=>> Building biology/mapm3 build started at Mon Apr 1 15:02:57 BST 2024 port directory: /usr/ports/biology/mapm3 package name: mapm3-3.0_1 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: tphilipp@potion-studios.com Makefile datestamp: -rw-r--r-- 1 root wheel 1178 Mar 8 2023 /usr/ports/biology/mapm3/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: c014f9c79a Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/06/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- tphilipp@potion-studios.com --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mapm3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mapm3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mapm3/work/.cache HOME=/wrkdirs/usr/ports/biology/mapm3/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/mapm3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mapm3/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mapm3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mapm3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/mapm3/work/.cache HOME=/wrkdirs/usr/ports/biology/mapm3/work TMPDIR="/tmp" PATH=/ccache/libexec/ccache:/wrkdirs/usr/ports/biology/mapm3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/mapm3/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing " CCACHE_DIR="/root/.ccache" 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-- OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/mapm3" EXAMPLESDIR="share/examples/mapm3" DATADIR="share/mapm3" WWWDIR="www/mapm3" ETCDIR="etc/mapm3" --End PLIST_SUB-- --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 FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.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) 8192 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-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> mapm3-3.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> mapm3-3.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mapm3-3.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mapm3-3.0_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mapm3-3.0_1 for building => SHA256 Checksum OK for mapm3-source.tar.Z. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by mapm3-3.0_1 for building ===> Extracting for mapm3-3.0_1 => SHA256 Checksum OK for mapm3-source.tar.Z. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for mapm3-3.0_1 ===> Applying FreeBSD patches for mapm3-3.0_1 from /usr/ports/biology/mapm3/files cp -f /wrkdirs/usr/ports/biology/mapm3/work/mapm3-3.0_1/sun/* /wrkdirs/usr/ports/biology/mapm3/work/mapm3-3.0_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for mapm3-3.0_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for mapm3-3.0_1 cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -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 -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/mathlib.c -o ./lib/mathlib.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/iolib.c -o ./lib/iolib.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/msglib.c -o ./lib/msglib.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/strlib.c -o ./lib/strlib.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/shell.c -o ./lib/shell.o ./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,""); ~~~~~~ ^ 2 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/table.c -o ./lib/table.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/eqn.c -o ./lib/eqn.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/stats.c -o ./lib/stats.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -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:236:44: note: treat the string as an argument to avoid this (*(mstrmsg[msg]))(ps_); fprintf(stderr,ps_); fprintf(stderr,"\n"); ^ "%s", ./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:245:44: note: treat the string as an argument to avoid this (*(mstrmsg[msg]))(ps_); fprintf(stderr,ps_); fprintf(stderr,"\n"); ^ "%s", ./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:257:42: note: treat the string as an argument to avoid this (*(mstrmsg[msg]))(ps_); fprintf(stderr,ps_); ^ "%s", ./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:269:42: note: treat the string as an argument to avoid this (*(mstrmsg[msg]))(ps_); fprintf(stderr,ps_); ^ "%s", 7 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 -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -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 -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -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: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 