 |         igraph_error_type_t __c = func; \
      |                                   ^~~~
rinterface.c:8284:19: note: initialize the variable 'c_instream' to silence this warning
 8284 |   FILE* c_instream;
      |                   ^
      |                    = NULL
rinterface.c:8376:59: warning: variable 'c_outstream' is uninitialized when used here [-Wuninitialized]
 8376 |   IGRAPH_R_CHECK(igraph_write_graph_dimacs_flow(&c_graph, c_outstream, c_source, c_target, &c_capacity));
      |                                                           ^~~~~~~~~~~
./rinterface.h:40:35: note: expanded from macro 'IGRAPH_R_CHECK'
   40 |         igraph_error_type_t __c = func; \
      |                                   ^~~~
rinterface.c:8363:20: note: initialize the variable 'c_outstream' to silence this warning
 8363 |   FILE* c_outstream;
      |                    ^
      |                     = NULL
rinterface.c:9970:18: warning: 'igraph_subisomorphic_function_vf2' is deprecated [-Wdeprecated-declarations]
 9970 |   IGRAPH_R_CHECK(igraph_subisomorphic_function_vf2(&c_graph1, &c_graph2, (Rf_isNull(vertex_color1) ? 0 : (Rf_isNull(vertex_color1) ? 0 : &c_vertex_color1)), (Rf_isNull(vertex_color2) ? 0 : (Rf_isNull(vertex_color2) ? 0 : &c_vertex_color2)), (Rf_isNull(edge_color1) ? 0 : (Rf_isNull(edge_color1) ? 0 : &c_edge_color1)), (Rf_isNull(edge_color2) ? 0 : (Rf_isNull(edge_color2) ? 0 : &c_edge_color2)), &c_map12, &c_map21, 0, 0, 0, 0));
      |                  ^
vendor/cigraph/include/igraph_topology.h:209:15: note: 'igraph_subisomorphic_function_vf2' has been explicitly marked deprecated here
  209 | IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_subisomorphic_function_vf2(
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface.c:10808:33: warning: variable 'c_a' is uninitialized when used here [-Wuninitialized]
 10808 |   c_result=igraph_almost_equals(c_a, c_b, c_eps);
       |                                 ^~~
rinterface.c:10800:13: note: initialize the variable 'c_a' to silence this warning
 10800 |   double c_a;
       |             ^
       |              = 0.0
rinterface.c:10808:38: warning: variable 'c_b' is uninitialized when used here [-Wuninitialized]
 10808 |   c_result=igraph_almost_equals(c_a, c_b, c_eps);
       |                                      ^~~
rinterface.c:10801:13: note: initialize the variable 'c_b' to silence this warning
 10801 |   double c_b;
       |             ^
       |              = 0.0
rinterface.c:10808:43: warning: variable 'c_eps' is uninitialized when used here [-Wuninitialized]
 10808 |   c_result=igraph_almost_equals(c_a, c_b, c_eps);
       |                                           ^~~~~
rinterface.c:10802:15: note: initialize the variable 'c_eps' to silence this warning
 10802 |   double c_eps;
       |               ^
       |                = 0.0
rinterface.c:10827:7: warning: variable 'c_result' set but not used [-Wunused-but-set-variable]
 10827 |   int c_result;
       |       ^
rinterface.c:10832:31: warning: variable 'c_a' is uninitialized when used here [-Wuninitialized]
 10832 |   c_result=igraph_cmp_epsilon(c_a, c_b, c_eps);
       |                               ^~~
rinterface.c:10824:13: note: initialize the variable 'c_a' to silence this warning
 10824 |   double c_a;
       |             ^
       |              = 0.0
rinterface.c:10832:36: warning: variable 'c_b' is uninitialized when used here [-Wuninitialized]
 10832 |   c_result=igraph_cmp_epsilon(c_a, c_b, c_eps);
       |                                    ^~~
rinterface.c:10825:13: note: initialize the variable 'c_b' to silence this warning
 10825 |   double c_b;
       |             ^
       |              = 0.0
rinterface.c:10832:41: warning: variable 'c_eps' is uninitialized when used here [-Wuninitialized]
 10832 |   c_result=igraph_cmp_epsilon(c_a, c_b, c_eps);
       |                                         ^~~~~
rinterface.c:10826:15: note: initialize the variable 'c_eps' to silence this warning
 10826 |   double c_eps;
       |               ^
       |                = 0.0
rinterface.c:10839:10: warning: variable 'r_result' is uninitialized when used here [-Wuninitialized]
 10839 |   return(r_result);
       |          ^~~~~~~~
rinterface.c:10828:16: note: initialize the variable 'r_result' to silence this warning
 10828 |   SEXP r_result;
       |                ^
       |                 = NULL
rinterface.c:11635:7: warning: unused variable 'c_result' [-Wunused-variable]
 11635 |   int c_result;
       |       ^~~~~~~~
rinterface.c:11647:10: warning: variable 'r_result' is uninitialized when used here [-Wuninitialized]
 11647 |   return(r_result);
       |          ^~~~~~~~
rinterface.c:11636:16: note: initialize the variable 'r_result' to silence this warning
 11636 |   SEXP r_result;
       |                ^
