* Package: sci-biology/t-coffee-11.00-r2 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox >>> Unpacking source... >>> Unpacking T-COFFEE_distribution_Version_11.00.4466924.tar.gz to /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work >>> Source unpacked in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924 ... * Applying t-coffee-11.00-mayhem.patch ... [ ok ] * Applying t-coffee-11.00-set_proper_dir_permissions.patch ... [ ok ] * Applying t-coffee-11.00-cxx11.patch ... [ ok ] * Applying t-coffee-11.00-gcc7.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924 ... make -j4 V=1 CC=x86_64-pc-linux-gnu-g++ 'CFLAGS=-O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result' -C t_coffee_source t_coffee make: Entering directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source' x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_domain_dp_drivers.deps -c -o dp_lib/util_domain_dp_drivers.o dp_lib/util_domain_dp_drivers.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_sim.deps -c -o dp_lib/util_dp_sim.o dp_lib/util_dp_sim.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_domain_dp.deps -c -o dp_lib/util_domain_dp.o dp_lib/util_domain_dp.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/fsa_dp.deps -c -o dp_lib/fsa_dp.o dp_lib/fsa_dp.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_generic_fasta_nw.deps -c -o dp_lib/util_dp_generic_fasta_nw.o dp_lib/util_dp_generic_fasta_nw.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/pavie_dp.deps -c -o dp_lib/pavie_dp.o dp_lib/pavie_dp.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_mm_nw.deps -c -o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_mm_nw.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_cdna_fasta_nw.deps -c -o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_cdna_fasta_nw.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_drivers.deps -c -o dp_lib/util_dp_drivers.o dp_lib/util_dp_drivers.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_suboptimal_nw.deps -c -o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_suboptimal_nw.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_gotoh_sw.deps -c -o dp_lib/util_dp_gotoh_sw.o dp_lib/util_dp_gotoh_sw.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate.deps -c -o dp_lib/evaluate.o dp_lib/evaluate.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_graph_maln.deps -c -o dp_lib/util_graph_maln.o dp_lib/util_graph_maln.c dp_lib/evaluate.c: In function ‘Alignment* msa2distances(Alignment*, Constraint_list*, float, float, int)’: dp_lib/evaluate.c:2909:53: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘int’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 2909 | fprintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~~~^ ~~~ | | | | double int | %3.2d dp_lib/evaluate.c:2909:67: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘double’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 2909 | rintf (stdout, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~^ ~~~~~~~ | | | | int double | %3f dp_lib/evaluate.c:2909:79: warning: format ‘%f’ expects argument of type ‘double’, but argument 6 has type ‘int’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 2909 | t, "##Groups s1: %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~~^ ~~~~~~~~ | | | | double int | %.3d dp_lib/evaluate.c:2909:95: warning: format ‘%d’ expects argument of type ‘int’, but argument 7 has type ‘double’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 2909 | %20s std_th: %3.2f min_size: %3d min_aa %.3f GroupIndex: %3d GroupSize: %3d pdbr: ", A->name[s1], a+1,clus_th, clus_min, min_aa, gsize); | ~~^ ~~~~~~ | | | | int double | %3f x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate_for_domain.deps -c -o dp_lib/evaluate_for_domain.o dp_lib/evaluate_for_domain.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate_dirichlet.deps -c -o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_dirichlet.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/evaluate_for_struc.deps -c -o dp_lib/evaluate_for_struc.o dp_lib/evaluate_for_struc.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_clean_maln.deps -c -o dp_lib/util_dp_clean_maln.o dp_lib/util_dp_clean_maln.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/CUSTOM_evaluate_for_struc.deps -c -o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/CUSTOM_evaluate_for_struc.