2 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/ctm.c -o ./mapm/ctm.o In file included from ./mapm/ctm.c:18: 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 -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/print.c -o ./mapm/print.o In file included from ./mapm/print.c:19: 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/print.c:367:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sf(line2,empty_loc_str); sf(line1,empty_loc_str); ^~~~~~~~~~~~~ ./mapm/print.c:21:23: note: expanded from macro 'empty_loc_str' #define empty_loc_str loc2str(-1) ^~~~~~~~~~~ ./mapm/print.c:367:14: note: treat the string as an argument to avoid this sf(line2,empty_loc_str); sf(line1,empty_loc_str); ^ "%s", ./mapm/print.c:21:23: note: expanded from macro 'empty_loc_str' #define empty_loc_str loc2str(-1) ^ ./mapm/print.c:367:39: warning: format string is not a string literal (potentially insecure) [-Wformat-security] sf(line2,empty_loc_str); sf(line1,empty_loc_str); ^~~~~~~~~~~~~ ./mapm/print.c:21:23: note: expanded from macro 'empty_loc_str' #define empty_loc_str loc2str(-1) ^~~~~~~~~~~ ./mapm/print.c:367:39: note: treat the string as an argument to avoid this sf(line2,empty_loc_str); sf(line1,empty_loc_str); ^ "%s", ./mapm/print.c:21:23: note: expanded from macro 'empty_loc_str' #define empty_loc_str loc2str(-1) ^ ./mapm/print.c:532:8: warning: incomplete format specifier [-Wformat] sf(ps,LIST_LINE,locus[i]+1,locname(locus[i],haplo), ^~~~~~~~~ ./mapm/print.c:503:46: note: expanded from macro 'LIST_LINE' "%4d %-9s %10s %5.2lf%% %-8s %-8s %-9s %-" ^~ 4 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/sequence.c -o ./mapm/sequence.o In file included from ./mapm/sequence.c:18: 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 -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/main.c -o ./mapm/main.o In file included from ./mapm/main.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. ^ ./mapm/main.c:62:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] } on_error { print("error opening photo file\n"); } ^ ./lib/msglib.h:168:41: note: expanded from macro 'on_error' #define on_error while(--lvl>10000); } else ^ ./mapm/main.c:68:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] } on_error { print("error opening load or prep file\n"); } ^ ./lib/msglib.h:168:41: note: expanded from macro 'on_error' #define on_error while(--lvl>10000); } else ^ ./mapm/main.c:72:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] } on_error { print("error opening run file\n"); } ^ ./lib/msglib.h:168:41: note: expanded from macro 'on_error' #define on_error while(--lvl>10000); } else ^ 4 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/quick23.c -o ./mapm/quick23.o In file included from ./mapm/quick23.c:15: 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 -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/maps.c -o ./mapm/maps.o In file included from ./mapm/maps.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 -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/info.c -o ./mapm/info.o In file included from ./mapm/info.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. ^ ./mapm/info.c:401:12: warning: expression result unused [-Wunused-value] for (p; p->next_same2 != NULL; p= p->next_same2) {} ^ 2 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/chroms.c -o ./mapm/chroms.o In file included from ./mapm/chroms.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/chroms.c:404:12: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] sf(ps,ANCHOR_ISFRAME,loc2str(locus[j]),chrom2str(old_chrom)); ^~~~~~~~~~~~~~ ./mapm/chroms.c:387:58: note: expanded from macro 'ANCHOR_ISFRAME' "%s is a framework marker on %s...cannot re-assign to %s\n" ~^ ./mapm/chroms.c:408:13: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] sf(ps,ANCHOR_ISANCH,loc2str(locus[j]),chrom2str(old_chrom)); ^~~~~~~~~~~~~ ./mapm/chroms.c:389:58: note: expanded from macro 'ANCHOR_ISANCH' "%s is a framework marker on %s...cannot re-assign to %s\n" ~^ ./mapm/chroms.c:856:7: warning: format string is not a string literal (potentially insecure) [-Wformat-security] chrom2str(j)); pr(); ^~~~~~~~~~~~ ./mapm/map_info.h:218:22: note: expanded from macro 'chrom2str' #define chrom2str(x) ((x)>=0 ? chromosome->map_list[x]->map_name : WRS("none")) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./mapm/chroms.c:856:7: note: treat the string as an argument to avoid this chrom2str(j)); pr(); ^ "%s", ./mapm/map_info.h:218:22: note: expanded from macro 'chrom2str' #define chrom2str(x) ((x)>=0 ? chromosome->map_list[x]->map_name : WRS("none")) ^ 4 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/orders.c -o ./mapm/orders.o In file included from ./mapm/orders.