       |                 = NULL
rinterface.c:11657:7: warning: unused variable 'c_result' [-Wunused-variable]
 11657 |   int c_result;
       |       ^~~~~~~~
rinterface.c:11669:10: warning: variable 'r_result' is uninitialized when used here [-Wuninitialized]
 11669 |   return(r_result);
       |          ^~~~~~~~
rinterface.c:11658:16: note: initialize the variable 'r_result' to silence this warning
 11658 |   SEXP r_result;
       |                ^
       |                 = NULL
rinterface.c:11678:15: warning: variable 'c_result' set but not used [-Wunused-but-set-variable]
 11678 |   const char* c_result;
       |               ^
rinterface.c:11683:28: warning: variable 'c_igraph_errno' is uninitialized when used here [-Wuninitialized]
 11683 |   c_result=igraph_strerror(c_igraph_errno);
       |                            ^~~~~~~~~~~~~~
rinterface.c:11677:21: note: initialize the variable 'c_igraph_errno' to silence this warning
 11677 |   int c_igraph_errno;
       |                     ^
       |                      = 0
rinterface.c:11690:10: warning: variable 'r_result' is uninitialized when used here [-Wuninitialized]
 11690 |   return(r_result);
       |          ^~~~~~~~
rinterface.c:11679:16: note: initialize the variable 'r_result' to silence this warning
 11679 |   SEXP r_result;
       |                ^
       |                 = NULL
rinterface.c:11798:31: warning: variable 'version_string' is uninitialized when used here [-Wuninitialized]
 11798 |   SET_VECTOR_ELT(r_result, 0, version_string);
       |                               ^~~~~~~~~~~~~~
rinterface.c:11784:22: note: initialize the variable 'version_string' to silence this warning
 11784 |   SEXP version_string;
       |                      ^
       |                       = NULL
rinterface.c:11799:31: warning: variable 'major' is uninitialized when used here [-Wuninitialized]
 11799 |   SET_VECTOR_ELT(r_result, 1, major);
       |                               ^~~~~
rinterface.c:11785:13: note: initialize the variable 'major' to silence this warning
 11785 |   SEXP major;
       |             ^
       |              = NULL
rinterface.c:11800:31: warning: variable 'minor' is uninitialized when used here [-Wuninitialized]
 11800 |   SET_VECTOR_ELT(r_result, 2, minor);
       |                               ^~~~~
rinterface.c:11786:13: note: initialize the variable 'minor' to silence this warning
 11786 |   SEXP minor;
       |             ^
       |              = NULL
rinterface.c:11801:31: warning: variable 'subminor' is uninitialized when used here [-Wuninitialized]
 11801 |   SET_VECTOR_ELT(r_result, 3, subminor);
       |                               ^~~~~~~~
rinterface.c:11787:16: note: initialize the variable 'subminor' to silence this warning
 11787 |   SEXP subminor;
       |                ^
       |                 = NULL
rinterface.c:11829:18: warning: 'igraph_get_stochastic_sparsemat' is deprecated [-Wdeprecated-declarations]
 11829 |   IGRAPH_R_CHECK(igraph_get_stochastic_sparsemat(&c_graph, &c_sparsemat, c_column_wise));
       |                  ^
vendor/cigraph/include/igraph_conversion.h:65:15: note: 'igraph_get_stochastic_sparsemat' has been explicitly marked deprecated here
   65 | IGRAPH_EXPORT IGRAPH_DEPRECATED igraph_error_t igraph_get_stochastic_sparsemat(const igraph_t *graph,
      |               ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
rinterface.c:11853:18: warning: 'igraph_hrg_dendrogram' is deprecated [-Wdeprecated-declarations]
 11853 |   IGRAPH_R_CHECK(igraph_hrg_dendrogram(&c_graph, &c_hrg));
       |                  ^
vendor/cigraph/include/igraph_hrg.h:126:1: note: 'igraph_hrg_dendrogram' has been explicitly marked deprecated here
  126 | IGRAPH_DEPRECATED IGRAPH_EXPORT igraph_error_t igraph_hrg_dendrogram(
      | ^
vendor/igraph_export.h:7:43: note: expanded from macro 'IGRAPH_DEPRECATED'
    7 | #define IGRAPH_DEPRECATED __attribute__ ((__deprecated__))
      |                                           ^
29 warnings generated.
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rrandom.c -o rrandom.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/dl-parser.c -o vendor/io/dl-parser.o
src/vendor/cigraph/src/io/dl-parser.y:242:55: warning: STR() is deprecated. Use igraph_strvector_get() instead. [-W#pragma-messages]
  242 |       IGRAPH_YY_CHECK(igraph_trie_get(&context->trie, STR(context->labels, i), &id));
      |                                                       ^
vendor/cigraph/include/igraph_strvector.h:62:6: note: expanded from macro 'STR'
   62 |     (IGRAPH_PREPROCESSOR_WARNING("STR() is deprecated. Use igraph_strvector_get() instead.") \
      |      ^
vendor/cigraph/include/igraph_error.h:72:45: note: expanded from macro 'IGRAPH_PREPROCESSOR_WARNING'
   72 | #define IGRAPH_PREPROCESSOR_WARNING(reason) _Pragma(IGRAPH_I_STRINGIFY(GCC warning reason))
