[package - main-armv7-default][biology/emboss] Failed for emboss-6.6.0_7 in build
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Date: Sat, 13 Sep 2025 18:59:00 UTC
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: wen@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere2/data/main-armv7-default/p6fecc51c6cfb_s1344979687/logs/emboss-6.6.0_7.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p6fecc51c6cfb_s1344979687
Log:
=>> Building biology/emboss
build started at Sat Sep 13 18:44:57 UTC 2025
port directory: /usr/ports/biology/emboss
package name: emboss-6.6.0_7
building for: FreeBSD main-armv7-default-job-03 15.0-PRERELEASE FreeBSD 15.0-PRERELEASE 1500063 arm
maintained by: wen@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1771 Jan 6 2024 /usr/ports/biology/emboss/Makefile
Ports top last git commit: 6fecc51c6cf
Ports top unclean checkout: no
Port dir last git commit: ee6c86aea57
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.3
Host OSVERSION: 1500061
Jail OSVERSION: 1500063
Job Id: 03
!!! Jail is newer than host. (Jail: 1500063, Host: 1500061) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1500063
UNAME_v=FreeBSD 15.0-PRERELEASE 1500063
UNAME_r=15.0-PRERELEASE
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=3.4.3
MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=tmux-256color
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-armv7-default/03/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-armv7-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.3
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---
===> The following configuration options are available for emboss-6.6.0_7:
DOCS=on: Build and/or install documentation
MYSQL=off: MySQL database support
X11=on: X11 (graphics) support
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
wen@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--with-docroot=/usr/local/emboss/share/EMBOSS/doc --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local/emboss ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/emboss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/emboss/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/emboss/work/.cache HOME=/wrkdirs/usr/ports/biology/emboss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/emboss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/emboss/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
OPENSSLBASE=/usr OPENSSLDIR=/etc/ssl OPENSSLINC=/usr/include OPENSSLLIB=/usr/lib MOTIFLIB="-L/usr/local/lib -lXm" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/emboss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/emboss/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/emboss/work/.cache HOME=/wrkdirs/usr/ports/biology/emboss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/emboss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/emboss/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/emboss LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib -L/usr/local/lib " LIBS="" CX
X="c++" CXXFLAGS="-O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include " 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--
PORTDOCS="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local/emboss LIB32DIR=lib DOCSDIR="share/EMBOSS/doc" EXAMPLESDIR="share/examples/emboss" DATADIR="share/EMBOSS" WWWDIR="www/emboss" ETCDIR="etc/emboss"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local/emboss DATADIR=/usr/local/emboss/share/EMBOSS PREFIX=/usr/local/emboss LOCALBASE=/usr/local DATADIR=/usr/local/emboss/share/EMBOSS DOCSDIR=/usr/local/emboss/share/EMBOSS/doc EXAMPLESDIR=/usr/local/emboss/share/examples/emboss WWWDIR=/usr/local/emboss/www/emboss ETCDIR=/usr/local/emboss/etc/emboss
--End SUB_LIST--
---Begin 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 3 jobs
MAKE_JOBS_NUMBER=3
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# 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 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
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
pipebuf (-y) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> emboss-6.6.0_7 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.2.2.pkg
[main-armv7-default-job-03] Installing pkg-2.2.2...
[main-armv7-default-job-03] Extracting pkg-2.2.2: .......... done
===> emboss-6.6.0_7 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of emboss-6.6.0_7
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by emboss-6.6.0_7 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by emboss-6.6.0_7 for building
=> SHA256 Checksum OK for emboss/EMBOSS-6.6.0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by emboss-6.6.0_7 for building
===> Extracting for emboss-6.6.0_7
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by emboss-6.6.0_7 for building
=> SHA256 Checksum OK for emboss/EMBOSS-6.6.0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for emboss-6.6.0_7
===> Applying FreeBSD patches for emboss-6.6.0_7 from /usr/ports/biology/emboss/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> emboss-6.6.0_7 depends on executable: clustalw - not found
<snip>
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
