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Date:      Thu, 23 Mar 2017 03:30:47 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:  <201703230330.v2N3UlFT041407@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/436687/logs/t_coffee-9.03_4.log
Build URL:      http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=436687
Log:

====>> Building biology/t_coffee
build started at Thu Mar 23 03:29:03 UTC 2017
port directory: /usr/ports/biology/t_coffee
building for: FreeBSD 110armv6-quarterly-job-26 11.0-RELEASE-p8 FreeBSD 11.0-RELEASE-p8 r314125 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: 3.1.16-15-g422980c5
Host OSVERSION: 1200020
Jail OSVERSION: 1100122
Job Id: 26

---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1100122
UNAME_v=FreeBSD 11.0-RELEASE-p8 r314125
UNAME_r=11.0-RELEASE-p8
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/ref
QEMU_EMULATING=1
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=t_coffee-9.03_4
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool
MASTERNAME=110armv6-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.16-15-g422980c5
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
POUDRIEREPATH=/usr/local/bin/poudriere
---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
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
ARCH=armv6
CONFIGURE_MAX_CMD_LEN=262144
OPSYS=FreeBSD
OSREL=11.0
OSVERSION=1100122
PYTHONBASE=/usr/local
UID=0
_JAVA_OS_LIST_REGEXP=native\|linux
_JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun
_JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+
_OSRELEASE=11.0-RELEASE-p8
#### Misc Poudriere ####
GID=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
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---
--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

===>  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-26] Installing pkg-1.9.4_1...
[110armv6-quarterly-job-26] 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       >============================
<snip>
              ~~ ~~~~^~~~~~~
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: 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
util.o: In function `get_os':
util.c:(.text+0x109cc): 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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