      |                                             ^
yy.tab.c:1376:9: warning: variable 'igraph_dl_yynerrs' set but not used [-Wunused-but-set-variable]
 1376 |     int yynerrs = 0;
      |         ^
vendor/io/dl-parser.c:72:25: note: expanded from macro 'yynerrs'
   72 | #define yynerrs         igraph_dl_yynerrs
      |                         ^
2 warnings generated.
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/ncol-lexer.c -o vendor/io/ncol-lexer.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/gml-parser.c -o vendor/io/gml-parser.o
yy.tab.c:1293:9: warning: variable 'igraph_gml_yynerrs' set but not used [-Wunused-but-set-variable]
 1293 |     int yynerrs = 0;
      |         ^
vendor/io/gml-parser.c:72:25: note: expanded from macro 'yynerrs'
   72 | #define yynerrs         igraph_gml_yynerrs
      |                         ^
1 warning generated.
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/ncol-parser.c -o vendor/io/ncol-parser.o
yy.tab.c:1239:9: warning: variable 'igraph_ncol_yynerrs' set but not used [-Wunused-but-set-variable]
 1239 |     int yynerrs = 0;
      |         ^
vendor/io/ncol-parser.c:72:25: note: expanded from macro 'yynerrs'
   72 | #define yynerrs         igraph_ncol_yynerrs
      |                         ^
1 warning generated.
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/gml-lexer.c -o vendor/io/gml-lexer.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/dl-lexer.c -o vendor/io/dl-lexer.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/lgl-parser.c -o vendor/io/lgl-parser.o
yy.tab.c:1246:9: warning: variable 'igraph_lgl_yynerrs' set but not used [-Wunused-but-set-variable]
 1246 |     int yynerrs = 0;
      |         ^
vendor/io/lgl-parser.c:72:25: note: expanded from macro 'yynerrs'
   72 | #define yynerrs         igraph_lgl_yynerrs
      |                         ^
1 warning generated.
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/lgl-lexer.c -o vendor/io/lgl-lexer.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/pajek-lexer.c -o vendor/io/pajek-lexer.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/io/pajek-parser.c -o vendor/io/pajek-parser.o
yy.tab.c:1531:9: warning: variable 'igraph_pajek_yynerrs' set but not used [-Wunused-but-set-variable]
 1531 |     int yynerrs = 0;
      |         ^
vendor/io/pajek-parser.c:72:25: note: expanded from macro 'yynerrs'
   72 | #define yynerrs         igraph_pajek_yynerrs
      |                         ^
1 warning generated.
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/version.c -o vendor/cigraph/src/version.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/parse_utils.c -o vendor/cigraph/src/io/parse_utils.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/dl.c -o vendor/cigraph/src/io/dl.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/edgelist.c -o vendor/cigraph/src/io/edgelist.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/dimacs.c -o vendor/cigraph/src/io/dimacs.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/gml.c -o vendor/cigraph/src/io/gml.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/graphml.c -o vendor/cigraph/src/io/graphml.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/ncol.c -o vendor/cigraph/src/io/ncol.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/dot.c -o vendor/cigraph/src/io/dot.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/lgl.c -o vendor/cigraph/src/io/lgl.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/pajek.c -o vendor/cigraph/src/io/pajek.o
vendor/cigraph/src/io/pajek.c:517:22: warning: variable 'notop' set but not used [-Wunused-but-set-variable]
  517 |     igraph_integer_t notop = 0, nobottom = 0;
      |                      ^
1 warning generated.
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/leda.c -o vendor/cigraph/src/io/leda.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/gml-tree.c -o vendor/cigraph/src/io/gml-tree.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/io/graphdb.c -o vendor/cigraph/src/io/graphdb.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/misc/degree_sequence.cpp -o vendor/cigraph/src/misc/degree_sequence.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/misc/feedback_arc_set.c -o vendor/cigraph/src/misc/feedback_arc_set.o
In file included from vendor/cigraph/src/misc/feedback_arc_set.c:35:
vendor/cigraph/src/internal/glpk_support.h:39:10: fatal error: 'glpk.h' file not found
   39 | #include <glpk.h>
      |          ^~~~~~~~
1 error generated.
make: *** [vendor/cigraph/src/misc/feedback_arc_set.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/igraph’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/igraph’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T//RtmpWf22dv/fileb55024570071/igraph_1.6.0.9007.tar.gz’ had non-zero exit status