mv -f .deps/libajax_la-ajphylo.Tpo .deps/libajax_la-ajphylo.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrange.lo -MD -MP -MF .deps/libajax_la-ajrange.Tpo -c -o libajax_la-ajrange.lo `test -f 'ajrange.c' || echo './'`ajrange.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrange.lo -MD -MP -MF .deps/libajax_la-ajrange.Tpo -c ajrange.c -fPIC -DPIC -o .libs/libajax_la-ajrange.o
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajindex.lo -MD -MP -MF .deps/libajax_la-ajindex.Tpo -c ajindex.c -o libajax_la-ajindex.o >/dev/null 2>&1
In file included from ajrange.c:35:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajquery.lo -MD -MP -MF .deps/libajax_la-ajquery.Tpo -c ajquery.c -o libajax_la-ajquery.o >/dev/null 2>&1
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrange.lo -MD -MP -MF .deps/libajax_la-ajrange.Tpo -c ajrange.c -o libajax_la-ajrange.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajquery.Tpo .deps/libajax_la-ajquery.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajreg.lo -MD -MP -MF .deps/libajax_la-ajreg.Tpo -c -o libajax_la-ajreg.lo `test -f 'ajreg.c' || echo './'`ajreg.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajreg.lo -MD -MP -MF .deps/libajax_la-ajreg.Tpo -c ajreg.c -fPIC -DPIC -o .libs/libajax_la-ajreg.o
In file included from ajreg.c:32:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajreg.lo -MD -MP -MF .deps/libajax_la-ajreg.Tpo -c ajreg.c -o libajax_la-ajreg.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajrange.Tpo .deps/libajax_la-ajrange.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajreport.lo -MD -MP -MF .deps/libajax_la-ajreport.Tpo -c -o libajax_la-ajreport.lo `test -f 'ajreport.c' || echo './'`ajreport.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajreport.lo -MD -MP -MF .deps/libajax_la-ajreport.Tpo -c ajreport.c -fPIC -DPIC -o .libs/libajax_la-ajreport.o
In file included from ajreport.c:31:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
mv -f .deps/libajax_la-ajreg.Tpo .deps/libajax_la-ajreg.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrefseq.lo -MD -MP -MF .deps/libajax_la-ajrefseq.Tpo -c -o libajax_la-ajrefseq.lo `test -f 'ajrefseq.c' || echo './'`ajrefseq.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrefseq.lo -MD -MP -MF .deps/libajax_la-ajrefseq.Tpo -c ajrefseq.c -fPIC -DPIC -o .libs/libajax_la-ajrefseq.o
In file included from ajrefseq.c:30:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrefseq.lo -MD -MP -MF .deps/libajax_la-ajrefseq.Tpo -c ajrefseq.c -o libajax_la-ajrefseq.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajrefseq.Tpo .deps/libajax_la-ajrefseq.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrefseqread.lo -MD -MP -MF .deps/libajax_la-ajrefseqread.Tpo -c -o libajax_la-ajrefseqread.lo `test -f 'ajrefseqread.c' || echo './'`ajrefseqread.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrefseqread.lo -MD -MP -MF .deps/libajax_la-ajrefseqread.Tpo -c ajrefseqread.c -fPIC -DPIC -o .libs/libajax_la-ajrefseqread.o
In file included from ajrefseqread.c:31:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrefseqread.lo -MD -MP -MF .deps/libajax_la-ajrefseqread.Tpo -c ajrefseqread.c -o libajax_la-ajrefseqread.o >/dev/null 2>&1
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajreport.lo -MD -MP -MF .deps/libajax_la-ajreport.Tpo -c ajreport.c -o libajax_la-ajreport.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajrefseqread.Tpo .deps/libajax_la-ajrefseqread.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrefseqwrite.lo -MD -MP -MF .deps/libajax_la-ajrefseqwrite.Tpo -c -o libajax_la-ajrefseqwrite.lo `test -f 'ajrefseqwrite.c' || echo './'`ajrefseqwrite.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrefseqwrite.lo -MD -MP -MF .deps/libajax_la-ajrefseqwrite.Tpo -c ajrefseqwrite.c -fPIC -DPIC -o .libs/libajax_la-ajrefseqwrite.o
In file included from ajrefseqwrite.c:28:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajrefseqwrite.lo -MD -MP -MF .deps/libajax_la-ajrefseqwrite.Tpo -c ajrefseqwrite.c -o libajax_la-ajrefseqwrite.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajreport.Tpo .deps/libajax_la-ajreport.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajresource.lo -MD -MP -MF .deps/libajax_la-ajresource.Tpo -c -o libajax_la-ajresource.lo `test -f 'ajresource.c' || echo './'`ajresource.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajresource.lo -MD -MP -MF .deps/libajax_la-ajresource.Tpo -c ajresource.c -fPIC -DPIC -o .libs/libajax_la-ajresource.o
mv -f .deps/libajax_la-ajrefseqwrite.Tpo .deps/libajax_la-ajrefseqwrite.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajresourceread.lo -MD -MP -MF .deps/libajax_la-ajresourceread.Tpo -c -o libajax_la-ajresourceread.lo `test -f 'ajresourceread.c' || echo './'`ajresourceread.c
In file included from ajresource.c:31:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajresourceread.lo -MD -MP -MF .deps/libajax_la-ajresourceread.Tpo -c ajresourceread.c -fPIC -DPIC -o .libs/libajax_la-ajresourceread.o
In file included from ajresourceread.c:31:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajresource.lo -MD -MP -MF .deps/libajax_la-ajresource.Tpo -c ajresource.c -o libajax_la-ajresource.o >/dev/null 2>&1
