=> Building biology/t_coffee build started at Tue Oct 4 22:08:18 PDT 2016 port directory: /usr/ports/biology/t_coffee building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: ports@FreeBSD.org ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../03//usr/ports/biology/t_coffee/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=t_coffee-9.03_3 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for t_coffee-9.03_3: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/wrkdirs/biology/t_coffee XDG_CONFIG_HOME=/wrkdirs/biology/t_coffee HOME=/wrkdirs/biology/t_coffee TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --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=/wrkdirs/biology/t_coffee XDG_CONFIG_HOME=/wrkdirs/biology/t_coffee HOME=/wrkdirs/biology/t_coffee TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 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 LIBDIR="/usr/lib" 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 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" 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" --End PLIST_SUB-- --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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> 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 =========================================================================== =================================================== ===> t_coffee-9.03_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> t_coffee-9.03_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of t_coffee-9.03_3 =========================================================================== =================================================== =========================================================================== =================================================== ===> 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_3 for building =========================================================================== =================================================== ===> 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_3 for building => SHA256 Checksum OK for T-COFFEE_distribution_Version_9.03.r1318.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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_3 for building ===> Extracting for t_coffee-9.03_3 => SHA256 Checksum OK for T-COFFEE_distribution_Version_9.03.r1318.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for t_coffee-9.03_3 ===> Applying ports patches for t_coffee-9.03_3 =========================================================================== =================================================== ===> t_coffee-9.03_3 depends on executable: gfortran5 - not found ===> Installing existing package /packages/All/gcc5-5.4.0.txz Installing gcc5-5.4.0... `-- Installing indexinfo-0.2.5... `-- Extracting indexinfo-0.2.5: .... done `-- Installing mpc-1.0.3... | `-- Installing gmp-5.1.3_3... | `-- Extracting gmp-5.1.3_3: .......... done | `-- Installing mpfr-3.1.5... | `-- Extracting mpfr-3.1.5: .......... done `-- Extracting mpc-1.0.3: ...... done `-- Installing binutils-2.27_4,1... | `-- Installing gettext-runtime-0.19.8.1... | `-- Extracting gettext-runtime-0.19.8.1: .......... done `-- Extracting binutils-2.27_4,1: .......... done Extracting gcc5-5.4.0: .......... done Message from gcc5-5.4.0: 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. ===> t_coffee-9.03_3 depends on executable: gfortran5 - found ===> Returning to build of t_coffee-9.03_3 ===> t_coffee-9.03_3 depends on file: /usr/local/bin/as - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for t_coffee-9.03_3 =========================================================================== =================================================== ===> Building for t_coffee-9.03_3 --- 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' [-Wimplicit-function-declaration] return constraint_list2max (CL); ^ --- 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' [-Wimplicit-function-declaration] wait((pid_t*)-1); ^ util.c: In function 'vwaitpid': util.c:4271:5: warning: implicit declaration of function 'waitpid' [-Wimplicit-function-declaration] p=waitpid (p, status, options); ^ --- 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' [-Wimplicit-function-declaration] if ( is_stockholm_aln (file))sprintf (format, "stockholm_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' [-Wimplicit-function-declaration] sp_triplet_coffee_evaluate_output (D1->A, (D1->A)->CL, out_file); ^ reformat.c:3058:6: warning: implicit declaration of function 'output_header_mat' [-Wimplicit-function-declaration] output_header_mat(D1->M, out_file); ^ reformat.c: In function 'modify_data': reformat.c:10759:5: warning: implicit declaration of function 'redundate' [-Wimplicit-function-declaration] redundate (D1->S, D2->T,seq, tree); ^ reformat.c:10775:5: warning: implicit declaration of function 'tree2nnode_unresolved' [-Wimplicit-function-declaration] tree2nnode_unresolved (D1->T, l); ^ --- 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' [-Wimplicit-function-declaration] proba_pair_wise (NULL, NULL, NULL, NULL); ^ --- 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' [-Wimplicit-function-declaration] while (sa_align_groups (A,CL,used,0,50)!=-1); ^ 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_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' [-Wimplicit-function-declaration] complete_agreement_score(arguments.aln2test, arguments.aln_ref); ^ fastal.c:3793:3: warning: implicit declaration of function 'compute_ref_alignments' [-Wimplicit-function-declaration] compute_ref_alignments(arguments.sequence_file, arguments.aln_ref, arguments.num_ref_aln, arguments.num_seq_in_ref); ^ --- 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' [-Wimplicit-function-declaration] free_nw((Nw_param*)method_arguments_p, alphabet_size); ^ --- 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 kmeans.c: In function 'kkz_init': kmeans.c:87:7: warning: implicit declaration of function 'l2norm' [-Wimplicit-function-declaration] tmp=l2norm(vec_set->vecs[i], dim); ^ --- km_coffee.o --- cc -pipe -Wno-return-type -O2 -fno-strict-aliasing -c km_coffee.c --- 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' [-Wimplicit-function-declaration] return fastal_main(argc, argv); ^ --- 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 -lmutil.o:util.c:function get_os.part.12: warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() =========================================================================== =================================================== ===> t_coffee-9.03_3 depends on executable: clustalw - not found ===> Installing existing package /packages/All/clustalw-2.1_1.txz Installing clustalw-2.1_1... Extracting clustalw-2.1_1: .. done Message from clustalw-2.1_1: ===> NOTICE: The clustalw 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 ===> t_coffee-9.03_3 depends on executable: clustalw - found ===> Returning to build of t_coffee-9.03_3 ===> t_coffee-9.03_3 depends on executable: gfortran5 - found =========================================================================== =================================================== ===> Staging for t_coffee-9.03_3 ===> Generating temporary packing list (cd /wrkdirs/biology/t_coffee/T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source && install -s -m 555 TMalign t_coffee /wrkdirs/biology/t_coffee/stage/usr/local/bin) /bin/mkdir -p /wrkdirs/biology/t_coffee/stage/usr/local/share/examples/t_coffee (cd /wrkdirs/biology/t_coffee/T-COFFEE_distribution_Version_9.03.r1318/example && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null 2>&1) && /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; && /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' -- . /wrkdirs/biology/t_coffee/stage/usr/local/share/examples/t_coffee) ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for t_coffee-9.03_3 file sizes/checksums [195]: .. done packing files [195]: .. done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for t_coffee-9.03_3 build of biology/t_coffee ended at Tue Oct 4 22:09:27 PDT 2016 build time: 00:01:09