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_fasta_nw.deps -c -o dp_lib/util_dp_fasta_nw.o dp_lib/util_dp_fasta_nw.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/showpair.deps -c -o dp_lib/showpair.o dp_lib/showpair.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_est.deps -c -o dp_lib/util_dp_est.o dp_lib/util_dp_est.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_gotoh_nw.deps -c -o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_gotoh_nw.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_fasta_sw.deps -c -o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_fasta_sw.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dp_lib/util_dp_ssec_pwaln.deps -c -o dp_lib/util_dp_ssec_pwaln.o dp_lib/util_dp_ssec_pwaln.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF io_lib/pb_util_read_sequence.deps -c -o io_lib/pb_util_read_sequence.o io_lib/pb_util_read_sequence.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF io_lib/io_func.deps -c -o io_lib/io_func.o io_lib/io_func.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF io_lib/pb_util_read_seq_util.deps -c -o io_lib/pb_util_read_seq_util.o io_lib/pb_util_read_seq_util.c io_lib/io_func.c: In function ‘int output_raw_score(Alignment*, Alignment*, char*)’: io_lib/io_func.c:1235:17: warning: converting to non-pointer type ‘int’ from NULL []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wconversion-null-Wconversion-null]8;;] 1235 | if (!A)return NULL; | ^~~~ io_lib/io_func.c: In function ‘int aln2compressed_ps(Alignment*, char*)’: io_lib/io_func.c:2076:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 2076 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF io_lib/tree_util.deps -c -o io_lib/tree_util.o io_lib/tree_util.c io_lib/tree_util.c: In function ‘Alignment* phylotrim(Alignment*, NT_node, char*, char*, char*)’: io_lib/tree_util.c:1299:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 1299 | } | ^ io_lib/tree_util.c: In function ‘tnode* no_rec_free_tree(NT_node)’: io_lib/tree_util.c:2317:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 2317 | } | ^ io_lib/tree_util.c: In function ‘int node_sort(char*, NT_node)’: io_lib/tree_util.c:6067:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 6067 | } | ^ io_lib/tree_util.c: In function ‘int treelist2leafgroup(Sequence*, Sequence*, char*)’: io_lib/tree_util.c:6321:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 6321 | } | ^ io_lib/tree_util.c: In function ‘int count_tree_groups(Sequence*, char*)’: io_lib/tree_util.c:6424:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 6424 | } | ^ io_lib/tree_util.c: In function ‘int treelist2splits(Sequence*, Sequence*)’: io_lib/tree_util.c:6802:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 6802 | } | ^ io_lib/tree_util.c: In function ‘int treelist2splits_old(Sequence*, Sequence*)’: io_lib/tree_util.c:6886:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 6886 | } | ^ io_lib/tree_util.c: In function ‘int treelist2frame(Sequence*, Sequence*)’: io_lib/tree_util.c:6959:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 6959 | } | ^ io_lib/tree_util.c: In function ‘char* graph2cons_d(long unsigned int, int)’: io_lib/tree_util.c:9328:27: warning: NULL used in arithmetic []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wpointer-arith-Wpointer-arith]8;;] 9328 | while ((c=rn_c(s))!=NULL) | ^~~~ io_lib/tree_util.c: In function ‘long unsigned int insert_gap_in_graph_d(long unsigned int)’: io_lib/tree_util.c:9346:20: warning: converting to non-pointer type ‘long unsigned int’ from NULL []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wconversion-null-Wconversion-null]8;;] 9346 | unsigned long pn=NULL; | ^~~~ io_lib/tree_util.c:9348:22: warning: converting to non-pointer type ‘long unsigned int’ from NULL []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wconversion-null-Wconversion-null]8;;] 9348 | if (!start) return NULL; | ^~~~ io_lib/tree_util.c:9361:14: warning: passing NULL to non-pointer argument 2 of ‘void wn_c(long unsigned int, long unsigned int)’ []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wconversion-null-Wconversion-null]8;;] 9361 | wn_c(n,NULL); | ^~~~ io_lib/tree_util.c:9112:46: note: declared here 9112 | void wn_c (unsigned long n, unsigned long t); | ~~~~~~~~~~~~~~^ io_lib/tree_util.c: In function ‘int check_node(ALN_node, char*)’: io_lib/tree_util.c:8937:1: warning: control reaches end of non-void function []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 8937 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/random.deps -c -o util_lib/random.o util_lib/random.