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. ^ 1 warning generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/sys_cmds.c -o ./mapm/sys_cmds.o In file included from ./mapm/sys_cmds.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 -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/two_cmds.c -o ./mapm/two_cmds.o In file included from ./mapm/two_cmds.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/two_cmds.c:500:9: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat] cm_dist(thetam),cm_dist(thetaf)); pr(); ^~~~~~~~~~~~~~~ ./mapm/map_info.h:418:24: note: expanded from macro 'cm_dist' #define cm_dist(theta) ((*mapfunction->rec_to_dist)(theta)*100.0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ./mapm/two_cmds.c:500:25: warning: format specifies type 'char *' but the argument has type 'double' [-Wformat] cm_dist(thetam),cm_dist(thetaf)); pr(); ^~~~~~~~~~~~~~~ ./mapm/map_info.h:418:24: note: expanded from macro 'cm_dist' #define cm_dist(theta) ((*mapfunction->rec_to_dist)(theta)*100.0) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/npt_cmds.c -o ./mapm/npt_cmds.o ./mapm/npt_cmds.c:11:1: warning: '/*' within block comment [-Wcomment] /* This file is part of MAPMAKER 3.0b, Copyright 1987-1992, Whitehead Institute ^ In file included from ./mapm/npt_cmds.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. ^ 2 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/auto_cmd.c -o ./mapm/auto_cmd.o In file included from ./mapm/auto_cmd.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. ^ 1 warning generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./lib/makehelp.c -o ./lib/makehelp.o cc ./lib/makehelp.o lib.o -fstack-protector-strong -lm -lncurses -o ./lib/makehelp ./lib/makehelp ./mapm/mapmhelp.src ./mapm/mapmhelp.c mapmaker.help mapmaker.ps General Information... About MAPMAKER... Release Notes... Starting MAPMAKER... Tutorial... entering commands... abbreviating commands... keyboard editing... PostScript Output... Basic Commands... help... photo... prepare data... load data... save data... quit... Sequences... sequence... history... expand sequence... insert... append... delete... edit sequence... let... names... forget named sequence... translate... Two-Point Analysis... two point... lod table... big lods... near... links... pairwise... group... default linkage criteria... suggest subset... informativeness criteria... Multipoint Analysis... map... draw map... compare... try... ripple... order... build... multipoint criteria... Genome Analysis... make chromosome... assign... attach... unassign... anchor... framework... place... together... list loci... list status... list chromosomes... list assignments... draw chromosome... draw all chromosomes... age... class... make class... Error Detection... error detection... error probability... error thresholds... genotypes... Three Point... use three point... three point... triple linkage criteria... triple exclusion criteria... triple error detection... forget three point... Joining Haplotypes... join haplotypes... list haplotypes... restore haplotypes... Parameters and Options... print names... print maps... tolerance... auto save data... units... centimorgan function... more mode... Miscellaneous Commands... previous commands... review output... change directory... run... time... comment... remark... system... import data... export data... wizard mode... ./lib/makehelp done cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/mapmhelp.c -o ./mapm/mapmhelp.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/database.c -o ./mapm/database.o In file included from ./mapm/database.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 -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./mapm/ps_maps.c -o ./mapm/ps_maps.o In file included from ./mapm/ps_maps.