Date: Sat, 27 Oct 2018 00:44:31 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv7-default][biology/t_coffee] Failed for t_coffee-9.03_8 in stage Message-ID: <201810270044.w9R0iVqH000552@beefy16.nyi.freebsd.org>
next in thread | raw e-mail | index | archive | help
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: head/biology/t_coffee/Makefile 475857 2018-07-29 22:18:44Z gerald $ Log URL: http://beefy16.nyi.freebsd.org/data/head-armv7-default/p482948_s339695/logs/t_coffee-9.03_8.log Build URL: http://beefy16.nyi.freebsd.org/build.html?mastername=head-armv7-default&build=p482948_s339695 Log: =>> Building biology/t_coffee build started at Sat Oct 27 00:43:01 UTC 2018 port directory: /usr/ports/biology/t_coffee package name: t_coffee-9.03_8 building for: FreeBSD head-armv7-default-job-24 13.0-CURRENT FreeBSD 13.0-CURRENT 1300000 arm maintained by: ports@FreeBSD.org Makefile ident: $FreeBSD: head/biology/t_coffee/Makefile 475857 2018-07-29 22:18:44Z gerald $ Poudriere version: 3.2.8 Host OSVERSION: 1200085 Jail OSVERSION: 1300000 Job Id: 24 !!! Jail is newer than host. (Jail: 1300000, Host: 1200085) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300000 UNAME_v=FreeBSD 13.0-CURRENT 1300000 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/usr/local/poudriere/data/.m/head-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv7-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for t_coffee-9.03_8: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran7" FC="gfortran7" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc7" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc7" 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" PATH=/wrkdirs/usr/ports/biology/t_coffee/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- FCC="gfortran7 -O -Wl,-rpath=/usr/local/lib/gcc7" F77="gfortran7" FC="gfortran7" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc7" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc7" 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" PATH=/wrkdirs/usr/ports/biology/t_coffee/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin 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 CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -p ipe -Wno-return-type -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc7 -L/usr/local/lib/gcc7 -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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTEXAMPLES="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local 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 PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 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 # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 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 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--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<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 <snip> 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: implicitly declaring library function 'tolower' with type 'int (int)' [-Wimplicit-function-declaration] r1=tolower(A->seq_al[k][i]); ^ dev1.c:76:9: note: include the header <ctype.h> or explicitly provide a declaration for 'tolower' 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: implicitly declaring library function 'toupper' with type 'int (int)' [-Wimplicit-function-declaration] list[list_pos][2] = M[toupper(seq1[tmpx-1])-'A'][toupper(seq2[tmpy-1])-'A']; ^ diagonal.c:284:27: note: include the header <ctype.h> or explicitly provide a declaration for 'toupper' 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 gfortran7 -O -Wl,-rpath=/usr/local/lib/gcc7 TMalign.f -o TMalign =========================================================================== =======================<phase: run-depends >============================ ===> t_coffee-9.03_8 depends on executable: clustalw - not found ===> Installing existing package /packages/All/clustalw-2.1_2.txz [head-armv7-default-job-24] Installing clustalw-2.1_2... [head-armv7-default-job-24] Extracting clustalw-2.1_2: ..... done ===> t_coffee-9.03_8 depends on executable: clustalw - found ===> Returning to build of t_coffee-9.03_8 ===> t_coffee-9.03_8 depends on executable: gfortran7 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for t_coffee-9.03_8 ===> Generating temporary packing list (cd /wrkdirs/usr/ports/biology/t_coffee/work/T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source && install -s -m 555 TMalign t_coffee /wrkdirs/usr/ports/biology/t_coffee/work/stage/usr/local/bin) /bin/mkdir -p /wrkdirs/usr/ports/biology/t_coffee/work/stage/usr/local/share/examples/t_coffee (cd /wrkdirs/usr/ports/biology/t_coffee/work/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 . /wrkdirs/usr/ports/biology/t_coffee/work/stage/usr/local/share/examples/t_coffee) Abort trap *** Error code 134 Stop. make: stopped in /usr/ports/biology/t_coffee
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201810270044.w9R0iVqH000552>