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/aln_compare.deps -c -o util_lib/aln_compare.o util_lib/aln_compare.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/aln_convertion_util.deps -c -o util_lib/aln_convertion_util.o util_lib/aln_convertion_util.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/hsearch.deps -c -o util_lib/hsearch.o util_lib/hsearch.c util_lib/aln_convertion_util.c: In function ‘Alignment* aln2conservation(Alignment*, int, char*)’: util_lib/aln_convertion_util.c:4446:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 4446 | } | ^ util_lib/aln_convertion_util.c: In function ‘Alignment* aln2N_replicate(Alignment*, char*, char*)’: util_lib/aln_convertion_util.c:7698:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 7698 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_declare.deps -c -o util_lib/util_declare.o util_lib/util_declare.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_aln_analyze.deps -c -o util_lib/util_aln_analyze.o util_lib/util_aln_analyze.c util_lib/util_aln_analyze.c: In function ‘Alignment* sar_analyze(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:713:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 713 | } | ^ util_lib/util_aln_analyze.c: In function ‘Alignment* or_scan(Alignment*, Alignment*, char*)’: util_lib/util_aln_analyze.c:4480:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 4480 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/reformat_struc.deps -c -o util_lib/reformat_struc.o util_lib/reformat_struc.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_analyse_constraints_list.deps -c -o util_lib/util_analyse_constraints_list.o util_lib/util_analyse_constraints_list.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_make_tree.deps -c -o util_lib/util_make_tree.o util_lib/util_make_tree.c util_lib/util_make_tree.c: In function ‘tnode* redundate(Sequence*, NT_node, char*, char*)’: util_lib/util_make_tree.c:66:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 66 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util.deps -c -o util_lib/util.o util_lib/util.c util_lib/util.c: In function ‘int cherry(int, char**)’: util_lib/util.c:1009:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 1009 | } | ^ util_lib/util.c: In function ‘int dump_nfc(char*, char*)’: util_lib/util.c:4435:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 4435 | } | ^ util_lib/util.c: In function ‘int set_nproc(int)’: util_lib/util.c:5468:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 5468 | } | ^ util_lib/util.c: In function ‘char* vremove3(char*, char*)’: util_lib/util.c:6899:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 6899 | } | ^ util_lib/util.c: In function ‘int printf_system_direct_check(char*, ...)’: util_lib/util.c:4419:19: warning: control reaches end of non-void function []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 4419 | printf_exit ( EXIT_FAILURE, stderr, "ERROR: Could not run %s\n", buf); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util_lib/util.c: In function ‘int get_cl_param(int, char**, FILE**, const char*, int*, const char*, int, int, const char*, ...)’: util_lib/util.c:7533:2: warning: second parameter of ‘va_start’ not last named argument []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wvarargs-Wvarargs]8;;] 7533 | va_start (ap, usage); | ^~~~~~~~ util_lib/util.c: In function ‘int check_internet_connection(int)’: util_lib/util.c:8416:10: warning: control reaches end of non-void function []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 8416 | myexit (EXIT_FAILURE); | ~~~~~~~^~~~~~~~~~~~~~ util_lib/util.c: In function ‘int km_main(int, char**)’: util_lib/util.c:10318:1: warning: control reaches end of non-void function []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 10318 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/reformat.deps -c -o util_lib/reformat.o util_lib/reformat.