=> Building biology/t_coffee Started : Thursday, 7 MAR 2019 at 18:40:36 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for t_coffee-9.03_9: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/construction/biology/t_coffee XDG_CONFIG_HOME=/construction/biology/t_coffee HOME=/construction/biology/t_coffee TMPDIR="/tmp" PATH=/construction/biology/t_coffee/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- FCC="gfortran5 -O -Wl,-rpath=/usr/local/lib/gcc5" F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/construction/biology/t_coffee XDG_CONFIG_HOME=/construction/biology/t_coffee HOME=/construction/biology/t_coffee TMPDIR="/tmp" PATH=/construction/biology/t_coffee/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -Wno-return-type -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin " LIBS="" CXX="c++" CXXFLAGS=" -pipe -Wno-return-type -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/t_coffee/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTEXAMPLES="" OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/t_coffee" EXAMPLESDIR="share/examples/t_coffee" DATADIR="share/t_coffee" WWWDIR="www/t_coffee" ETCDIR="etc/t_coffee" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/t_coffee DOCSDIR=/usr/local/share/doc/t_coffee EXAMPLESDIR=/usr/local/share/examples/t_coffee WWWDIR=/usr/local/www/t_coffee ETCDIR=/usr/local/etc/t_coffee -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> NOTICE: The t_coffee port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> t_coffee-9.03_9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> t_coffee-9.03_9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of t_coffee-9.03_9 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The t_coffee port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by t_coffee-9.03_9 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The t_coffee port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by t_coffee-9.03_9 for building => SHA256 Checksum OK for T-COFFEE_distribution_Version_9.03.r1318.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The t_coffee port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by t_coffee-9.03_9 for building ===> Extracting for t_coffee-9.03_9 => SHA256 Checksum OK for T-COFFEE_distribution_Version_9.03.r1318.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for t_coffee-9.03_9 ===> Applying ports patches for t_coffee-9.03_9 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> t_coffee-9.03_9 depends on executable: gfortran5 - not found ===> Installing existing package /packages/All/gcc5-5.5.0_6.txz Installing gcc5-5.5.0_6... `-- Installing binutils-2.32,1... | `-- Installing gettext-runtime-0.19.8.1_2... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done `-- Extracting binutils-2.32,1: .......... done `-- Installing gmp-6.1.2_1... `-- Extracting gmp-6.1.2_1: .......... done `-- Installing mpc-1.1.0_2... | `-- Installing mpfr-4.0.2... | `-- Extracting mpfr-4.0.2: .......... done `-- Extracting mpc-1.1.0_2: ......... done Extracting gcc5-5.5.0_6: .......... done Message from gcc5-5.5.0_6: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unsupported by upstream. Use GCC 7 or newer instead.. ===> t_coffee-9.03_9 depends on executable: gfortran5 - found ===> Returning to build of t_coffee-9.03_9 ===> t_coffee-9.03_9 depends on file: /usr/local/bin/as - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for t_coffee-9.03_9 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for t_coffee-9.03_9 --- TMalign --- --- util_constraints_list.o --- --- util_job_handling.o --- --- util_dps.o --- --- util_domain_constraints_list.o --- --- TMalign --- gfortran5 -O -Wl,-rpath=/usr/local/lib/gcc5 TMalign.f -o TMalign --- util_constraints_list.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_constraints_list.c --- util_job_handling.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_job_handling.c --- util_dps.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dps.c --- util_domain_constraints_list.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_domain_constraints_list.c --- util_analyse_constraints_list.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_analyse_constraints_list.c --- util_aln_analyze.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_aln_analyze.c --- util_constraints_list.o --- util_constraints_list.c: In function 'return_max_constraint_list': util_constraints_list.c:2013:9: warning: implicit declaration of function 'constraint_list2max'; did you mean 'constraint_list2avg'? [-Wimplicit-function-declaration] return constraint_list2max (CL); ^~~~~~~~~~~~~~~~~~~ constraint_list2avg --- aln_convertion_util.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c aln_convertion_util.c --- util_declare.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_declare.c --- hsearch.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c hsearch.c --- random.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c random.c --- util_make_tree.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_make_tree.c --- util.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util.c util.c: In function 'vvfork': util.c:4222:7: warning: implicit declaration of function 'wait'; did you mean 'vwait'? [-Wimplicit-function-declaration] wait((pid_t*)-1); ^~~~ vwait util.c: In function 'vwaitpid': util.c:4271:5: warning: implicit declaration of function 'waitpid'; did you mean 'vwaitpid'? [-Wimplicit-function-declaration] p=waitpid (p, status, options); ^~~~~~~ vwaitpid --- reformat_struc.