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build.

Maintainer:     tphil...@potion-studios.com
Last committer: b...@freebsd.org
Ident:          $FreeBSD: head/biology/mapm3/Makefile 300895 2012-07-14 
12:56:14Z beat $
Log URL:        
http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2013-09-19_01h04m14s/logs/mapm3-3.0.log
Build URL:      
http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2013-09-19_01h04m14s
Log:

====>> Building biology/mapm3
build started at Thu Sep 19 06:36:08 UTC 2013
port directory: /usr/ports/biology/mapm3
building for: FreeBSD head-amd64-default-job-17 10.0-CURRENT FreeBSD 
10.0-CURRENT amd64
maintained by: tphil...@potion-studios.com
Makefile ident:      $FreeBSD: head/biology/mapm3/Makefile 300895 2012-07-14 
12:56:14Z beat $
Poudriere version: 3.1-pre

---Begin Environment---
OSVERSION=1000055
UNAME_v=FreeBSD 10.0-CURRENT
UNAME_r=10.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
MASTERMNT=/usr/local/poudriere/data/build/head-amd64-default/ref
PKG_EXT=txz
tpid=3901
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
NBPARALLEL=24
PKGNG=1
PKGNAME=mapm3-3.0
PKG_DELETE=/usr/local/sbin/pkg delete -y -f
PKG_ADD=/usr/local/sbin/pkg add
PWD=/root
MASTERNAME=head-amd64-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
SKIPSANITY=0
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
---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
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=yes
---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-1.1.4_2.txz
Installing pkg-1.1.4_2... 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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