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_dps.deps -c -o util_lib/util_dps.o util_lib/util_dps.c util_lib/reformat.c: In function ‘int output_suchard_aln(char*, Alignment*)’: util_lib/reformat.c:7395:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 7395 | } | ^ util_lib/reformat.c: In function ‘int output_header_mat(int**, char*)’: util_lib/reformat.c:14267:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 14267 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_job_handling.deps -c -o util_lib/util_job_handling.o util_lib/util_job_handling.c util_lib/reformat.c: In function ‘Sequence* quick_read_seq(char*)’: util_lib/reformat.c:1320:1: warning: control reaches end of non-void function []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 1320 | } | ^ util_lib/reformat.c: In function ‘Alignment* quick_read_aln(char*)’: util_lib/reformat.c:1362:1: warning: control reaches end of non-void function []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 1362 | } | ^ util_lib/reformat.c: In function ‘int fast_format_determination(char*)’: util_lib/reformat.c:2444:1: warning: control reaches end of non-void function []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 2444 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_domain_constraints_list.deps -c -o util_lib/util_domain_constraints_list.o util_lib/util_domain_constraints_list.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF util_lib/util_constraints_list.deps -c -o util_lib/util_constraints_list.o util_lib/util_constraints_list.c util_lib/util_constraints_list.c: In function ‘Constraint_list* unfreeze_constraint_list(Constraint_list*)’: util_lib/util_constraints_list.c:1312:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 1312 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF dev_lib/dev1.deps -c -o dev_lib/dev1.o dev_lib/dev1.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF t_coffee_lib/t_coffee.deps -c -o t_coffee_lib/t_coffee.o t_coffee_lib/t_coffee.c t_coffee_lib/t_coffee.c: In function ‘char** km_coffee(int, char**)’: t_coffee_lib/t_coffee.c:6527:1: warning: no return statement in function returning non-void []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 6527 | } | ^ t_coffee_lib/t_coffee.c: In function ‘Alignment* km_align_seq_slow(char*, Alignment*, int, char**, int, int)’: t_coffee_lib/t_coffee.c:6766:1: warning: control reaches end of non-void function []8;;https://gcc.gnu.org/onlinedocs/gfortran/Error-and-Warning-Options.html#index-Wreturn-type-Wreturn-type]8;;] 6766 | } | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF fastal/fastal.deps -c -o fastal/fastal.o fastal/fastal.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF fastal/fastal_opt_parsing.deps -c -o fastal/fastal_opt_parsing.o fastal/fastal_opt_parsing.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF fastal/parttree.deps -c -o fastal/parttree.o fastal/parttree.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF fastal/scoring.deps -c -o fastal/scoring.o fastal/scoring.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF fastal/diagonal.deps -c -o fastal/diagonal.o fastal/diagonal.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF fastal/tree.deps -c -o fastal/tree.o fastal/tree.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF fastal/iteration.deps -c -o fastal/iteration.o fastal/iteration.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF km_coffee/Vector.deps -c -o km_coffee/Vector.o km_coffee/Vector.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF km_coffee/kmeans.deps -c -o km_coffee/kmeans.o km_coffee/kmeans.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF km_coffee/km_coffee.deps -c -o km_coffee/km_coffee.o km_coffee/km_coffee.