krlmlr commented 8 months ago

@Antonov548: The failing compilation line is:

clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c vendor/cigraph/src/misc/feedback_arc_set.c -o vendor/cigraph/src/misc/feedback_arc_set.o

Do we need to find the installed glpk, or maybe use an autobrew approach as in RPostgres?

szhorvat commented 8 months ago

There's also a vendored GLPK ... The only reason not to use it is that CRAN would keep asking us to fix things in it (lots of compiler warnings). Otherwise, as far as I can see, there are only advantages to using the vendored version: You get the latest version, and you get slightly better error handling thanks to some small patches we made.

krlmlr commented 6 months ago

@joshua-zh: Did you manage to install igraph? Version 2.0.2 has hit CRAN, with all binaries built.

To install from source, you probably need brew install glpk .

joshua-zh commented 6 months ago

Thank you for your response. I have installed glpk via Brew, but the error appeared again, and the installation still failed for the version 2.0.2.

szhorvat commented 6 months ago

Why are you compiling igraph yourself instead of using the binaries provided by CRAN, as suggested in the troubleshooting instructions?

If you just want to try a recent development version, you can still get binaries from R-universe: https://igraph.r-universe.dev/igraph

If you choose to compile it yourself, expect to have to do additional setup, such as communicating the location of the required libraries to R by setting the appropriate entries in your ~/.R/Makevars file.

krlmlr commented 6 months ago

Weird. Can you please share the complete log from install.packages() ?

szhorvat commented 6 months ago

I wasn't able to finish my comment earlier. I use MacPorts to install libraries, and I need to provide this information in my Makevars file, otherwise the compiler won't find the libraries. MacPorts uses /opt/local as the prefix, so I have:

CPPFLAGS=-I/opt/local/include
LDFLAGS=-L/opt/local/lib

(And a bunch of other things necessary with MacPorts, which I won't share to avoid confusion. For Homebrew it wouldn't be the same.)

joshua-zh commented 6 months ago

pak::pak("igraph/rigraph")
! Using bundled GitHub PAT. Please add your own PAT using `gitcreds::gitcreds_set()`.
✔ Updated metadata database: 4.96 MB in 8 files.                           
ℹ R 4.3 aarch64-apple-darwin20 packages are missing from Bioconductor       
✔ Updating metadata database ... done                                      

→ Will update 1 package.
→ Will download 1 package with unknown size.
+ igraph 2.0.2 → 2.0.2.9003 👷🏽‍♂️🔧 ⬇ (GitHub: 63dfd0f)
? Do you want to continue (Y/n) Y
ℹ Getting 1 pkg with unknown size
✔ Cached copy of igraph 2.0.2.9003 (source) is the latest build
✔ No downloads needed, all packages are cached
ℹ Building igraph 2.0.2.9003
✖ Failed to build igraph 2.0.2.9003                               
Error:                                                            
! error in pak subprocess
Caused by error in `stop_task_build(state, worker)`:
! Failed to build source package 'igraph'
Full installation output:
* installing *source* package ‘igraph’ ...
staged installation is only possible with locking
** using non-staged installation
libxml2 include directories: -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
libxml2 library link flags: -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -lxml2 -lz -lpthread -licucore -lm
** libs
using C compiler: ‘Homebrew clang version 17.0.6’
using C++ compiler: ‘Homebrew clang version 17.0.6’
using SDK: ‘MacOSX14.2.sdk’
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c simpleraytracer.cpp -o simpleraytracer.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c rinterface_extra.c -o rinterface_extra.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c rrandom.c -o rrandom.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c rinterface.c -o rinterface.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c cpp11.cpp -o cpp11.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c cpprinterface.cpp -o cpprinterface.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c lazyeval.c -o lazyeval.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c init.cpp -o init.o
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dnaupd.f -o vendor/arpack/dnaupd.o
vendor/arpack/dnaupd.f:541:25:

  541 |          if (nb .le. 0)                         nb = 1
      |                         1~~~~~~~
Warning: Nonconforming tab character at (1) [-Wtabs]
vendor/arpack/dnaupd.f:542:29:

  542 |          if (tol .le. zero)                     tol = dlamch('EpsMach')
      |                                 1~~~~~~~
Warning: Nonconforming tab character at (1) [-Wtabs]
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dstatn.f -o vendor/arpack/dstatn.o
stat.h:8:19:

