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Maintainer: tphil...@potion-studios.com Last committer: b...@freebsd.org Ident: $FreeBSD: head/biology/mapm3/Makefile 327709 2013-09-20 15:55:44Z bapt $ Log URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2013-12-13_10h32m20s/logs/mapm3-3.0.log Build URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2013-12-13_10h32m20s Log: ====>> Building biology/mapm3 build started at Fri Dec 13 23:04:44 UTC 2013 port directory: /usr/ports/biology/mapm3 building for: FreeBSD head-amd64-default-job-09 11.0-CURRENT FreeBSD 11.0-CURRENT r256430 amd64 maintained by: tphil...@potion-studios.com Makefile ident: $FreeBSD: head/biology/mapm3/Makefile 327709 2013-09-20 15:55:44Z bapt $ Poudriere version: 3.1-pre ---Begin Environment--- OSVERSION=1100000 UNAME_v=FreeBSD 11.0-CURRENT r256430 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin STATUS=1 MASTERMNT=/usr/local/poudriere/data/build/head-amd64-default/ref PKG_EXT=txz tpid=37730 POUDRIERE_BUILD_TYPE=bulk PKGNG=1 PKGNAME=mapm3-3.0 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add PWD=/root MASTERNAME=head-amd64-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/poudriere/pkg-static version PKG_BIN=/usr/local/sbin/pkg-static ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- TMPDIR="/tmp" SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mapm3 DOCSDIR=/usr/local/share/doc/mapm3 EXAMPLESDIR=/usr/local/share/examples/mapm3 WWWDIR=/usr/local/www/mapm3 ETCDIR=/usr/local/etc/mapm3 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes NO_RESTRICTED=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ===> Cleaning for mapm3-3.0 =======================<phase: check-config >============================ =========================================================================== =======================<phase: pkg-depends >============================ ===> mapm3-3.0 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.2.3.txz Installing pkg-1.2.3... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of mapm3-3.0 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> Fetching all distfiles required by mapm3-3.0 for building =========================================================================== =======================<phase: checksum >============================ ===> Fetching all distfiles required by mapm3-3.0 for building => SHA256 Checksum OK for mapm3-source.tar.Z. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> Fetching all distfiles required by mapm3-3.0 for building ===> Extracting for mapm3-3.0 => SHA256 Checksum OK for mapm3-source.tar.Z. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for mapm3-3.0 ===> Applying FreeBSD patches for mapm3-3.0 /bin/cp /wrkdirs/usr/ports/biology/mapm3/work/sun/* /wrkdirs/usr/ports/biology/mapm3/work =========================================================================== =======================<phase: build-depends >============================ =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for mapm3-3.0 =========================================================================== =======================<phase: build >============================ ===> Building for mapm3-3.0 cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/memlib.c -o ./lib/memlib.o ./lib/memlib.c:51:28: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] sf(ps_,ALLOC_FAIL_MSG,num,cell_sizeof,n_alloced); ^~~ ./lib/memlib.c:51:32: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] sf(ps_,ALLOC_FAIL_MSG,num,cell_sizeof,n_alloced); ^~~~~~~~~~~ ./lib/memlib.c:59:29: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] sprintf(ps_,ALLOC_MSG,num,cell_sizeof,((long)p),n_alloced); ^~~ ./lib/memlib.c:59:33: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat] sprintf(ps_,ALLOC_MSG,num,cell_sizeof,((long)p),n_alloced); ^~~~~~~~~~~ 4 warnings generated. cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/mathlib.c -o ./lib/mathlib.o cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/iolib.c -o ./lib/iolib.o ./lib/iolib.c:143:7: warning: implicit declaration of function 'get_directory' is invalid in C99 [-Wimplicit-function-declaration] if (!get_directory(dir)) { ^ ./lib/iolib.c:149:7: warning: implicit declaration of function 'get_home_directory' is invalid in C99 [-Wimplicit-function-declaration] if (!get_home_directory(dir)) { ^ ./lib/iolib.c:155:7: warning: implicit declaration of function 'get_code_directory' is invalid in C99 [-Wimplicit-function-declaration] if (!get_code_directory(dir)) { ^ ./lib/iolib.c:931:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ 4 warnings generated. cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/msglib.c -o ./lib/msglib.o cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/strlib.c -o ./lib/strlib.o cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/shell.c -o ./lib/shell.o ./lib/shell.c:1024:5: warning: implicit declaration of function 'do_hold' is invalid in C99 [-Wimplicit-function-declaration] hold (more_mode) { ^ ./lib/iolib.h:172:8: note: expanded from macro 'hold' for (do_hold(TRUE,with_more_on); holding>0; do_hold(FALSE,FALSE)) ^ ./lib/shell.c:1045:37: warning: data argument not used by format string [-Wformat-extra-args] else sf(str,"%s",cmd[i]->name,""); ~~~~ ^ ./lib/shell.c:1062:38: warning: data argument not used by format string [-Wformat-extra-args] else sf(ps,"%s\n",cmd[i]->name,""); ~~~~~~ ^ 3 warnings generated. cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/table.c -o ./lib/table.o ./lib/table.c:239:38: warning: control reaches end of non-void function [-Wreturn-type] { send(CRASH); /* NOT IMPLEMENTED */ } ^ 1 warning generated. cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/eqn.c -o ./lib/eqn.o cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/stats.c -o ./lib/stats.o cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/syscode.c -o ./lib/syscode.o ./lib/syscode.c:234:47: warning: trigraph ignored [-Wtrigraphs] { fprintf(stderr, "Untrapped error %d (???)