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF km_coffee/km_util.deps -c -o km_coffee/km_util.o km_coffee/km_util.c km_coffee/Vector.c: In function ‘void print_vecs(VectorSet*, char*)’: km_coffee/Vector.c:869:20: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 869 | fprintf(out_F, "%i ", i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %li km_coffee/km_util.c: In function ‘char* my_make_temp_dir(char*, char*)’: km_coffee/km_util.c:96:55: warning: format ‘%s’ expects a matching ‘char*’ argument []8;;https://gcc.gnu.org/onlinedocs/gcc/Warning-Options.html#index-Wformat=-Wformat=]8;;] 96 | fprintf(stderr, "This error was caused by '%s' in '%s'\n", function); | ~^ | | | char* x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF km_coffee/classes.deps -c -o km_coffee/classes.o km_coffee/classes.c x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -frecord-gcc-switches -Wno-write-strings -Wno-unused-result -I. -MD -MF km_coffee/Stack.deps -c -o km_coffee/Stack.o km_coffee/Stack.c x86_64-pc-linux-gnu-g++ dp_lib/util_domain_dp_drivers.o dp_lib/util_dp_sim.o dp_lib/util_domain_dp.o dp_lib/fsa_dp.o dp_lib/util_dp_generic_fasta_nw.o dp_lib/pavie_dp.o dp_lib/util_dp_mm_nw.o dp_lib/util_dp_cdna_fasta_nw.o dp_lib/util_dp_drivers.o dp_lib/util_dp_suboptimal_nw.o dp_lib/util_dp_gotoh_sw.o dp_lib/evaluate.o dp_lib/util_graph_maln.o dp_lib/evaluate_for_domain.o dp_lib/evaluate_dirichlet.o dp_lib/evaluate_for_struc.o dp_lib/util_dp_clean_maln.o dp_lib/CUSTOM_evaluate_for_struc.o dp_lib/util_dp_fasta_nw.o dp_lib/showpair.o dp_lib/util_dp_est.o dp_lib/util_dp_gotoh_nw.o dp_lib/util_dp_fasta_sw.o dp_lib/util_dp_ssec_pwaln.o io_lib/pb_util_read_sequence.o io_lib/io_func.o io_lib/pb_util_read_seq_util.o io_lib/tree_util.o util_lib/random.o util_lib/aln_compare.o util_lib/aln_convertion_util.o util_lib/hsearch.o util_lib/util_declare.o util_lib/util_aln_analyze.o util_lib/reformat_struc.o util_lib/util_analyse_constraints_list.o util_lib/util_make_tree.o util_lib/util.o util_lib/reformat.o util_lib/util_dps.o util_lib/util_job_handling.o util_lib/util_domain_constraints_list.o util_lib/util_constraints_list.o dev_lib/dev1.o t_coffee_lib/t_coffee.o fastal/fastal.o fastal/fastal_opt_parsing.o fastal/parttree.o fastal/scoring.o fastal/diagonal.o fastal/tree.o fastal/iteration.o km_coffee/Vector.o km_coffee/kmeans.o km_coffee/km_coffee.o km_coffee/km_util.o km_coffee/classes.o km_coffee/Stack.o -o t_coffee -lm /usr/lib/gcc/x86_64-pc-linux-gnu/10.1.0/../../../../x86_64-pc-linux-gnu/bin/ld: dp_lib/util_dp_drivers.o: in function `hh_pair(TC_method*, char*, Constraint_list*)': util_dp_drivers.c:(.text+0x2959): warning: the use of `tmpnam' is dangerous, better use `mkstemp' make: Leaving directory '/var/tmp/portage/sci-biology/t-coffee-11.00-r2/work/T-COFFEE_distribution_Version_11.00.4466924/t_coffee_source' >>> Source compiled. >>> Test phase: sci-biology/t-coffee-11.00-r2 >>> Completed testing sci-biology/t-coffee-11.00-r2 >>> Install sci-biology/t-coffee-11.00-r2 into /var/tmp/portage/sci-biology/t-coffee-11.00-r2/image/ >>> Completed installing sci-biology/t-coffee-11.00-r2 into /var/tmp/portage/sci-biology/t-coffee-11.00-r2/image/ * Final size of build directory: 22372 KiB (21.8 MiB) * Final size of installed tree: 7664 KiB ( 7.4 MiB) * QA Notice: Files built without respecting LDFLAGS have been detected * Please include the following list of files in your report: * /usr/bin/t_coffee strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version /usr/bin/t_coffee >>> Done. emerge --info: Portage 2.3.100 (python 3.7.7-final-0, default/linux/amd64/17.1, gcc-10.1.0, glibc-2.31-r3, 5.4.0-1009-aws x86_64) ================================================================= System uname: Linux-5.4.0-1009-aws-x86_64-AMD_EPYC_7571-with-gentoo-2.7 KiB Mem: 16011344 total, 1832892 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Mon, 25 May 2020 12:35:49 +0000 sh bash 5.0_p17 ld GNU ld (Gentoo 2.34 p4) 2.34.0 app-shells/bash: 5.0_p17::gentoo dev-lang/perl: 5.30.2-r2::gentoo dev-lang/python: 2.7.18::gentoo, 3.7.7-r2::gentoo, 3.8.3::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.18::gentoo sys-devel/autoconf: 2.69-r5::gentoo sys-devel/automake: 1.16.2::gentoo sys-devel/binutils: 2.34-r1::gentoo sys-devel/gcc: 10.1.0::gentoo sys-devel/gcc-config: 2.3::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers) sys-libs/glibc: 2.31-r3::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXX="x86_64-pc-linux-gnu-g++" CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="--with-bdeps=y --binpkg-respect-use=y -1 -b -k" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="C.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j4" PKGDIR="/root/.packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" USE="acl amd64 berkdb bzip2 cli crypt dri fortran gdbm iconv ipv6 libtirpc multilib ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS