Date: Tue, 31 Jan 2017 11:07:26 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110armv6-quarterly][biology/t_coffee] Failed for t_coffee-9.03_4 in build Message-ID: <201701311107.v0VB7Q6A050459@beefy15.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: ports@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: branches/2017Q1/biology/t_coffee/Makefile 428057 2016-12-07 13:24:56Z gerald $ Log URL: http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/432890/logs/t_coffee-9.03_4.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=432890 Log: ====>> Building biology/t_coffee build started at Tue Jan 31 11:05:08 UTC 2017 port directory: /usr/ports/biology/t_coffee building for: FreeBSD 110armv6-quarterly-job-19 11.0-RELEASE-p5 FreeBSD 11.0-RELEASE-p5 r309692 arm maintained by: ports@FreeBSD.org Makefile ident: $FreeBSD: branches/2017Q1/biology/t_coffee/Makefile 428057 2016-12-07 13:24:56Z gerald $ Poudriere version: 3.1.14 Host OSVERSION: 1200018 Jail OSVERSION: 1100122 Job Id: 19 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o UNAME_v=FreeBSD 11.0-RELEASE-p5 r309692 UNAME_r=11.0-RELEASE-p5 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=armv6 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/ref QEMU_EMULATING=1 UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=t_coffee-9.03_4 OSREL=11.0 _OSRELEASE=11.0-RELEASE-p5 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=28 PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool MASTERNAME=110armv6-quarterly SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=1100122 ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for t_coffee-9.03_4: 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="gfortran49" FC="gfortran49" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc49" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc49" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/t_coffee/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/t_coffee/work HOME=/wrkdirs/usr/ports/biology/t_coffee/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- FCC="gfortran49 -O -Wl,-rpath=/usr/local/lib/gcc49" F77="gfortran49" FC="gfortran49" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc49" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc49" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/t_coffee/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/t_coffee/work HOME=/wrkdirs/usr/ports/biology/t_coffee/work TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES 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" CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -Wno-return-type -fno-strict-aliasing" CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -W l,-rpath=/usr/local/lib/gcc49 -L/usr/local/lib/gcc49 -B/usr/local/bin" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -Wno-return-type -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=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib 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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed READELF=/nxb-bin/usr/bin/readelf RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- =======================<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_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4_1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-19] Installing pkg-1.9.4_1... [110armv6-quarterly-job-19] Extracting pkg-1.9.4_1: .......... done ===> t_coffee-9.03_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of t_coffee-9.03_4 =========================================================================== =======================<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_4 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_4 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 <snip> util_dp_drivers.c:3615:22: warning: address of array 'CL->dp_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( CL && CL->dp_mode && strstr (CL->dp_mode, "collapse"))dump_constraint_list (CL, tmp, "w"); ~~ ~~~~^~~~~~~ util_dp_drivers.c:3618:22: warning: address of array 'CL->dp_mode' will always evaluate to 'true' [-Wpointer-bool-conversion] if ( CL && CL->dp_mode && strstr (CL->dp_mode, "collapse")) ~~ ~~~~^~~~~~~ 8 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c util_domain_dp.c -o util_domain_dp.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c CUSTOM_evaluate_for_struc.c -o CUSTOM_evaluate_for_struc.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c evaluate_for_struc.c -o evaluate_for_struc.o evaluate_for_struc.c:926:21: warning: comparison of array 'S->T[i]->P->template_file' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (S->T[i]->P->template_file != NULL) ~~~~~~~~~~~~^~~~~~~~~~~~~ ~~~~ 1 warning generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c evaluate_for_domain.c -o evaluate_for_domain.