[package - 135arm64-default][biology/gkl] Failed for gkl-0.9.1 in build
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Date: Fri, 26 Sep 2025 23:21:03 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/ampere3/data/135arm64-default/fcc5efebc7d0/logs/gkl-0.9.1.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=135arm64-default&build=fcc5efebc7d0
Log:
=>> Building biology/gkl
build started at Fri Sep 26 23:20:41 -00 2025
port directory: /usr/ports/biology/gkl
package name: gkl-0.9.1
building for: FreeBSD 135arm64-default-job-09 13.5-RELEASE-p4 FreeBSD 13.5-RELEASE-p4 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 464 Aug 28 01:03 /usr/ports/biology/gkl/Makefile
Ports top last git commit: fcc5efebc7d
Ports top unclean checkout: no
Port dir last git commit: 25848df4724
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.3
Host OSVERSION: 1600000
Jail OSVERSION: 1305000
Job Id: 09
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yuri@FreeBSD.org
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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"
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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.
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=======================<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-0.9.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.3.1.pkg
[135arm64-default-job-09] Installing pkg-2.3.1...
[135arm64-default-job-09] Extracting pkg-2.3.1: .......... done
===> gkl-0.9.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of gkl-0.9.1
===========================================================================
=======================<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
===> Fetching all distfiles required by gkl-0.9.1 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-0.9.1 for building
=> SHA256 Checksum OK for Intel-HLS-GKL-0.9.1_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-0.9.1 for building
===> Extracting for gkl-0.9.1
=> SHA256 Checksum OK for Intel-HLS-GKL-0.9.1_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-0.9.1
===> Applying FreeBSD patches for gkl-0.9.1 from /usr/ports/biology/gkl/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> gkl-0.9.1 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[135arm64-default-job-09] Installing gmake-4.4.1...
[135arm64-default-job-09] `-- Installing gettext-runtime-0.23.1...
[135arm64-default-job-09] | `-- Installing indexinfo-0.3.1_1...
[135arm64-default-job-09] | `-- Extracting indexinfo-0.3.1_1: .... done
[135arm64-default-job-09] `-- Extracting gettext-runtime-0.23.1: .......... done
[135arm64-default-job-09] Extracting gmake-4.4.1: .......... done
===> gkl-0.9.1 depends on executable: gmake - found
===> Returning to build of gkl-0.9.1
===> gkl-0.9.1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.31.7_1.pkg
[135arm64-default-job-09] Installing cmake-core-3.31.7_1...
[135arm64-default-job-09] `-- Installing expat-2.7.2...
[135arm64-default-job-09] `-- Extracting expat-2.7.2: .......... done
[135arm64-default-job-09] `-- Installing jsoncpp-1.9.6_1...
[135arm64-default-job-09] `-- Extracting jsoncpp-1.9.6_1: .......... done
[135arm64-default-job-09] `-- Installing libidn2-2.3.8...
[135arm64-default-job-09] | `-- Installing libunistring-1.3...
[135arm64-default-job-09] | `-- Extracting libunistring-1.3: .......... done
[135arm64-default-job-09] `-- Extracting libidn2-2.3.8: .......... done
[135arm64-default-job-09] `-- Installing libuv-1.51.0...
[135arm64-default-job-09] `-- Extracting libuv-1.51.0: .......... done
[135arm64-default-job-09] `-- Installing rhash-1.4.4_1...
[135arm64-default-job-09] `-- Extracting rhash-1.4.4_1: .......... done
[135arm64-default-job-09] Extracting cmake-core-3.31.7_1: .......... done
<snip>
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)
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33:
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:32:
In file included from /usr/lib/clang/19/include/x86intrin.h:13:
/usr/lib/clang/19/include/ia32intrin.h:312:10: error: use of undeclared identifier '__builtin_ia32_readeflags_u32'
312 | return __builtin_ia32_readeflags_u32();
| ^
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
/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_omp.dir/all ---
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33:
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:32:
In file included from /usr/lib/clang/19/include/x86intrin.h:13:
/usr/lib/clang/19/include/ia32intrin.h:312:10: error: use of undeclared identifier '__builtin_ia32_readeflags_u32'
312 | return __builtin_ia32_readeflags_u32();
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:327:3: error: use of undeclared identifier '__builtin_ia32_writeeflags_u32'
327 | __builtin_ia32_writeeflags_u32(__f);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:327:3: error: use of undeclared identifier '__builtin_ia32_writeeflags_u32'
327 | __builtin_ia32_writeeflags_u32(__f);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:408:10: error: use of undeclared identifier '__builtin_ia32_crc32qi'
408 | return __builtin_ia32_crc32qi(__C, __D);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:408:10: error: use of undeclared identifier '__builtin_ia32_crc32qi'
408 | return __builtin_ia32_crc32qi(__C, __D);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:428:10: error: use of undeclared identifier '__builtin_ia32_crc32hi'; did you mean '__builtin_arm_crc32h'?
