[package - main-arm64-default][biology/gkl] Failed for gkl-0.8.11.9 in build
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Date: Tue, 22 Jul 2025 15:45:44 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p853f568b31ec_s4be9c6f38e7/logs/gkl-0.8.11.9.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p853f568b31ec_s4be9c6f38e7
Log:
=>> Building biology/gkl
build started at Tue Jul 22 15:42:33 UTC 2025
port directory: /usr/ports/biology/gkl
package name: gkl-0.8.11.9
building for: FreeBSD main-arm64-default-job-10 15.0-CURRENT FreeBSD 15.0-CURRENT 1500052 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 496 Jan 4 2025 /usr/ports/biology/gkl/Makefile
Ports top last git commit: 853f568b31e
Ports top unclean checkout: no
Port dir last git commit: 0835676e361
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2-12-g74a54a88
Host OSVERSION: 1500035
Jail OSVERSION: 1500052
Job Id: 10
!!! Jail is newer than host. (Jail: 1500052, Host: 1500035) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
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UNAME_r=15.0-CURRENT
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LANG=C.UTF-8
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HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
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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--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gkl/work/.cache HOME=/wrkdirs/usr/ports/biology/gkl/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gkl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gkl/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"
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gkl/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gkl/work/.cache HOME=/wrkdirs/usr/ports/biology/gkl/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gkl/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gkl/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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 06
44" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
CMAKE_BUILD_TYPE="release" JAVASHAREDIR="share/java" JAVAJARDIR="share/java/classes" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gkl" EXAMPLESDIR="share/examples/gkl" DATADIR="share/gkl" WWWDIR="www/gkl" ETCDIR="etc/gkl"
--End PLIST_SUB--
--SUB_LIST--
JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gkl DOCSDIR=/usr/local/share/doc/gkl EXAMPLESDIR=/usr/local/share/examples/gkl WWWDIR=/usr/local/www/gkl ETCDIR=/usr/local/etc/gkl
--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) 1048576
stack size (kbytes, -s) 1048576
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 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gkl-0.8.11.9 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.2.1.pkg
[main-arm64-default-job-10] Installing pkg-2.2.1...
[main-arm64-default-job-10] Extracting pkg-2.2.1: .......... done
===> gkl-0.8.11.9 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gkl-0.8.11.9
===========================================================================
=======================<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 MIT accepted by the user
=> Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz doesn't seem to exist in /portdistfiles.
=> Attempting to fetch https://codeload.github.com/Intel-HLS/GKL/tar.gz/0.8.11-9-g25670d8?dummy=/Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz
fetch: https://codeload.github.com/Intel-HLS/GKL/tar.gz/0.8.11-9-g25670d8?dummy=/Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/Intel-HLS/GKL/tar.gz/0.8.11-9-g25670d8?dummy=/Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz: size of remote file is not known
Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.tar.gz 5186 kB 7984 kBps 00s
===> Fetching all distfiles required by gkl-0.8.11.9 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by gkl-0.8.11.9 for building
=> SHA256 Checksum OK for Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.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 MIT accepted by the user
===> Fetching all distfiles required by gkl-0.8.11.9 for building
===> Extracting for gkl-0.8.11.9
=> SHA256 Checksum OK for Intel-HLS-GKL-0.8.11-9-g25670d8_GH0.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 gkl-0.8.11.9
===> Applying FreeBSD patches for gkl-0.8.11.9 from /usr/ports/biology/gkl/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gkl-0.8.11.9 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[main-arm64-default-job-10] Installing gmake-4.4.1...
<snip>
/usr/lib/clang/19/include/crc32intrin.h:33:10: error: use of undeclared identifier '__builtin_ia32_crc32qi'
33 | return __builtin_ia32_crc32qi(__C, __D);
| ^
/usr/lib/clang/19/include/crc32intrin.h:53:10: error: use of undeclared identifier '__builtin_ia32_crc32hi'; did you mean '__builtin_arm_crc32h'?
53 | return __builtin_ia32_crc32hi(__C, __D);
| ^
/usr/lib/clang/19/include/ia32intrin.h:428:10: note: '__builtin_arm_crc32h' declared here
428 | return __builtin_ia32_crc32hi(__C, __D);
| ^
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33:
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32:
In file included from /usr/lib/clang/19/include/x86intrin.h:15:
In file included from /usr/lib/clang/19/include/immintrin.h:17:
In file included from /usr/lib/clang/19/include/x86gprintrin.h:26:
/usr/lib/clang/19/include/crc32intrin.h:73:10: error: use of undeclared identifier '__builtin_ia32_crc32si'
73 | return __builtin_ia32_crc32si(__C, __D);
| ^
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/IntelPairHmm.cc:33:
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.8.11-9-g25670d8/src/main/native/pairhmm/../common/avx.h:32:
In file included from /usr/lib/clang/19/include/x86intrin.h:15:
In file included from /usr/lib/clang/19/include/immintrin.h:17:
In file included from /usr/lib/clang/19/include/x86gprintrin.h:34:
/usr/lib/clang/19/include/raointintrin.h:39:3: error: use of undeclared identifier '__builtin_ia32_aadd32'; did you mean '__builtin_arm_addg'?
