* Package: sci-biology/grappa-2.0 * Repository: science * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking GRAPPA20.tar.gz to /var/tmp/portage/sci-biology/grappa-2.0/work >>> Source unpacked in /var/tmp/portage/sci-biology/grappa-2.0/work >>> Preparing source in /var/tmp/portage/sci-biology/grappa-2.0/work/GRAPPA20 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/grappa-2.0/work/GRAPPA20 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/grappa-2.0/work/GRAPPA20 ... make -j1 Makefile:156: *** mixed implicit and normal rules: deprecated syntax Makefile:160: warning: overriding recipe for target 'GRAPPA-2' Makefile:157: warning: ignoring old recipe for target 'GRAPPA-2' Makefile:159: *** mixed implicit and normal rules: deprecated syntax gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c convert.c -o convert.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c labeltree.c -o labeltree.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c main.c -o main.o main.c: In function ‘main’: main.c:364:9: warning: variable ‘treelevel2count2’ set but not used [-Wunused-but-set-variable] 364 | int treelevel2count2; | ^~~~~~~~~~~~~~~~ main.c:363:9: warning: variable ‘treelevel2count’ set but not used [-Wunused-but-set-variable] 363 | int treelevel2count; | ^~~~~~~~~~~~~~~ main.c:338:55: warning: variable ‘YTESTARG’ set but not used [-Wunused-but-set-variable] 338 | int BOUND, NJ, COUNT, COND, CIRCULAR, OPT, YTEST, YTESTARG, CORRECTION, | ^~~~~~~~ main.c:742:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 742 | fscanf ( constFile, "%[0123456789,()]", constString ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:1031:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1031 | fscanf ( DCMInput, "%d", &DCMNum ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:1040:13: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1040 | fscanf ( DCMInput, "%s\n", tmpString ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c:1501:13: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1501 | system ( DCMCacheFName ); | ^~~~~~~~~~~~~~~~~~~~~~~~ main.c:1930:21: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1930 | fscanf ( cacheFile, "%lld", &workLob[k] ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.c: In function ‘readDCMCacheLine’: main.c:2674:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2674 | fscanf ( cacheFile, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c binencode.c -o binencode.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c gen_tree.c -o gen_tree.o gen_tree.c: In function ‘next’: gen_tree.c:241:5: warning: ‘dif_lev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 241 | gen_tree ( n, exp, dif_lev, env ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gen_tree.c: In function ‘testonelevel’: gen_tree.c:558:5: warning: ‘dif_lev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 558 | gen_tree ( n - 1, old_trees, dif_lev, env ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gen_tree.c: In function ‘testtwolevel’: gen_tree.c:629:10: warning: ‘dif_lev’ may be used uninitialized in this function [-Wmaybe-uninitialized] 629 | if ( gen_tree_levels | ^~~~~~~~~~~~~~~ 630 | ( n - 1, old_trees, tpool, dif_lev, env, NUM_GENOMES, distmatrix, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 631 | best_so_far, minidist ) == -1 ) | ~~~~~~~~~~~~~~~~~~~~~~~ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c inittree.c -o inittree.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c circ_order.c -o circ_order.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c lk_main.c -o lk_main.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c bbtsp.c -o bbtsp.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c condense.c -o condense.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c const_tree.c -o const_tree.o const_tree.c: In function ‘rooted2unrooted’: const_tree.c:393:32: warning: variable ‘rchild_bin’ set but not used [-Wunused-but-set-variable] 393 | struct tNode *lchild_bin, *rchild_bin; | ^~~~~~~~~~ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c greedy_median.c -o greedy_median.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c invdist.c -o invdist.o invdist.c: In function ‘calc_invmatrix’: invdist.c:15:9: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable] 15 | int dist; | ^~~~ invdist.c: In function ‘calc_invmatrix_BH’: invdist.c:65:9: warning: variable ‘dist’ set but not used [-Wunused-but-set-variable] 65 | int dist; | ^~~~ invdist.c: In function ‘num_hurdles_and_fortress’: invdist.c:463:26: warning: variable ‘labeled’ set but not used [-Wunused-but-set-variable] 463 | int *oriented, *cc, *labeled; | ^~~~~~~ invdist.c: In function ‘connected_component_BH’: invdist.c:701:18: warning: variable ‘components’ set but not used [-Wunused-but-set-variable] 701 | component_t *components; | ^~~~~~~~~~ invdist.c:700:10: warning: variable ‘oriented’ set but not used [-Wunused-but-set-variable] 700 | int *oriented, *cc, *labeled; | ^~~~~~~~ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c uf.c -o uf.