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c reformat_struc.c --- reformat.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c reformat.c reformat.c: In function 'identify_seq_format': reformat.c:1272:13: warning: implicit declaration of function 'is_stockholm_aln'; did you mean 'is_stockhom_aln'? [-Wimplicit-function-declaration] if ( is_stockholm_aln (file))sprintf (format, "stockholm_aln"); ^~~~~~~~~~~~~~~~ is_stockhom_aln reformat.c:1275:27: warning: implicit declaration of function 'fast_format_determination' [-Wimplicit-function-declaration] else if (format_val = fast_format_determination(file)) ^~~~~~~~~~~~~~~~~~~~~~~~~ reformat.c: In function 'main_output': reformat.c:2256:6: warning: implicit declaration of function 'sp_triplet_coffee_evaluate_output'; did you mean 'triplet_coffee_evaluate_output'? [-Wimplicit-function-declaration] sp_triplet_coffee_evaluate_output (D1->A, (D1->A)->CL, out_file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ triplet_coffee_evaluate_output reformat.c:3058:6: warning: implicit declaration of function 'output_header_mat'; did you mean 'output_header'? [-Wimplicit-function-declaration] output_header_mat(D1->M, out_file); ^~~~~~~~~~~~~~~~~ output_header reformat.c: In function 'modify_data': reformat.c:10759:5: warning: implicit declaration of function 'redundate'; did you mean 'truncate'? [-Wimplicit-function-declaration] redundate (D1->S, D2->T,seq, tree); ^~~~~~~~~ truncate reformat.c:10775:5: warning: implicit declaration of function 'tree2nnode_unresolved'; did you mean 'tree2_nnode_unresolved'? [-Wimplicit-function-declaration] tree2nnode_unresolved (D1->T, l); ^~~~~~~~~~~~~~~~~~~~~ tree2_nnode_unresolved --- aln_compare.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c aln_compare.c --- io_func.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c io_func.c --- pb_util_read_sequence.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c pb_util_read_sequence.c --- pb_util_read_seq_util.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c pb_util_read_seq_util.c --- tree_util.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c tree_util.c --- util_graph_maln.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_graph_maln.c --- util_dp_clean_maln.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_clean_maln.c --- util_dp_ssec_pwaln.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_ssec_pwaln.c --- util_dp_sim.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_sim.c --- util_dp_mm_nw.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_mm_nw.c --- util_dp_gotoh_nw.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_gotoh_nw.c util_dp_gotoh_nw.c: In function 'aln2prf': util_dp_gotoh_nw.c:2625:6: warning: implicit declaration of function 'tolower' [-Wimplicit-function-declaration] r=tolower(A->seq_al[b][a]); ^~~~~~~ --- util_dp_suboptimal_nw.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_suboptimal_nw.c util_dp_suboptimal_nw.c: In function 'suboptimal_pair_wise': util_dp_suboptimal_nw.c:200:6: warning: implicit declaration of function 'idscore_pairseq' [-Wimplicit-function-declaration] id=idscore_pairseq(seqI,seqJ,-12, -1, CL->M, "idmat"); ^~~~~~~~~~~~~~~ util_dp_suboptimal_nw.c: In function 'free_proba_pair_wise': util_dp_suboptimal_nw.c:616:3: warning: implicit declaration of function 'proba_pair_wise'; did you mean 'free_pair_wise'? [-Wimplicit-function-declaration] proba_pair_wise (NULL, NULL, NULL, NULL); ^~~~~~~~~~~~~~~ free_pair_wise --- util_dp_cdna_fasta_nw.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_cdna_fasta_nw.c --- util_dp_generic_fasta_nw.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_generic_fasta_nw.c --- util_dp_fasta_nw.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_fasta_nw.c --- util_dp_fasta_sw.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_fasta_sw.c --- util_dp_gotoh_sw.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_gotoh_sw.c --- util_dp_est.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_est.c --- util_domain_dp_drivers.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_domain_dp_drivers.c --- util_dp_drivers.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_dp_drivers.c util_dp_drivers.c: In function 'sap_pair': util_dp_drivers.c:1647:12: warning: implicit declaration of function 'isalpha' [-Wimplicit-function-declaration] if (!isalpha(r1) || !isalpha(r2))continue; ^~~~~~~ util_dp_drivers.c: In function 'sorted_aln_old': util_dp_drivers.c:3170:10: warning: implicit declaration of function 'sa_align_groups'; did you mean 'seq2aln_group'? [-Wimplicit-function-declaration] while (sa_align_groups (A,CL,used,0,50)!=-1); ^~~~~~~~~~~~~~~ seq2aln_group util_dp_drivers.c: In function 'sa2sc': util_dp_drivers.c:3233:14: warning: implicit declaration of function 'tolower' [-Wimplicit-function-declaration] int r1=tolower(s1[a]); ^~~~~~~ util_dp_drivers.c: In function 'sa_get_next_group': util_dp_drivers.c:3347:12: warning: type defaults to 'int' in declaration of 'sim2' [-Wimplicit-int] static **sim2; ^~~~ util_dp_drivers.c: In function 'rec_tree_aln_N': util_dp_drivers.c:5747:11: warning: 'return' with no value, in function returning non-void if (!P) return; ^~~~~~ util_dp_drivers.c:5745:8: note: declared here char * rec_tree_aln_N ( NT_node P,Sequence *S,int N, int argv, char **argc) ^~~~~~~~~~~~~~ --- util_domain_dp.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c util_domain_dp.c --- CUSTOM_evaluate_for_struc.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c CUSTOM_evaluate_for_struc.c --- evaluate_for_struc.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c evaluate_for_struc.c --- evaluate_for_domain.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c evaluate_for_domain.c --- evaluate_dirichlet.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c evaluate_dirichlet.c --- evaluate.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c evaluate.c --- showpair.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c showpair.c --- fsa_dp.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c fsa_dp.c --- pavie_dp.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c pavie_dp.c --- dev1.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c dev1.c dev1.c: In function 'aln2hitMat': dev1.c:76:9: warning: implicit declaration of function 'tolower' [-Wimplicit-function-declaration] r1=tolower(A->seq_al[k][i]); ^~~~~~~ --- dev2.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c dev2.c --- dev3.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c dev3.c --- dev4.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c dev4.c --- fastal.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c fastal.c fastal.c: In function 'fastal_main': fastal.c:3786:3: warning: implicit declaration of function 'complete_agreement_score'; did you mean 'agreement_score'? [-Wimplicit-function-declaration] complete_agreement_score(arguments.aln2test, arguments.aln_ref); ^~~~~~~~~~~~~~~~~~~~~~~~ agreement_score fastal.c:3793:3: warning: implicit declaration of function 'compute_ref_alignments'; did you mean 'make_ref_alignment'? [-Wimplicit-function-declaration] compute_ref_alignments(arguments.sequence_file, arguments.aln_ref, arguments.num_ref_aln, arguments.num_seq_in_ref); ^~~~~~~~~~~~~~~~~~~~~~ make_ref_alignment --- parttree.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c parttree.c --- tree.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c tree.c --- diagonal.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c diagonal.c diagonal.c: In function 'segments2int': diagonal.c:284:27: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] list[list_pos][2] = M[toupper(seq1[tmpx-1])-'A'][toupper(seq2[tmpy-1])-'A']; ^~~~~~~ --- fastal_opt_parsing.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c fastal_opt_parsing.c --- scoring.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c scoring.c scoring.c:578:1: warning: return type defaults to 'int' [-Wimplicit-int] complete_agreement_score(char *aln_file_name, const char *ref_directory) ^~~~~~~~~~~~~~~~~~~~~~~~ --- iteration.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c iteration.c iteration.c: In function 'iterate': iteration.c:387:22: warning: implicit declaration of function 'gotoh_dyn' [-Wimplicit-function-declaration] alignment_length = gotoh_dyn(profiles, param, method_arguments_p, 0, edit_file, profile_file, 0); ^~~~~~~~~ iteration.c:411:7: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration] if (!strcmp(param->method, "fast")) ^~~~~~ iteration.c:417:3: warning: implicit declaration of function 'free_nw'; did you mean 'free_int'? [-Wimplicit-function-declaration] free_nw((Nw_param*)method_arguments_p, alphabet_size); ^~~~~~~ free_int --- Stack.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c Stack.c --- Vector.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c Vector.c --- classes.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c classes.c --- km_util.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c km_util.c --- kmeans.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c kmeans.c --- km_coffee.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c km_coffee.c --- kmeans.o --- kmeans.c: In function 'kkz_init': kmeans.c:87:7: warning: implicit declaration of function 'l2norm'; did you mean 'minor'? [-Wimplicit-function-declaration] tmp=l2norm(vec_set->vecs[i], dim); ^~~~~~ minor --- t_coffee.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c t_coffee.c t_coffee.c: In function 'run_other_pg': t_coffee.c:5388:10: warning: implicit declaration of function 'fastal_main'; did you mean 'batch_main'? [-Wimplicit-function-declaration] return fastal_main(argc, argv); ^~~~~~~~~~~ batch_main --- t_coffee --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o -lm util.o:util.c:function get_os.part.22: warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> t_coffee-9.03_9 depends on executable: clustalw - not found ===> Installing existing package /packages/All/clustalw-2.1_2.txz Installing clustalw-2.1_2... Extracting clustalw-2.1_2: ..... done ===> t_coffee-9.03_9 depends on executable: clustalw - found ===> Returning to build of t_coffee-9.03_9 ===> t_coffee-9.03_9 depends on executable: gfortran5 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for t_coffee-9.03_9 ===> Generating temporary packing list (cd /construction/biology/t_coffee/T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source && install -s -m 555 TMalign t_coffee /construction/biology/t_coffee/stage/usr/local/bin) /bin/mkdir -p /construction/biology/t_coffee/stage/usr/local/share/examples/t_coffee (cd /construction/biology/t_coffee/T-COFFEE_distribution_Version_9.03.r1318/example && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /construction/biology/t_coffee/stage/usr/local/share/examples/t_coffee) ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for t_coffee-9.03_9 file sizes/checksums [195]: .. done packing files [195]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 18:41:42 UTC Duration: 00:01:05