39 | __builtin_ia32_aadd32((int *)__A, __B);
| ^
/usr/lib/clang/19/include/raointintrin.h:39:3: error: argument to '__builtin_arm_addg' must be a constant integer
39 | __builtin_ia32_aadd32((int *)__A, __B);
| ^ ~~~
/usr/lib/clang/19/include/raointintrin.h:61:3: error: use of undeclared identifier '__builtin_ia32_aand32'
61 | __builtin_ia32_aand32((int *)__A, __B);
| ^
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
11 warnings generated.
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/19/include/raointintrin.h:83:3: error: use of undeclared identifier '__builtin_ia32_aor32'
83 | __builtin_ia32_aor32((int *)__A, __B);
| ^
/usr/lib/clang/19/include/raointintrin.h:105:3: error: use of undeclared identifier '__builtin_ia32_axor32'
105 | __builtin_ia32_axor32((int *)__A, __B);
| ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
--- minigzip64.o ---
cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -I/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/ -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:351:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
351 | void error(msg)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:362:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
362 | void gz_compress(in, out)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:430:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
430 | void gz_uncompress(in, out)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:457:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
457 | void file_compress(file, mode)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:496:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
496 | void file_uncompress(file)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/minigzip.c:556:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
556 | int main(argc, argv)
| ^
6 warnings generated.
--- example.o ---
cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -I/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/ -c -o example.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:88:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
88 | void test_compress(compr, comprLen, uncompr, uncomprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:114:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
114 | void test_gzio(fname, uncompr, uncomprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:200:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
200 | void test_deflate(compr, comprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:238:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
238 | void test_inflate(compr, comprLen, uncompr, uncomprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:279:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
279 | void test_large_deflate(compr, comprLen, uncompr, uncomprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:334:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
334 | void test_large_inflate(compr, comprLen, uncompr, uncomprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:375:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
375 | void test_flush(compr, comprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:413:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
413 | void test_sync(compr, comprLen, uncompr, uncomprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:456:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
456 | void test_dict_deflate(compr, comprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:493:6: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
493 | void test_dict_inflate(compr, comprLen, uncompr, uncomprLen)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/test/example.c:544:5: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
544 | int main(argc, argv)
| ^
11 warnings generated.
--- adler32.o ---
cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o adler32.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:63:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
63 | uLong ZEXPORT adler32_z(adler, buf, len)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:150:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
150 | uLong ZEXPORT adler32(adler, buf, len)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:159:13: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
159 | local uLong adler32_combine_(adler1, adler2, len2)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:188:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
188 | uLong ZEXPORT adler32_combine(adler1, adler2, len2)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/adler32.c:196:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
196 | uLong ZEXPORT adler32_combine64(adler1, adler2, len2)
| ^
5 warnings generated.
--- crc32.o ---
cc -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fPIC -O3 -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -include zconf.h -c -o crc32.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:126:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
126 | local z_word_t byte_swap(word)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:551:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
551 | local z_crc_t multmodp(a, b)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:575:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
575 | local z_crc_t x2nmodp(n, k)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:726:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
726 | local z_crc_t crc_word(data)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:735:16: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
735 | local z_word_t crc_word_big(data)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:748:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
748 | unsigned long ZEXPORT crc32_z(crc, buf, len)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1072:23: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1072 | unsigned long ZEXPORT crc32(crc, buf, len)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1081:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1081 | uLong ZEXPORT crc32_combine64(crc1, crc2, len2)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1093:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1093 | uLong ZEXPORT crc32_combine(crc1, crc2, len2)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1102:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1102 | uLong ZEXPORT crc32_combine_gen64(len2)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1112:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1112 | uLong ZEXPORT crc32_combine_gen(len2)
| ^
/wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc32.c:1119:15: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]
1119 | uLong ZEXPORT crc32_combine_op(crc1, crc2, op)
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
1 warning and 20 errors generated.
*** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/IntelPairHmm.cc.o] Error code 1
make[2]: stopped making "src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/build" in /wrkdirs/usr/ports/biology/gkl/work/.build
make[2]: 1 error
make[2]: stopped making "src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/build" in /wrkdirs/usr/ports/biology/gkl/work/.build
*** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all] Error code 2
make[1]: stopped making "all" in /wrkdirs/usr/ports/biology/gkl/work/.build
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
12 warnings generated.
*** [src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-build] Error code 6
make[2]: stopped making "src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/build" in /wrkdirs/usr/ports/biology/gkl/work/.build
make[2]: 1 error
make[2]: stopped making "src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/build" in /wrkdirs/usr/ports/biology/gkl/work/.build
*** [src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all] Error code 2
make[1]: stopped making "all" in /wrkdirs/usr/ports/biology/gkl/work/.build
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
1 warning and 20 errors generated.
make[2]: stopped making "src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/build" in /wrkdirs/usr/ports/biology/gkl/work/.build
*** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all] Error code 2
make[1]: stopped making "all" in /wrkdirs/usr/ports/biology/gkl/work/.build
make[1]: 3 errors
make[1]: stopped making "all" in /wrkdirs/usr/ports/biology/gkl/work/.build
*** [all] Error code 2
make: stopped making "all" in /wrkdirs/usr/ports/biology/gkl/work/.build
make: 1 error
make: stopped making "all" in /wrkdirs/usr/ports/biology/gkl/work/.build
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped making "build" in /usr/ports/biology/gkl