Warning: Unused variable 't0' declared at (1) [-Wunused-variable]
stat.h:8:23:

Warning: Unused variable 't1' declared at (1) [-Wunused-variable]
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dsaupd.f -o vendor/arpack/dsaupd.o
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dvout.f -o vendor/arpack/dvout.o
vendor/arpack/dvout.f:32:26:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                          1
Warning: Unused variable 'i' declared at (1) [-Wunused-variable]
vendor/arpack/dvout.f:18:49:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                                 1
Warning: Unused dummy argument 'idigit' at (1) [-Wunused-dummy-argument]
vendor/arpack/dvout.f:18:55:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                                       1
Warning: Unused dummy argument 'ifmt' at (1) [-Wunused-dummy-argument]
vendor/arpack/dvout.f:32:30:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                              1
Warning: Unused variable 'k1' declared at (1) [-Wunused-variable]
vendor/arpack/dvout.f:32:34:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                                  1
Warning: Unused variable 'k2' declared at (1) [-Wunused-variable]
vendor/arpack/dvout.f:31:29:

   31 |       CHARACTER*80       LINE
      |                             1
Warning: Unused variable 'line' declared at (1) [-Wunused-variable]
vendor/arpack/dvout.f:32:39:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                                       1
Warning: Unused variable 'lll' declared at (1) [-Wunused-variable]
vendor/arpack/dvout.f:18:34:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                  1
Warning: Unused dummy argument 'lout' at (1) [-Wunused-dummy-argument]
vendor/arpack/dvout.f:18:37:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                     1
Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument]
vendor/arpack/dvout.f:32:47:

   32 |       INTEGER            I, K1, K2, LLL, NDIGIT
      |                                               1
Warning: Unused variable 'ndigit' declared at (1) [-Wunused-variable]
vendor/arpack/dvout.f:18:41:

   18 |       SUBROUTINE IGRAPHDVOUT( LOUT, N, SX, IDIGIT, IFMT )
      |                                         1
Warning: Unused dummy argument 'sx' at (1) [-Wunused-dummy-argument]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dstqrb.f -o vendor/arpack/dstqrb.o
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dlaqrb.f -o vendor/arpack/dlaqrb.o
vendor/arpack/dlaqrb.f:495:16:

  495 |             if( i2.gt.i )
      |                ^
Warning: 'i2' may be used uninitialized [-Wmaybe-uninitialized]
vendor/arpack/dlaqrb.f:141:26:

  141 |       integer    i, i1, i2, itn, its, j, k, l, m, nh, nr
      |                          ^
note: 'i2' was declared here
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dsaup2.f -o vendor/arpack/dsaup2.o
vendor/arpack/dsaup2.f:812:5:

  812 |   130    continue
      |     1
Warning: Label 130 at (1) defined but not used [-Wunused-label]
vendor/arpack/dsaup2.f:326:5:

  326 |    10 continue
      |     1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
vendor/arpack/dsaup2.f:180:63:

  180 |      &   ( ido, bmat, n, which, nev, np, tol, resid, mode, iupd,
      |                                                               1
Warning: Unused dummy argument 'iupd' at (1) [-Wunused-dummy-argument]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dmout.f -o vendor/arpack/dmout.o
vendor/arpack/dmout.f:21:43:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                           1
Warning: Unused dummy argument 'a' at (1) [-Wunused-dummy-argument]
vendor/arpack/dmout.f:35:26:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                          1
Warning: Unused variable 'i' declared at (1) [-Wunused-variable]
vendor/arpack/dmout.f:21:56:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                                        1
Warning: Unused dummy argument 'idigit' at (1) [-Wunused-dummy-argument]
vendor/arpack/dmout.f:21:62:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                                              1
Warning: Unused dummy argument 'ifmt' at (1) [-Wunused-dummy-argument]
vendor/arpack/dmout.f:35:29:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                             1
Warning: Unused variable 'j' declared at (1) [-Wunused-variable]
vendor/arpack/dmout.f:35:33:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                                 1
Warning: Unused variable 'k1' declared at (1) [-Wunused-variable]
vendor/arpack/dmout.f:35:37:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                                     1
Warning: Unused variable 'k2' declared at (1) [-Wunused-variable]
vendor/arpack/dmout.f:34:29:

   34 |       CHARACTER*80       LINE
      |                             1
Warning: Unused variable 'line' declared at (1) [-Wunused-variable]
vendor/arpack/dmout.f:35:42:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                                          1
Warning: Unused variable 'lll' declared at (1) [-Wunused-variable]
vendor/arpack/dmout.f:21:34:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                  1
Warning: Unused dummy argument 'lout' at (1) [-Wunused-dummy-argument]
vendor/arpack/dmout.f:21:37:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                     1
Warning: Unused dummy argument 'm' at (1) [-Wunused-dummy-argument]
vendor/arpack/dmout.f:21:40:

   21 |       SUBROUTINE IGRAPHDMOUT( LOUT, M, N, A, LDA, IDIGIT, IFMT )
      |                                        1
Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument]
vendor/arpack/dmout.f:35:50:

   35 |       INTEGER            I, J, K1, K2, LLL, NDIGIT
      |                                                  1
Warning: Unused variable 'ndigit' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dngets.f -o vendor/arpack/dngets.o
vendor/arpack/dngets.f:96:33:

   96 |      &     bounds, shiftr, shifti )
      |                                 1
Warning: Unused dummy argument 'shifti' at (1) [-Wunused-dummy-argument]
vendor/arpack/dngets.f:96:25:

   96 |      &     bounds, shiftr, shifti )
      |                         1
Warning: Unused dummy argument 'shiftr' at (1) [-Wunused-dummy-argument]
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dneupd.f -o vendor/arpack/dneupd.o
stat.h:8:19:

Warning: Unused variable 't0' declared at (1) [-Wunused-variable]
stat.h:8:23:

Warning: Unused variable 't1' declared at (1) [-Wunused-variable]
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
vendor/arpack/dneupd.f:537:72:

  537 |      &           '_neupd: Threshold eigenvalue used for re-ordering')
      |                                                                        ^
Warning: 'thres' may be used uninitialized [-Wmaybe-uninitialized]
vendor/arpack/dneupd.f:347:47:

  347 |      &           conds, rnorm, sep, temp, thres, vl(1,1), temp1, eps23
      |                                               ^
note: 'thres' was declared here
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dsortc.f -o vendor/arpack/dsortc.o
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dnaup2.f -o vendor/arpack/dnaup2.o
vendor/arpack/dnaup2.f:315:5:

  315 |    10 continue
      |     1
Warning: Label 10 at (1) defined but not used [-Wunused-label]
vendor/arpack/dnaup2.f:175:63:

  175 |      &   ( ido, bmat, n, which, nev, np, tol, resid, mode, iupd,
      |                                                               1
Warning: Unused dummy argument 'iupd' at (1) [-Wunused-dummy-argument]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dseigt.f -o vendor/arpack/dseigt.o
vendor/arpack/dseigt.f:124:18:

  124 |       integer    i, k, msglvl
      |                  1
Warning: Unused variable 'i' declared at (1) [-Wunused-variable]
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dneigh.f -o vendor/arpack/dneigh.o
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dseupd.f -o vendor/arpack/dseupd.o
stat.h:8:19:

Warning: Unused variable 't0' declared at (1) [-Wunused-variable]
stat.h:8:23:

Warning: Unused variable 't1' declared at (1) [-Wunused-variable]
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
vendor/arpack/dseupd.f:557:49:

  557 |                if ( workl(irz+j) .le. thres1 .or.
      |                                                 ^
Warning: 'thres1' may be used uninitialized [-Wmaybe-uninitialized]
vendor/arpack/dseupd.f:259:44:

  259 |      &           bnorm2, rnorm, temp, thres1, thres2, tempbnd, eps23
      |                                            ^
note: 'thres1' was declared here
vendor/arpack/dseupd.f:557:49:

  557 |                if ( workl(irz+j) .le. thres1 .or.
      |                                                 ^
Warning: 'thres2' may be used uninitialized [-Wmaybe-uninitialized]
vendor/arpack/dseupd.f:259:52:

  259 |      &           bnorm2, rnorm, temp, thres1, thres2, tempbnd, eps23
      |                                                    ^
note: 'thres2' was declared here
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dsgets.f -o vendor/arpack/dsgets.o
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dnapps.f -o vendor/arpack/dnapps.o
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dsaitr.f -o vendor/arpack/dsaitr.o
vendor/arpack/dsaitr.f:484:72:

  484 |          tmvopx = tmvopx + (t3 - t2)
      |                                                                        ^
Warning: 't2' may be used uninitialized [-Wmaybe-uninitialized]
stat.h:8:27:

note: 't2' declared here
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dstats.f -o vendor/arpack/dstats.o
stat.h:8:19:

Warning: Unused variable 't0' declared at (1) [-Wunused-variable]
stat.h:8:23:

Warning: Unused variable 't1' declared at (1) [-Wunused-variable]
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dnconv.f -o vendor/arpack/dnconv.o
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/second.f -o vendor/arpack/second.o
vendor/arpack/second.f:23:30:

   23 |       REAL               ETIME
      |                              1
Warning: Unused variable 'etime' declared at (1) [-Wunused-variable]
vendor/arpack/second.f:17:27:

   17 |       REAL               T1
      |                           1
Warning: Unused variable 't1' declared at (1) [-Wunused-variable]
vendor/arpack/second.f:20:36:

   20 |       REAL               TARRAY( 2 )
      |                                    1
Warning: Unused variable 'tarray' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dsesrt.f -o vendor/arpack/dsesrt.o
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dsapps.f -o vendor/arpack/dsapps.o
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dgetv0.f -o vendor/arpack/dgetv0.o
vendor/arpack/dgetv0.f:120:26:

  120 |      &   ( ido, bmat, itry, initv, n, j, v, ldv, resid, rnorm,
      |                          1
Warning: Unused dummy argument 'itry' at (1) [-Wunused-dummy-argument]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
vendor/arpack/dgetv0.f:269:72:

  269 |          tmvopx = tmvopx + (t3 - t2)
      |                                                                        ^
Warning: 't2' may be used uninitialized [-Wmaybe-uninitialized]
stat.h:8:27:

note: 't2' declared here
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dnaitr.f -o vendor/arpack/dnaitr.o
vendor/arpack/dnaitr.f:210:33:

  210 |      &   (ido, bmat, n, k, np, nb, resid, rnorm, v, ldv, h, ldh,
      |                                 1
Warning: Unused dummy argument 'nb' at (1) [-Wunused-dummy-argument]
vendor/arpack/dnaitr.f:494:72:

  494 |          tmvopx = tmvopx + (t3 - t2)
      |                                                                        ^
Warning: 't2' may be used uninitialized [-Wmaybe-uninitialized]
stat.h:8:27:

note: 't2' declared here
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dsortr.f -o vendor/arpack/dsortr.o
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/dsconv.f -o vendor/arpack/dsconv.o
stat.h:8:27:

Warning: Unused variable 't2' declared at (1) [-Wunused-variable]
stat.h:8:31:

Warning: Unused variable 't3' declared at (1) [-Wunused-variable]
stat.h:8:35:

Warning: Unused variable 't4' declared at (1) [-Wunused-variable]
stat.h:8:39:

Warning: Unused variable 't5' declared at (1) [-Wunused-variable]
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/wrap.f -o vendor/arpack/wrap.o
gfortran -arch arm64 -fopenmp -fallow-argument-mismatch  -fPIC  -Wall -g -O2  -c vendor/arpack/ivout.f -o vendor/arpack/ivout.o
vendor/arpack/ivout.f:25:18:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                  1
Warning: Unused variable 'i' declared at (1) [-Wunused-variable]
vendor/arpack/ivout.f:18:49:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                                 1
Warning: Unused dummy argument 'idigit' at (1) [-Wunused-dummy-argument]
vendor/arpack/ivout.f:18:55:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                                       1
Warning: Unused dummy argument 'ifmt' at (1) [-Wunused-dummy-argument]
vendor/arpack/ivout.f:18:41:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                         1
Warning: Unused dummy argument 'ix' at (1) [-Wunused-dummy-argument]
vendor/arpack/ivout.f:25:30:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                              1
Warning: Unused variable 'k1' declared at (1) [-Wunused-variable]
vendor/arpack/ivout.f:25:34:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                                  1
Warning: Unused variable 'k2' declared at (1) [-Wunused-variable]
vendor/arpack/ivout.f:26:23:

   26 |       CHARACTER*80 LINE
      |                       1
Warning: Unused variable 'line' declared at (1) [-Wunused-variable]
vendor/arpack/ivout.f:25:39:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                                       1
Warning: Unused variable 'lll' declared at (1) [-Wunused-variable]
vendor/arpack/ivout.f:18:34:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                  1
Warning: Unused dummy argument 'lout' at (1) [-Wunused-dummy-argument]
vendor/arpack/ivout.f:18:37:

   18 |       SUBROUTINE IGRAPHIVOUT (LOUT, N, IX, IDIGIT, IFMT)
      |                                     1
Warning: Unused dummy argument 'n' at (1) [-Wunused-dummy-argument]
vendor/arpack/ivout.f:25:26:

   25 |       INTEGER    I, NDIGIT, K1, K2, LLL
      |                          1
Warning: Unused variable 'ndigit' declared at (1) [-Wunused-variable]
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/version.c -o vendor/cigraph/src/version.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/eigenvector.c -o vendor/cigraph/src/centrality/eigenvector.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/truss.cpp -o vendor/cigraph/src/centrality/truss.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack.cpp -o vendor/cigraph/src/centrality/prpack.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/pagerank.c -o vendor/cigraph/src/centrality/pagerank.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/closeness.c -o vendor/cigraph/src/centrality/closeness.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/hub_authority.c -o vendor/cigraph/src/centrality/hub_authority.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/coreness.c -o vendor/cigraph/src/centrality/coreness.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/centralization.c -o vendor/cigraph/src/centrality/centralization.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/betweenness.c -o vendor/cigraph/src/centrality/betweenness.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/centrality_other.c -o vendor/cigraph/src/centrality/centrality_other.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack/prpack_utils.cpp -o vendor/cigraph/src/centrality/prpack/prpack_utils.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_scc_graph.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_ge_graph.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack/prpack_base_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_base_graph.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_schur_graph.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_igraph_graph.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.cpp -o vendor/cigraph/src/centrality/prpack/prpack_preprocessed_gs_graph.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack/prpack_result.cpp -o vendor/cigraph/src/centrality/prpack/prpack_result.o
clang++ -arch arm64 -std=gnu++17 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/centrality/prpack/prpack_solver.cpp -o vendor/cigraph/src/centrality/prpack/prpack_solver.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/cliques/glet.c -o vendor/cigraph/src/cliques/glet.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/cliques/maximal_cliques.c -o vendor/cigraph/src/cliques/maximal_cliques.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/cliques/cliquer_wrapper.c -o vendor/cigraph/src/cliques/cliquer_wrapper.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/cliques/cliques.c -o vendor/cigraph/src/cliques/cliques.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/cliques/cliquer/cliquer.c -o vendor/cigraph/src/cliques/cliquer/cliquer.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/cliques/cliquer/reorder.c -o vendor/cigraph/src/cliques/cliquer/reorder.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/cliques/cliquer/cliquer_graph.c -o vendor/cigraph/src/cliques/cliquer/cliquer_graph.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -c vendor/cigraph/src/community/voronoi.c -o vendor/cigraph/src/community/voronoi.o
clang -arch arm64 -flax-vector-conversions -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -Wall -pedantic -fdiagnostics-color=always -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' file not found
   39 | #include <glpk.h>
      |          ^~~~~~~~
1 error generated.
make: *** [vendor/cigraph/src/community/optimal_modularity.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/private/var/folders/sj/jdgnsm9n14vgsjctfrk5x2_80000gn/T/RtmpcbYC44/pkg-lib4ddc46878d02/igraph’
Type .Last.error to see the more details.

krlmlr commented 6 months ago

Thanks. How did you install R?

My compilation lines look like this:

ccache clang -arch arm64 -I"/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/include" -DNDEBUG -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor -Ivendor/mini-gmp -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -DNDEBUG -DNTIMER -DNPRINT -DIGRAPH_THREAD_LOCAL= -DPRPACK_IGRAPH_SUPPORT -DHAVE_GFORTRAN=1 -D_GNU_SOURCE=1 -I'/Users/kirill/Library/R/arm64/4.3/library/cpp11/include' -I/opt/homebrew/include    -fPIC  -O0 -g -Wmacro-redefined -Wno-everything -w -c vendor/cigraph/src/operators/rewire.c -o vendor/cigraph/src/operators/rewire.o

Note -I/opt/homebrew/include -- that's where glpk.h lives on my system.

szhorvat commented 6 months ago

You did not mention why you are trying to compile igraph instead of using the binaries from CRAN.

If you did not install R from CRAN, then all packages that have C extensions will need to be compiled from sources. This involves setting things up so that libraries can be found, and ensuring that you are using compilers that have ABIs compatible with your specific version of R. If you are not comfortable with all this, then I suggest you simply use the official R distribution from https://www.r-project.org/

I don't see anything that we need to fix on the igraph side here. It is entirely normal that libraries that are installed with Homebrew won't be found without extra setup.

krlmlr commented 6 months ago

Some installations of R don't support binary packages. Is this MacPorts? Or something else?

joshua-zh commented 6 months ago

Sorry to bother you. I compile igraph just out of curiosity. I installed the R from R-4.3.2-arm64.pkg. Every configuration kept the default settings.

This program has ABSOLUTELY NO WARRANTY.

This program is free software; you may re-distribute it under the terms of the GNU General Public License version 3 or later.

krlmlr commented 6 months ago

I have the following in my ~/.R/Makevars :

MAKEFLAGS = -j8
CPPFLAGS = -I/opt/homebrew/include
LDFLAGS = -L/opt/homebrew/lib

FC      = /opt/homebrew/bin/gfortran
F77     = /opt/homebrew/bin/gfortran
F95     = /opt/homebrew/bin/gfortran
FLIBS   = -L/opt/homebrew/lib/gcc

This explains the difference. Useful StackOverflow answer: https://stackoverflow.com/a/74534903/946850 . Is there a better traditional resource that describes this? (I should have added a comment into that file when I added the definitions...)

joshua-zh commented 6 months ago

Thank you very much. This setting makes it perfect!

igraph / rigraph

'glpk.h' file not found on MacOS #1002

What happens?

To Reproduce