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 ./mapm/state.o ./mapm/reader.o ./mapm/ctm.o ./mapm/print.o ./mapm/sequence.o ./mapm/main.o ./mapm/quick23.o ./mapm/maps.o ./mapm/info.o ./mapm/chroms.o ./mapm/orders.o ./mapm/sys_cmds.o ./mapm/two_cmds.o ./mapm/npt_cmds.o ./mapm/auto_cmd.o ./mapm/mapmhelp.o ./mapm/database.o ./mapm/ps_maps.o lib.o -fstack-protector-strong -lm -lncurses -o mapmaker cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qcmds.c -o ./quant/qcmds.o ./quant/qcmds.c:1068:24: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] fprintf(fp,"*loci\t \%AA\t \%AB \%BB\t n_indivs"); ~~^ ./quant/qcmds.c:1077:7: warning: format specifies type 'double' but the argument has type 'int' [-Wformat] 100*tot_aa/total_num,100*tot_bb/total_num,100*tot_ab/total_num, ^~~~~~~~~~~~~~~~~~~~ ./quant/qcmds.c:1077:28: warning: format specifies type 'double' but the argument has type 'int' [-Wformat] 100*tot_aa/total_num,100*tot_bb/total_num,100*tot_ab/total_num, ^~~~~~~~~~~~~~~~~~~~ ./quant/qcmds.c:1077:49: warning: format specifies type 'double' but the argument has type 'int' [-Wformat] 100*tot_aa/total_num,100*tot_bb/total_num,100*tot_ab/total_num, ^~~~~~~~~~~~~~~~~~~~ ./quant/qcmds.c:1413:6: warning: format specifies type 'int' but the argument has type 'char *' [-Wformat] temp,BADDATA_line_num); pr(); ^~~~ ./quant/qcmds.c:1413:11: warning: data argument not used by format string [-Wformat-extra-args] temp,BADDATA_line_num); pr(); ^ 6 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qctm.c -o ./quant/qctm.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qdata.c -o ./quant/qdata.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qseq.c -o ./quant/qseq.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qtop.c -o ./quant/qtop.o ./quant/qtop.c:128:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] } on_error { print("error opening photo file\n"); } ^ ./lib/msglib.h:168:41: note: expanded from macro 'on_error' #define on_error while(--lvl>10000); } else ^ ./quant/qtop.c:132:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] } on_error { print("error opening run file\n"); } ^ ./lib/msglib.h:168:41: note: expanded from macro 'on_error' #define on_error while(--lvl>10000); } else ^ 2 warnings generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qraw.c -o ./quant/qraw.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qprint.c -o ./quant/qprint.o ./quant/qprint.c:703:33: warning: data argument not used by format string [-Wformat-extra-args] genetics->a,genetics->b,genetics->c); ^ 1 warning generated. cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qcontext.c -o ./quant/qcontext.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qwiggle.c -o ./quant/qwiggle.o cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qps_scan.c -o ./quant/qps_scan.o ./lib/makehelp ./quant/qtlhelp.src ./quant/qtlhelp.c qtl.help qtl.ps General Information... About MAPMAKER/QTL... Release Notes... Starting MAPMAKER/QTL... Tutorial... entering commands... abbreviating commands... keyboard editing... PostScript Output... Basic Commands... help... photo... load data... save data... quit... Sequences... sequence... history... list loci... edit sequence... let... names... forget named sequence... Traits... trait... make trait... show trait... list traits... forget trait... Mapping Commands... map... scan... list scans... show scan... draw scan... forget scan... forget all scans... show peaks... show trys... compare... list compares... show compare... forget compare... forget all compares... show best maps... show linkage map... Parameters and Options... print names... units... auto save data... more mode... Miscellaneous Commands... run... change directory... system... previous commands... review output... time... comment... wizard mode... ./lib/makehelp done cc -O2 -pipe -fcommon -Wno-return-type -fstack-protector-strong -fno-strict-aliasing -std=gnu89 -I./lib/ -D_SYS_BSD -D_BIG_DATASETS -c ./quant/qtlhelp.c -o ./quant/qtlhelp.o cc ./quant/qcmds.o ./quant/qctm.o ./quant/qdata.o ./quant/qseq.o ./quant/qtop.o ./quant/qraw.o ./quant/qprint.o ./quant/qcontext.o ./quant/qwiggle.o ./quant/qps_scan.o ./quant/qtlhelp.o lib.o -fstack-protector-strong -lm -lncurses -o qtl =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for mapm3-3.0_1 ===> Generating temporary packing list cp mapmaker mapmaker.help xmapmaker /wrkdirs/usr/ports/biology/mapm3/work/stage/usr/local/bin cp qtl qtl.help xqtl /wrkdirs/usr/ports/biology/mapm3/work/stage/usr/local/bin /usr/bin/strip /wrkdirs/usr/ports/biology/mapm3/work/stage/usr/local/bin/mapmaker /usr/bin/strip /wrkdirs/usr/ports/biology/mapm3/work/stage/usr/local/bin/qtl ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-01T14:02:57+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=c014f9c79a' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for mapm3-3.0_1 ===> Building mapm3-3.0_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for mapm3-3.0_1 build of biology/mapm3 | mapm3-3.0_1 ended at Mon Apr 1 15:03:23 BST 2024 build time: 00:00:26