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c neighborj.c -o neighborj.o neighborj.c: In function ‘neighborj_score_one’: neighborj.c:775:12: warning: variable ‘invscore_d’ set but not used [-Wunused-but-set-variable] 775 | double invscore_d; | ^~~~~~~~~~ neighborj.c: In function ‘neighborj_SK_trees’: neighborj.c:849:9: warning: variable ‘score’ set but not used [-Wunused-but-set-variable] 849 | int score; | ^~~~~ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c condense3.c -o condense3.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c getopt3.c -o getopt3.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c randomBSD.c -o randomBSD.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c cheaptsp.c -o cheaptsp.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c specialtsp.c -o specialtsp.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c specialinit.c -o specialinit.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c read_input.c -o read_input.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c circular_ordering.c -o circular_ordering.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c correction.c -o correction.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c inversion_median.c -o inversion_median.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c inversion_median_alberto.c -o inversion_median_alberto.o inversion_median_alberto.c: In function ‘termin’: inversion_median_alberto.c:222:9: warning: variable ‘qmc’ set but not used [-Wunused-but-set-variable] 222 | int qmc; | ^~~ inversion_median_alberto.c: In function ‘albert_inversion_median_noncircular’: inversion_median_alberto.c:641:28: warning: variable ‘kbest’ set but not used [-Wunused-but-set-variable] 641 | int mindistk, totdist, kbest; | ^~~~~ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c priority_stack.c -o priority_stack.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c hashtable.c -o hashtable.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c med_util.c -o med_util.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c simpleio.c -o simpleio.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c vertex_factory.c -o vertex_factory.o vertex_factory.c: In function ‘get_vertex’: vertex_factory.c:96:9: warning: variable ‘oldcap’ set but not used [-Wunused-but-set-variable] 96 | int oldcap, i; | ^~~~~~ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c growTree.c -o growTree.o growTree.c: In function ‘addNewEdge’: growTree.c:184:29: warning: variable ‘rReturn’ set but not used [-Wunused-but-set-variable] 184 | struct tNode *lReturn, *rReturn; | ^~~~~~~ growTree.c:184:19: warning: variable ‘lReturn’ set but not used [-Wunused-but-set-variable] 184 | struct tNode *lReturn, *rReturn; | ^~~~~~~ growTree.c: In function ‘findOne’: growTree.c:552:24: warning: variable ‘tmp’ set but not used [-Wunused-but-set-variable] 552 | struct stack_node *tmp; | ^~~ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c bitvector.c -o bitvector.o bitvector.c: In function ‘bitvector_get_positions_of_ones’: bitvector.c:153:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 153 | push ( l, ( void * ) idx ); | ^ bitvector.c: In function ‘bitvector_set_positions_of_ones’: bitvector.c:168:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 168 | pos = ( int ) list_get ( l, i ); | ^ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c lists.c -o lists.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c sorting_reversal_median.c -o sorting_reversal_median.o sorting_reversal_median.c: In function ‘find_reversal_median’: sorting_reversal_median.c:35:45: warning: variable ‘nneighbors’ set but not used [-Wunused-but-set-variable] 35 | int i, j, k, pass, found_one = 0, stop, nneighbors; | ^~~~~~~~~~ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c mythread_rwlock.c -o mythread_rwlock.o gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -c all_sorting_reversals.c -o all_sorting_reversals.o all_sorting_reversals.c: In function ‘find_all_sorting_reversals’: all_sorting_reversals.c:145:16: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 145 | ( void * ) i ); | ^ all_sorting_reversals.c:167:16: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 167 | ( void * ) i ); | ^ all_sorting_reversals.c:179:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 179 | j = ( int ) list_get ( &mem->conn_comp[i].cyclelist, 0 ); | ^ all_sorting_reversals.c:299:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 299 | a = ( int ) list_get ( &mem->cyclelist[i], j ); | ^ all_sorting_reversals.c:300:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 300 | b = ( int ) list_get ( &mem->cyclelist[c + 1 + i], k ); | ^ all_sorting_reversals.c:351:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 351 | a = ( int ) list_get ( &mem-> | ^ all_sorting_reversals.c:354:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 354 | b = ( int ) list_get ( &mem-> | ^ all_sorting_reversals.c:460:43: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 460 | cyclelist[( int ) | ^ all_sorting_reversals.c:465:43: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 465 | cyclelist[( int ) | ^ all_sorting_reversals.c:473:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 473 | a = ( int ) list_get ( edges1, k ); | ^ all_sorting_reversals.c:474:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 474 | b = ( int ) list_get ( edges2, k2 ); | ^ all_sorting_reversals.c:497:35: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 497 | push ( mem->mhurdles, ( void * ) i ); | ^ all_sorting_reversals.c:515:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 515 | h1 = ( int ) list_get ( mem->mhurdles, i ); | ^ all_sorting_reversals.c:516:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 516 | h2 = ( int ) list_get ( mem->mhurdles, j ); | ^ all_sorting_reversals.c:565:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 565 | oc = ( int ) list_get ( &ocs[i], k ); | ^ all_sorting_reversals.c:569:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 569 | h = ( int ) list_get ( mem->mhurdles, j ); | ^ all_sorting_reversals.c:618:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 618 | int o1 = ( int ) list_get ( &ocs[i], k ); | ^ all_sorting_reversals.c:621:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 621 | int o2 = ( int ) list_get ( &ocs[j], k2 ); | ^ all_sorting_reversals.c:644:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 644 | push ( &non_separated_ocs, ( void * ) i ); | ^ all_sorting_reversals.c:658:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 658 | int h = ( int ) list_get ( mem->mhurdles, i ); | ^ all_sorting_reversals.c:659:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 659 | push ( &to_merge1, ( void * ) h ); | ^ all_sorting_reversals.c:664:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 664 | int oc = ( int ) list_get ( &ocs[lidx[h]], j ); | ^ all_sorting_reversals.c:665:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 665 | push ( &to_merge1, ( void * ) oc ); | ^ all_sorting_reversals.c:672:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 672 | ( void * ) mem->conn_comp[h].anchor ); | ^ all_sorting_reversals.c:683:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 683 | push ( &to_merge2, ( void * ) j ); | ^ all_sorting_reversals.c:693:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 693 | ( int ) list_get ( &non_separated_ocs, j ); | ^ all_sorting_reversals.c:698:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 698 | push ( &to_merge2, ( void * ) bc ); | ^ all_sorting_reversals.c:703:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 703 | int c1 = ( int ) list_get ( &to_merge1, j ); | ^ all_sorting_reversals.c:706:42: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 706 | int c2 = ( int ) list_get ( &to_merge2, k ); | ^ all_sorting_reversals.c:730:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 730 | int hrdl = ( int ) list_get ( mem->mhurdles, i ); | ^ all_sorting_reversals.c:734:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 734 | ( void * ) mem->conn_comp[hrdl].anchor ); | ^ all_sorting_reversals.c:739:43: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 739 | push ( &tmpl, ( void * ) hrdl ); | ^ all_sorting_reversals.c:758:55: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 758 | push ( &tmpl, ( void * ) j ); | ^ all_sorting_reversals.c:766:55: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 766 | push ( &tmpl, ( void * ) j ); | ^ all_sorting_reversals.c:775:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 775 | ( int ) list_get ( &non_separated_ocs, j ); | ^ all_sorting_reversals.c:783:47: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 783 | push ( &tmpl, ( void * ) bc ); | ^ all_sorting_reversals.c:790:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 790 | if ( ( int ) | ^ all_sorting_reversals.c:797:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 797 | ( int ) list_get ( &mem->conn_comp[hrdl]. | ^ all_sorting_reversals.c:800:47: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 800 | push ( &tmpl, ( void * ) partner ); | ^ all_sorting_reversals.c:816:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 816 | int comp = ( int ) list_get ( &tmpl, j ); | ^ all_sorting_reversals.c:833:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 833 | ( int ) list_get ( &ocs[lidx[hrdl]], | ^ all_sorting_reversals.c:856:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 856 | ( int ) list_get ( &ocs[lidx[hrdl]], k ); | ^ all_sorting_reversals.c:862:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 862 | ( int ) list_get ( &ocs[lidx[hrdl]], | ^ all_sorting_reversals.c: In function ‘find_connected_components’: all_sorting_reversals.c:952:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 952 | push ( mem->stack, ( void * ) mem->cc_e[i] ); | ^ all_sorting_reversals.c:953:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 953 | top = ( int ) peek_stack ( mem->stack ); | ^ all_sorting_reversals.c:965:19: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 965 | top = ( int ) peek_stack ( mem->stack ); | ^ all_sorting_reversals.c: In function ‘build_uoc_list’: all_sorting_reversals.c:1027:30: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1027 | push ( uoc_list, ( void * ) current ); | ^ all_sorting_reversals.c: In function ‘find_superhurdles’: all_sorting_reversals.c:1050:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1050 | prevlbl = ( int ) list_get ( uoc_list, list_size ( uoc_list ) - 1 ); | ^ all_sorting_reversals.c:1058:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1058 | currentlbl = ( int ) list_get ( uoc_list, i ); | ^ all_sorting_reversals.c:1067:31: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1067 | ( void * ) ( idx[currentlbl] ) ) ) | ^ all_sorting_reversals.c:1073:45: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1073 | push ( &adj_list[idx[prevlbl]], ( void * ) idx[currentlbl] ); | ^ all_sorting_reversals.c:1074:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1074 | push ( &adj_list[idx[currentlbl]], ( void * ) idx[prevlbl] ); | ^ all_sorting_reversals.c:1093:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1093 | v = ( int ) pop_stack ( &S ); | ^ all_sorting_reversals.c:1100:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1100 | n = ( int ) list_get ( &adj_list[v], i ); | ^ all_sorting_reversals.c:1105:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1105 | push ( &cycles[n], ( void * ) ncycles ); | ^ all_sorting_reversals.c:1110:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1110 | push ( &cycles[u], ( void * ) ncycles ); | ^ all_sorting_reversals.c:1115:56: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1115 | push ( &three_cycles_memb, ( void * ) v ); | ^ all_sorting_reversals.c:1120:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1120 | push ( &S, ( void * ) n ); | ^ all_sorting_reversals.c:1165:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1165 | n = ( int ) list_get ( &adj_list[i], 0 ); | ^ all_sorting_reversals.c:1193:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1193 | u[0] = ( int ) list_get ( &three_cycles_memb, i ); | ^ all_sorting_reversals.c:1229:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1229 | ( void * ) label[w] ); | ^ all_sorting_reversals.c:1231:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1231 | ( void * ) label[v] ); | ^ all_sorting_reversals.c:1254:25: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1254 | j = ( int ) list_get ( &adj_list[i], 0 ); | ^ all_sorting_reversals.c:1283:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1283 | x1 = label[( int ) list_get ( &adj_list[i], 0 )]; | ^ all_sorting_reversals.c:1284:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1284 | x2 = label[( int ) list_get ( &adj_list[j], 0 )]; | ^ all_sorting_reversals.c:1296:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1296 | int newj = ( int ) list_get ( &adj_list[j], 0 ); | ^ all_sorting_reversals.c:1300:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1300 | j = ( int ) list_get ( &adj_list[j], 1 ); | ^ all_sorting_reversals.c: In function ‘find_single_hurdle’: all_sorting_reversals.c:1327:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1327 | v = ( int ) list_get ( &adj_list[u], i ); | ^ all_sorting_reversals.c:1345:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1345 | next = ( int ) list_get ( &adj_list[v], 0 ) == prev ? | ^ all_sorting_reversals.c:1346:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1346 | ( int ) list_get ( &adj_list[v], 1 ) : | ^ all_sorting_reversals.c:1347:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1347 | ( int ) list_get ( &adj_list[v], 0 ); | ^ all_sorting_reversals.c: In function ‘count_hurdles_after_reversal’: all_sorting_reversals.c:1687:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1687 | label = ( int ) list_get ( V, i ); | ^ all_sorting_reversals.c: In function ‘new_nhurdles_plus_nfortresses_cc’: all_sorting_reversals.c:1791:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 1791 | push ( &mem->comp_grey_edges[comp], ( void * ) mem->upi_cpy[i] ); | ^ all_sorting_reversals.c: In function ‘add_all_merging_reversals’: all_sorting_reversals.c:1860:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1860 | ( int ) list_get ( &c1->cyclelist, i )]; | ^ all_sorting_reversals.c:1863:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1863 | ( int ) list_get ( &c2->cyclelist, j )]; | ^ all_sorting_reversals.c:1868:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1868 | a = ( int ) list_get ( edges1, k ); | ^ all_sorting_reversals.c:1869:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1869 | b = ( int ) list_get ( edges2, k2 ); | ^ all_sorting_reversals.c: In function ‘add_all_cutting_reversals’: all_sorting_reversals.c:1892:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1892 | edges = &cyclelist[( int ) list_get ( &cc->cyclelist, j )]; | ^ all_sorting_reversals.c:1897:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1897 | a = ( int ) list_get ( edges, k ); | ^ all_sorting_reversals.c:1898:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1898 | b = ( int ) list_get ( edges, k2 ); | ^ all_sorting_reversals.c: In function ‘form_double_superhurdle’: all_sorting_reversals.c:1940:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1940 | ( int ) list_get ( &conn_comp[h1].double_superhurdle_partners, | ^ all_sorting_reversals.c:1943:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 1943 | && ( int ) list_get ( &conn_comp[h1]. | ^ all_sorting_reversals.c: In function ‘find_separating_hurdles’: all_sorting_reversals.c:2219:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2219 | comp = ( int ) pop_stack ( &tmpl ); | ^ all_sorting_reversals.c:2222:40: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2222 | push ( &separated_ocs, ( void * ) comp ); | ^ all_sorting_reversals.c:2223:45: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2223 | push ( &separating_hurdles, ( void * ) currenth ); | ^ all_sorting_reversals.c:2248:25: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2248 | int c = ( int ) pop_stack ( &tmpl ); | ^ all_sorting_reversals.c:2324:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2324 | push ( &tmpl, ( void * ) comp ); | ^ all_sorting_reversals.c:2347:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2347 | oc = ( int ) list_get ( &separated_ocs, i ); | ^ all_sorting_reversals.c:2349:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2349 | h = ( int ) list_get ( &separating_hurdles, i ); | ^ all_sorting_reversals.c:2357:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2357 | push ( &( *ocs )[j], ( void * ) oc ); | ^ gcc -O3 -Wall -DGCC -DLinux -O2 -pipe -march=native -fno-diagnostics-color -DINIT -o grappa convert.o labeltree.o main.o binencode.o gen_tree.o inittree.o circ_order.o lk_main.o bbtsp.o condense.o const_tree.o greedy_median.o invdist.o uf.o neighborj.o condense3.o getopt3.o randomBSD.o cheaptsp.o specialtsp.o specialinit.o read_input.o circular_ordering.o correction.o inversion_median.o inversion_median_alberto.o priority_stack.o hashtable.o med_util.o simpleio.o vertex_factory.o growTree.o bitvector.o lists.o sorting_reversal_median.o mythread_rwlock.o all_sorting_reversals.o -lm -lc -lpthread /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x28): multiple definition of `id'; labeltree.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x30): multiple definition of `genupd'; labeltree.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x38): multiple definition of `gen'; labeltree.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x40): multiple definition of `piupd'; labeltree.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x48): multiple definition of `metricub'; labeltree.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x4c): multiple definition of `realbest'; labeltree.o:(.bss+0x24): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x50): multiple definition of `realub'; labeltree.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x54): multiple definition of `tf'; labeltree.o:(.bss+0x2c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x58): multiple definition of `ti'; labeltree.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x5c): multiple definition of `millnodes'; labeltree.o:(.bss+0x34): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x60): multiple definition of `treenodes'; labeltree.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x68): multiple definition of `solmate'; labeltree.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x70): multiple definition of `permate'; labeltree.o:(.bss+0x48): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x78): multiple definition of `hamate'; labeltree.o:(.bss+0x50): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x80): multiple definition of `hamilmate'; labeltree.o:(.bss+0x58): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x88): multiple definition of `rdist'; labeltree.o:(.bss+0x60): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x90): multiple definition of `ncycles'; labeltree.o:(.bss+0x68): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x98): multiple definition of `inv_unreach'; labeltree.o:(.bss+0x70): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xa0): multiple definition of `unreach'; labeltree.o:(.bss+0x78): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xa8): multiple definition of `nunreach'; labeltree.o:(.bss+0x80): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xac): multiple definition of `best_now'; labeltree.o:(.bss+0x84): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xb0): multiple definition of `UB'; labeltree.o:(.bss+0x88): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xb8): multiple definition of `cycvar'; labeltree.o:(.bss+0x90): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xc0): multiple definition of `localDistmem'; labeltree.o:(.bss+0x98): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xc8): multiple definition of `fout'; labeltree.o:(.bss+0xa0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xd0): multiple definition of `fid'; labeltree.o:(.bss+0xa8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xd8): multiple definition of `pibest'; labeltree.o:(.bss+0xb0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xe0): multiple definition of `bestsol'; labeltree.o:(.bss+0xb8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xe8): multiple definition of `bestub'; labeltree.o:(.bss+0xc0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xf0): multiple definition of `at_root'; labeltree.o:(.bss+0xc8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xf4): multiple definition of `bsec'; labeltree.o:(.bss+0xcc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xf8): multiple definition of `nsec'; labeltree.o:(.bss+0xd0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0xfc): multiple definition of `bcyceq'; labeltree.o:(.bss+0xd4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x100): multiple definition of `ncyceq'; labeltree.o:(.bss+0xd8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x104): multiple definition of `bdegree'; labeltree.o:(.bss+0xdc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x108): multiple definition of `ndegree'; labeltree.o:(.bss+0xe0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x10c): multiple definition of `bcycvar'; labeltree.o:(.bss+0xe4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x110): multiple definition of `ncycnz'; labeltree.o:(.bss+0xe8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x114): multiple definition of `ncycvar'; labeltree.o:(.bss+0xec): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x118): multiple definition of `bedge'; labeltree.o:(.bss+0xf0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x11c): multiple definition of `nedge'; labeltree.o:(.bss+0xf4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x120): multiple definition of `inv_unexp'; labeltree.o:(.bss+0xf8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x128): multiple definition of `unexp'; labeltree.o:(.bss+0x100): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x130): multiple definition of `kmate'; labeltree.o:(.bss+0x108): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x138): multiple definition of `pmmate'; labeltree.o:(.bss+0x110): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x140): multiple definition of `ke'; labeltree.o:(.bss+0x118): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x148): multiple definition of `pme'; labeltree.o:(.bss+0x120): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x150): multiple definition of `pm'; labeltree.o:(.bss+0x128): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x158): multiple definition of `j_ind'; labeltree.o:(.bss+0x130): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x160): multiple definition of `i_ind'; labeltree.o:(.bss+0x138): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x168): multiple definition of `e_ind'; labeltree.o:(.bss+0x140): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x170): multiple definition of `ec'; labeltree.o:(.bss+0x148): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x174): multiple definition of `mc'; labeltree.o:(.bss+0x14c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x178): multiple definition of `vc'; labeltree.o:(.bss+0x150): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x180): multiple definition of `pi'; labeltree.o:(.bss+0x158): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x188): multiple definition of `MAXEDG'; labeltree.o:(.bss+0x160): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x18c): multiple definition of `MAXM'; labeltree.o:(.bss+0x164): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x190): multiple definition of `MAXNOD'; labeltree.o:(.bss+0x168): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: main.o:(.bss+0x194): multiple definition of `Num_Genes'; labeltree.o:(.bss+0x16c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: gen_tree.o:(.bss+0x0): multiple definition of `switchDist'; main.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: gen_tree.o:(.bss+0x20): multiple definition of `outfile'; main.