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajresourceread.lo -MD -MP -MF .deps/libajax_la-ajresourceread.Tpo -c ajresourceread.c -o libajax_la-ajresourceread.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajresource.Tpo .deps/libajax_la-ajresource.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajresourcewrite.lo -MD -MP -MF .deps/libajax_la-ajresourcewrite.Tpo -c -o libajax_la-ajresourcewrite.lo `test -f 'ajresourcewrite.c' || echo './'`ajresourcewrite.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajresourcewrite.lo -MD -MP -MF .deps/libajax_la-ajresourcewrite.Tpo -c ajresourcewrite.c -fPIC -DPIC -o .libs/libajax_la-ajresourcewrite.o
In file included from ajresourcewrite.c:28:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajresourcewrite.lo -MD -MP -MF .deps/libajax_la-ajresourcewrite.Tpo -c ajresourcewrite.c -o libajax_la-ajresourcewrite.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajresourceread.Tpo .deps/libajax_la-ajresourceread.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseq.lo -MD -MP -MF .deps/libajax_la-ajseq.Tpo -c -o libajax_la-ajseq.lo `test -f 'ajseq.c' || echo './'`ajseq.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseq.lo -MD -MP -MF .deps/libajax_la-ajseq.Tpo -c ajseq.c -fPIC -DPIC -o .libs/libajax_la-ajseq.o
In file included from ajseq.c:32:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
mv -f .deps/libajax_la-ajresourcewrite.Tpo .deps/libajax_la-ajresourcewrite.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseqabi.lo -MD -MP -MF .deps/libajax_la-ajseqabi.Tpo -c -o libajax_la-ajseqabi.lo `test -f 'ajseqabi.c' || echo './'`ajseqabi.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseqabi.lo -MD -MP -MF .deps/libajax_la-ajseqabi.Tpo -c ajseqabi.c -fPIC -DPIC -o .libs/libajax_la-ajseqabi.o
In file included from ajseqabi.c:30:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseqabi.lo -MD -MP -MF .deps/libajax_la-ajseqabi.Tpo -c ajseqabi.c -o libajax_la-ajseqabi.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajseqabi.Tpo .deps/libajax_la-ajseqabi.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseqbam.lo -MD -MP -MF .deps/libajax_la-ajseqbam.Tpo -c -o libajax_la-ajseqbam.lo `test -f 'ajseqbam.c' || echo './'`ajseqbam.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseqbam.lo -MD -MP -MF .deps/libajax_la-ajseqbam.Tpo -c ajseqbam.c -fPIC -DPIC -o .libs/libajax_la-ajseqbam.o
In file included from ajseqbam.c:31:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseqbam.lo -MD -MP -MF .deps/libajax_la-ajseqbam.Tpo -c ajseqbam.c -o libajax_la-ajseqbam.o >/dev/null 2>&1
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseq.lo -MD -MP -MF .deps/libajax_la-ajseq.Tpo -c ajseq.c -o libajax_la-ajseq.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajseqbam.Tpo .deps/libajax_la-ajseqbam.Plo
/bin/sh ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM="\"FreeBSD\"" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseqread.lo -MD -MP -MF .deps/libajax_la-ajseqread.Tpo -c -o libajax_la-ajseqread.lo `test -f 'ajseqread.c' || echo './'`ajseqread.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseqread.lo -MD -MP -MF .deps/libajax_la-ajseqread.Tpo -c ajseqread.c -fPIC -DPIC -o .libs/libajax_la-ajseqread.o
In file included from ajseqread.c:30:
In file included from ./ajlib.h:34:
./ajdefine.h:60:9: warning: '__deprecated' macro redefined [-Wmacro-redefined]
60 | #define __deprecated __attribute__((deprecated))
| ^
/usr/include/sys/cdefs.h:157:9: note: previous definition is here
157 | #define __deprecated __attribute__((__deprecated__))
| ^
ajseqread.c:16412:20: warning: implicit conversion from enumeration type 'SeqEDesSwiss' to different enumeration type 'SeqESubSwiss' [-Wenum-conversion]
16412 | isub = SWISS_DES_UNK;
| ~ ^~~~~~~~~~~~~
gmake[3]: *** [Makefile:1094: libajax_la-ajseq.lo] Error 1
gmake[3]: *** Waiting for unfinished jobs....
2 warnings generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I../../ajax/pcre -I../../ajax/expat -I../../ajax/zlib -I../../plplot -DNO_AUTH -I/usr/local/include -DAJAX_FIXED_ROOT=\"/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/emboss\" -DAJAX_SYSTEM=\"FreeBSD\" -DPREFIX=\"/usr/local/emboss\" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -DDOC_ROOT=\"/usr/local/emboss/share/EMBOSS/doc\" -DAJ_FreeBSDLF -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -O2 -I/usr/local/include -MT libajax_la-ajseqread.lo -MD -MP -MF .deps/libajax_la-ajseqread.Tpo -c ajseqread.c -o libajax_la-ajseqread.o >/dev/null 2>&1
mv -f .deps/libajax_la-ajindex.Tpo .deps/libajax_la-ajindex.Plo
mv -f .deps/libajax_la-ajseqread.Tpo .deps/libajax_la-ajseqread.Plo
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/ajax/core'
gmake[2]: *** [Makefile:538: all] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/ajax/core'
gmake[1]: *** [Makefile:329: all-recursive] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/emboss/work/EMBOSS-6.6.0/ajax'
gmake: *** [Makefile:375: all-recursive] Error 1
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make[1]: stopped making "build-message do-build post-build" in /usr/ports/biology/emboss
*** Error code 1
Stop.
make: stopped making "build" in /usr/ports/biology/emboss