\n",msg); exit(1); } ^ ./lib/syscode.c:236:44: warning: format string is not a string literal (potentially insecure) [-Wformat-security] (*(mstrmsg[msg]))(ps_); fprintf(stderr,ps_); fprintf(stderr,"\n"); ^~~ ./lib/syscode.c:243:36: warning: trigraph ignored [-Wtrigraphs] { fprintf(stderr,"Error %d (???)\n",msg); exit(1); } ^ ./lib/syscode.c:245:44: warning: format string is not a string literal (potentially insecure) [-Wformat-security] (*(mstrmsg[msg]))(ps_); fprintf(stderr,ps_); fprintf(stderr,"\n"); ^~~ ./lib/syscode.c:255:56: warning: trigraph ignored [-Wtrigraphs] if (msg<1 || msg>MSGS) { fprintf(stderr,"error #%d (???)\n",msg); exit(1); } ^ ./lib/syscode.c:257:42: warning: format string is not a string literal (potentially insecure) [-Wformat-security] (*(mstrmsg[msg]))(ps_); fprintf(stderr,ps_); ^~~ ./lib/syscode.c:269:42: warning: format string is not a string literal (potentially insecure) [-Wformat-security] (*(mstrmsg[msg]))(ps_); fprintf(stderr,ps_); ^~~ ./lib/syscode.c:502:2: warning: implicit declaration of function 'tgetent' is invalid in C99 [-Wimplicit-function-declaration] tgetent(bp,tty_type); ^ ./lib/syscode.c:503:9: warning: implicit declaration of function 'tgetnum' is invalid in C99 [-Wimplicit-function-declaration] if ((x=tgetnum("li"))>0) tty_lines=x; ^ ./lib/syscode.c:546:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ ./lib/syscode.c:744:6: warning: implicit declaration of function 'check_file_arg' is invalid in C99 [-Wimplicit-function-declaration] check_file_arg(*argc_ptr-i,argv[i+1],file_arg[LOAD_FILE_ARG], ^ ./lib/syscode.c:813:1: warning: control may reach end of non-void function [-Wreturn-type] } ^ 12 warnings generated. ld -r ./lib/memlib.o ./lib/mathlib.o ./lib/iolib.o ./lib/msglib.o ./lib/strlib.o ./lib/shell.o ./lib/table.o ./lib/eqn.o ./lib/stats.o ./lib/syscode.o -o lib.o cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/state.c -o ./mapm/state.o In file included from ./mapm/state.c:16: In file included from ./mapm/mapm.h:416: ./mapm/toplevel.h:46:1: warning: '/*' within block comment [-Wcomment] /* side-effects locus[], *num_loci; and, if verbose, may print a msg. ^ 1 warning generated. cc -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/reader.c -o ./mapm/reader.o In file included from ./mapm/reader.c:17: In file included from ./mapm/mapm.h:416: ./mapm/toplevel.h:46:1: warning: '/*' within block comment [-Wcomment] /* side-effects locus[], *num_loci; and, if verbose, may print a msg. ^ ./mapm/reader.c:424:16: warning: '&&' within '||' [-Wlogical-op-parentheses] if (first && xstreq(str,"symbols") || xstreq(str,"symbols:")) { ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ ~~ ./mapm/reader.c:424:16: note: place parentheses around the '&&' expression to silence this warning if (first && xstreq(str,"symbols") || xstreq(str,"symbols:")) { ^ ( ) ./mapm/reader.c:388:38: warning: while loop has empty body [-Wempty-body] getdataln(fp); while(nullstr(ln)); crunch(ln); ^ ./mapm/reader.c:388:38: note: put the semicolon on a separate line to silence this warning ./mapm/reader.c:697:6: warning: implicit declaration of function 'add_to_seg_dist' is invalid in C99 [-Wimplicit-function-declaration] add_to_seg_dist(converted,locus_num); ^ ./mapm/reader.c:704:5: warning: implicit declaration of function 'scale_seg_dist' is invalid in C99 [-Wimplicit-function-declaration] scale_seg_dist(locus_num); ^ ./mapm/reader.c:882:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] add_to_seg_dist(c,locus) ^~~~~~~~~~~~~~~ ./mapm/reader.c:889:6: error: non-void function 'add_to_seg_dist' should return a value [-Wreturn-type] return; ^ ./mapm/reader.c:893:6: error: non-void function 'add_to_seg_dist' should return a value [-Wreturn-type] return; ^ ./mapm/reader.c:905:6: error: non-void function 'add_to_seg_dist' should return a value [-Wreturn-type] return; ^ ./mapm/reader.c:917:6: error: non-void function 'add_to_seg_dist' should return a value [-Wreturn-type] return; ^ ./mapm/reader.c:922:6: error: non-void function 'add_to_seg_dist' should return a value [-Wreturn-type] return; ^ ./mapm/reader.c:927:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] scale_seg_dist(locus) ^~~~~~~~~~~~~~ 7 warnings and 5 errors generated. *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/mapm3/work *** Error code 1 Stop. make: stopped in /usr/ports/biology/mapm3 ===> Cleaning for mapm3-3.0 _______________________________________________ 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