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x0): multiple definition of `id'; labeltree.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x8): multiple definition of `genupd'; labeltree.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x10): multiple definition of `gen'; labeltree.o:(.bss+0x10): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x18): multiple definition of `piupd'; labeltree.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x20): multiple definition of `metricub'; labeltree.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x24): multiple definition of `realbest'; labeltree.o:(.bss+0x24): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x28): multiple definition of `realub'; labeltree.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x2c): multiple definition of `tf'; labeltree.o:(.bss+0x2c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x30): multiple definition of `ti'; labeltree.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x34): multiple definition of `millnodes'; labeltree.o:(.bss+0x34): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x38): multiple definition of `treenodes'; labeltree.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x40): multiple definition of `solmate'; 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labeltree.o:(.bss+0x128): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x130): multiple definition of `j_ind'; labeltree.o:(.bss+0x130): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x138): multiple definition of `i_ind'; labeltree.o:(.bss+0x138): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x140): multiple definition of `e_ind'; labeltree.o:(.bss+0x140): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x148): multiple definition of `ec'; labeltree.o:(.bss+0x148): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x14c): multiple definition of `mc'; labeltree.o:(.bss+0x14c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x150): multiple definition of `vc'; labeltree.o:(.bss+0x150): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x158): multiple definition of `pi'; labeltree.o:(.bss+0x158): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x160): multiple definition of `MAXEDG'; labeltree.o:(.bss+0x160): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x164): multiple definition of `MAXM'; labeltree.o:(.bss+0x164): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x168): multiple definition of `MAXNOD'; labeltree.o:(.bss+0x168): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inittree.o:(.bss+0x16c): multiple definition of `Num_Genes'; labeltree.o:(.bss+0x16c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x14c): multiple definition of `mc'; 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labeltree.o:(.bss+0x60): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x98): multiple definition of `localDistmem'; labeltree.o:(.bss+0x98): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x8): multiple definition of `genupd'; labeltree.o:(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xa8): multiple definition of `fid'; labeltree.o:(.bss+0xa8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x110): multiple definition of `pmmate'; labeltree.o:(.bss+0x110): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x108): multiple definition of `kmate'; labeltree.o:(.bss+0x108): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x128): multiple definition of `pm'; labeltree.o:(.bss+0x128): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x138): multiple definition of `i_ind'; labeltree.o:(.bss+0x138): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x130): multiple definition of `j_ind'; labeltree.o:(.bss+0x130): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x120): multiple definition of `pme'; labeltree.o:(.bss+0x120): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x118): multiple definition of `ke'; labeltree.o:(.bss+0x118): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x100): multiple definition of `unexp'; labeltree.o:(.bss+0x100): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xf8): multiple definition of `inv_unexp'; labeltree.o:(.bss+0xf8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x38): multiple definition of `treenodes'; labeltree.o:(.bss+0x38): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x34): multiple definition of `millnodes'; labeltree.o:(.bss+0x34): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x84): multiple definition of `best_now'; labeltree.o:(.bss+0x84): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x80): multiple definition of `nunreach'; labeltree.o:(.bss+0x80): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x50): multiple definition of `hamate'; labeltree.o:(.bss+0x50): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x78): multiple definition of `unreach'; labeltree.o:(.bss+0x78): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x40): multiple definition of `solmate'; labeltree.o:(.bss+0x40): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x18): multiple definition of `piupd'; labeltree.o:(.bss+0x18): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x28): multiple definition of `realub'; labeltree.o:(.bss+0x28): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x24): multiple definition of `realbest'; labeltree.o:(.bss+0x24): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xb0): multiple definition of `pibest'; labeltree.o:(.bss+0xb0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x48): multiple definition of `permate'; labeltree.o:(.bss+0x48): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x68): multiple definition of `ncycles'; labeltree.o:(.bss+0x68): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x70): multiple definition of `inv_unreach'; labeltree.o:(.bss+0x70): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x168): multiple definition of `MAXNOD'; labeltree.o:(.bss+0x168): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x164): multiple definition of `MAXM'; labeltree.o:(.bss+0x164): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x160): multiple definition of `MAXEDG'; labeltree.o:(.bss+0x160): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x0): multiple definition of `id'; labeltree.o:(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x140): multiple definition of `e_ind'; labeltree.o:(.bss+0x140): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x58): multiple definition of `hamilmate'; labeltree.o:(.bss+0x58): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x88): multiple definition of `UB'; labeltree.o:(.bss+0x88): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x20): multiple definition of `metricub'; labeltree.o:(.bss+0x20): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x2c): multiple definition of `tf'; labeltree.o:(.bss+0x2c): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x30): multiple definition of `ti'; labeltree.o:(.bss+0x30): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0x90): multiple definition of `cycvar'; labeltree.o:(.bss+0x90): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xa0): multiple definition of `fout'; labeltree.o:(.bss+0xa0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xb8): multiple definition of `bestsol'; labeltree.o:(.bss+0xb8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xc0): multiple definition of `bestub'; labeltree.o:(.bss+0xc0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xc8): multiple definition of `at_root'; labeltree.o:(.bss+0xc8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xcc): multiple definition of `bsec'; labeltree.o:(.bss+0xcc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xd0): multiple definition of `nsec'; labeltree.o:(.bss+0xd0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xd4): multiple definition of `bcyceq'; labeltree.o:(.bss+0xd4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xd8): multiple definition of `ncyceq'; labeltree.o:(.bss+0xd8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xdc): multiple definition of `bdegree'; labeltree.o:(.bss+0xdc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xe0): multiple definition of `ndegree'; labeltree.o:(.bss+0xe0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xe4): multiple definition of `bcycvar'; labeltree.o:(.bss+0xe4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xe8): multiple definition of `ncycnz'; labeltree.o:(.bss+0xe8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xec): multiple definition of `ncycvar'; labeltree.o:(.bss+0xec): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xf0): multiple definition of `bedge'; labeltree.o:(.bss+0xf0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: inversion_median_alberto.o:(.bss+0xf4): multiple definition of `nedge'; labeltree.o:(.bss+0xf4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: greedy_median.o: in function `greedy_median': greedy_median.c:(.text+0x3e9): undefined reference to `finish1' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: greedy_median.c:(.text+0x4c1): undefined reference to `finish2' collect2: error: ld returned 1 exit status make: *** [Makefile:128: grappa] Error 1 * ERROR: sci-biology/grappa-2.0::science failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/grappa-2.0::science'`, * the complete build log and the output of `emerge -pqv '=sci-biology/grappa-2.0::science'`. * The complete build log is located at '/var/log/portage/sci-biology:grappa-2.0:20201118-001535.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/grappa-2.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/grappa-2.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/grappa-2.0/work/GRAPPA20' * S: '/var/tmp/portage/sci-biology/grappa-2.0/work/GRAPPA20'