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c evaluate_dirichlet.c -o evaluate_dirichlet.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c evaluate.c -o evaluate.o evaluate.c:1218:13: warning: if statement has empty body [-Wempty-body] if (w);free_int (w, -1); ^ evaluate.c:1218:13: note: put the semicolon on a separate line to silence this warning evaluate.c:1368:13: warning: if statement has empty body [-Wempty-body] if (w);free_int (w, -1); ^ evaluate.c:1368:13: note: put the semicolon on a separate line to silence this warning 2 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c showpair.c -o showpair.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c fsa_dp.c -o fsa_dp.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c pavie_dp.c -o pavie_dp.o pavie_dp.c:1118:58: warning: operator '?:' has lower precedence than '*'; '*' will be evaluated first [-Wparentheses] gap_inY= F[i-1][j] + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ pavie_dp.c:1118:58: note: place parentheses around the '*' expression to silence this warning gap_inY= F[i-1][j] + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1); ^ ( ) pavie_dp.c:1118:58: note: place parentheses around the '?:' expression to evaluate it first gap_inY= F[i-1][j] + (CL->M[x[i-1]-'A'][gap]*(j==YL)?factor:1); ^ ( ) pavie_dp.c:1119:58: warning: operator '?:' has lower precedence than '*'; '*' will be evaluated first [-Wparentheses] gap_inX= F[i][j-1] + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ pavie_dp.c:1119:58: note: place parentheses around the '*' expression to silence this warning gap_inX= F[i][j-1] + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1); ^ ( ) pavie_dp.c:1119:58: note: place parentheses around the '?:' expression to evaluate it first gap_inX= F[i][j-1] + (CL->M[y[j-1]-'A'][gap]*(i==XL)?factor:1); ^ ( ) 2 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c dev1.c -o dev1.o dev1.c:63:42: warning: data argument not used by format string [-Wformat-extra-args] fprintf (stdout, "Process positions\n", i); ~~~~~~~~~~~~~~~~~~~~~ ^ dev1.c:76:9: warning: implicit declaration of function 'tolower' is invalid in C99 [-Wimplicit-function-declaration] r1=tolower(A->seq_al[k][i]); ^ 2 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c dev2.c -o dev2.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c dev3.c -o dev3.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c dev4.c -o dev4.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c fastal.c -o fastal.o fastal.c:3786:3: warning: implicit declaration of function 'complete_agreement_score' is invalid in C99 [-Wimplicit-function-declaration] complete_agreement_score(arguments.aln2test, arguments.aln_ref); ^ fastal.c:3793:3: warning: implicit declaration of function 'compute_ref_alignments' is invalid in C99 [-Wimplicit-function-declaration] compute_ref_alignments(arguments.sequence_file, arguments.aln_ref, arguments.num_ref_aln, arguments.num_seq_in_ref); ^ 2 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c parttree.c -o parttree.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c tree.c -o tree.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c diagonal.c -o diagonal.o diagonal.c:284:27: warning: implicit declaration of function 'toupper' is invalid in C99 [-Wimplicit-function-declaration] list[list_pos][2] = M[toupper(seq1[tmpx-1])-'A'][toupper(seq2[tmpy-1])-'A']; ^ 1 warning generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c fastal_opt_parsing.c -o fastal_opt_parsing.o fastal_opt_parsing.c:13:29: warning: result of comparison against a string literal is unspecified (use strncmp instead) [-Wstring-compare] if (arguments->tree_method == "parttree") ^ ~~~~~~~~~~ 1 warning generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c scoring.c -o scoring.o scoring.c:578:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] complete_agreement_score(char *aln_file_name, const char *ref_directory) ^ 1 warning generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c iteration.c -o iteration.o iteration.c:387:22: warning: implicit declaration of function 'gotoh_dyn' is invalid in C99 [-Wimplicit-function-declaration] alignment_length = gotoh_dyn(profiles, param, method_arguments_p, 0, edit_file, profile_file, 0); ^ iteration.c:411:7: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' [-Wimplicit-function-declaration] if (!strcmp(param->method, "fast")) ^ iteration.c:411:7: note: include the header <string.h> or explicitly provide a declaration for 'strcmp' iteration.c:417:3: warning: implicit declaration of function 'free_nw' is invalid in C99 [-Wimplicit-function-declaration] free_nw((Nw_param*)method_arguments_p, alphabet_size); ^ 3 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c Stack.c -o Stack.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c Vector.c -o Vector.o Vector.c:124:22: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] printf("DIM=%li\n", *vec_len); ~~~ ^~~~~~~~ %zu Vector.c:231:22: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] printf("DIM=%li\n", *vec_len); ~~~ ^~~~~~~~ %zu 2 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c classes.c -o classes.o /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c km_util.c -o km_util.o km_util.c:23:68: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); ~~~ ^~~~ %zu km_util.c:35:68: warning: format specifies type 'long' but the argument has type 'unsigned int' [-Wformat] fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size*num); ~~~ ^~~~~~~~ %u km_util.c:49:68: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] fprintf(stderr, "ERROR: Could not allocate space of size %li\n", size); ~~~ ^~~~ %zu 3 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c kmeans.c -o kmeans.o kmeans.c:87:7: warning: implicit declaration of function 'l2norm' is invalid in C99 [-Wimplicit-function-declaration] tmp=l2norm(vec_set->vecs[i], dim); ^ 1 warning generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c km_coffee.c -o km_coffee.o km_coffee.c:98:28: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command, "%li",current->id); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:100:99: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command,"clustalo --guidetree-out co_tree.dnd -i %li --force >/dev/null 2>/dev/null", current->id); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:107:174: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command,"t_coffee -usetree co_tree.dnd -in %li -output fasta_aln -dp_mode gotoh_pair_wise -outfile %li.fa -n_core %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, method); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:107:187: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command,"t_coffee -usetree co_tree.dnd -in %li -output fasta_aln -dp_mode gotoh_pair_wise -outfile %li.fa -n_core %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, method); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:109:173: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command,"t_coffee -usetree co_tree.dnd -in %li -output fasta_aln -dp_mode gotoh_pair_wise -outfile %s -n_core %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, method); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:118:28: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command, "%li",current->id); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:121:153: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command,"t_coffee -in %li -output fasta_aln -dp_mode gotoh_pair_wise -outfile %li.fa -n_core %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, method); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:121:166: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command,"t_coffee -in %li -output fasta_aln -dp_mode gotoh_pair_wise -outfile %li.fa -n_core %i -method %s -quiet >/dev/null 2>/dev/null", current->id, current->id, n_cores, method); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:123:152: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command,"t_coffee -in %li -output fasta_aln -dp_mode gotoh_pair_wise -outfile %s -n_core %i -method %s -quiet >/dev/null 2>/dev/null ", current->id, out_f, n_cores, method); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:132:31: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command, "%li.fa",current->id); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:142:169: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] sprintf(command, "t_coffee -output fasta_aln -dp_mode gotoh_pair_wise -quiet -outfile %li.fa -n_core %i -method %s -profile FILE::prf.fa 2>/dev/null >/dev/null", current->id,n_cores, method); ~~~ ^~~~~~~~~~~ %zu km_coffee.c:149:33: warning: format specifies type 'long' but the argument has type 'size_t' (aka 'unsigned int') [-Wformat] fprintf(prf_F, "%li.fa\n", current->children[j]->id); ~~~ ^~~~~~~~~~~~~~~~~~~~~~~~ %zu 12 warnings generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -fno-strict-aliasing -c t_coffee.c -o t_coffee.o t_coffee.c:5388:10: warning: implicit declaration of function 'fastal_main' is invalid in C99 [-Wimplicit-function-declaration] return fastal_main(argc, argv); ^ 1 warning generated. /nxb-bin/usr/bin/cc -O2 -pipe -Wno-return-type -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: In function `get_os': util.c:(.text+0x1075c): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp() gfortran49 -O -Wl,-rpath=/usr/local/lib/gcc49 TMalign.f -o TMalign /usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../libgfortran.so: undefined reference to `fpgetsticky' collect2: error: ld returned 1 exit status *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/t_coffee/work/T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source *** Error code 1 Stop. make: stopped in /usr/ports/biology/t_coffee
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