428 | return __builtin_ia32_crc32hi(__C, __D);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:428:10: error: use of undeclared identifier '__builtin_ia32_crc32hi'; did you mean '__builtin_arm_crc32h'?
428 | return __builtin_ia32_crc32hi(__C, __D);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:448:10: error: use of undeclared identifier '__builtin_ia32_crc32si'
448 | return __builtin_ia32_crc32si(__C, __D);
| ^
/usr/lib/clang/19/include/ia32intrin.h:487:10: error: use of undeclared identifier '__builtin_ia32_rdpmc'; did you mean '__builtin_arm_dmb'?
487 | return __builtin_ia32_rdpmc(__A);
| ^
/usr/lib/clang/19/include/ia32intrin.h:487:10: error: argument to '__builtin_arm_dmb' must be a constant integer
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:448:10: error: use of undeclared identifier '__builtin_ia32_crc32si'
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
487 | return __builtin_ia32_rdpmc(__A);
| ^ ~~~
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
448 | return __builtin_ia32_crc32si(__C, __D);
| ^
/usr/lib/clang/19/include/ia32intrin.h:487:10: error: use of undeclared identifier '__builtin_ia32_rdpmc'; did you mean '__builtin_arm_dmb'?
487 | return __builtin_ia32_rdpmc(__A);
| ^
/usr/lib/clang/19/include/ia32intrin.h:487:10: error: argument to '__builtin_arm_dmb' must be a constant integer
487 | return __builtin_ia32_rdpmc(__A);
| ^ ~~~
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:502:10: error: use of undeclared identifier '__builtin_ia32_rdtscp'; did you mean '__builtin_arm_rsrp'?
502 | return __builtin_ia32_rdtscp(__A);
| ^
/usr/lib/clang/19/include/ia32intrin.h:502:32: error: cannot initialize a parameter of type 'const char *' with an lvalue of type 'unsigned int *'
502 | return __builtin_ia32_rdtscp(__A);
| ^~~
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:502:10: error: use of undeclared identifier '__builtin_ia32_rdtscp'; did you mean '__builtin_arm_rsrp'?
502 | return __builtin_ia32_rdtscp(__A);
| ^
/usr/lib/clang/19/include/ia32intrin.h:502:32: error: cannot initialize a parameter of type 'const char *' with an lvalue of type 'unsigned int *'
502 | return __builtin_ia32_rdtscp(__A);
| ^~~
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:538:3: error: use of undeclared identifier '__builtin_ia32_wbinvd'
538 | __builtin_ia32_wbinvd();
| ^
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33:
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:32:
In file included from /usr/lib/clang/19/include/x86intrin.h:15:
/usr/lib/clang/19/include/immintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
14 | #error "This header is only meant to be used on x86 and x64 architecture"
| ^
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33:
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/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:14:
/usr/lib/clang/19/include/hresetintrin.h:42:27: error: invalid input constraint 'a' in asm
42 | __asm__ ("hreset $0" :: "a"(__eax));
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/19/include/ia32intrin.h:538:3: error: use of undeclared identifier '__builtin_ia32_wbinvd'
538 | __builtin_ia32_wbinvd();
| ^
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33:
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/../common/avx.h:32:
In file included from /usr/lib/clang/19/include/x86intrin.h:15:
/usr/lib/clang/19/include/immintrin.h:14:2: error: "This header is only meant to be used on x86 and x64 architecture"
14 | #error "This header is only meant to be used on x86 and x64 architecture"
| ^
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
12 warnings generated.
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33:
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/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:33:10: error: use of undeclared identifier '__builtin_ia32_crc32qi'
33 | return __builtin_ia32_crc32qi(__C, __D);
| ^
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
--- crc_folding.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 -mpclmul -msse4 -c -o crc_folding.o /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal/crc_folding.c
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/src/main/native/pairhmm/IntelPairHmm.cc:33:
In file included from /wrkdirs/usr/ports/biology/gkl/work/GKL-0.9.1/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:33:10: error: use of undeclared identifier '__builtin_ia32_crc32qi'
33 | return __builtin_ia32_crc32qi(__C, __D);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
/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);
| ^
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
cc: error: unsupported option '-mpclmul' for target 'aarch64-unknown-freebsd13.5'
cc: warning: argument unused during compilation: '-msse4' [-Wunused-command-line-argument]
*** [crc_folding.o] Error code 1
make[3]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build
1 error
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
*** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all] Error code 6
make[1]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
make[3]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
*** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all] Error code 6
make[1]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
*** [src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-build] Error code 2
make[2]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build
1 error
make[2]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build
*** [src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all] Error code 2
make[1]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build
3 errors
make[1]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build
*** [all] Error code 2
make: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build
1 error
make: stopped 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 in /usr/ports/biology/gkl