[package - 142arm64-default][biology/gkl] Failed for gkl-0.8.11.9 in build
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Date: Wed, 23 Jul 2025 12:19:54 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/142arm64-default/b3423aefe7f1/logs/gkl-0.8.11.9.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=142arm64-default&build=b3423aefe7f1
Log:
=>> Building biology/gkl
build started at Wed Jul 23 12:19:08 UTC 2025
port directory: /usr/ports/biology/gkl
package name: gkl-0.8.11.9
building for: FreeBSD 142arm64-default-job-10 14.2-RELEASE-p4 FreeBSD 14.2-RELEASE-p4 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: b3423aefe7f
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: 1402000
Job Id: 10
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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.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
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GID=0
UID=0
---End make.conf---
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cpu time (seconds, -t) unlimited
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--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
[142arm64-default-job-10] Installing pkg-2.2.1...
[142arm64-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
===> 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
[142arm64-default-job-10] Installing gmake-4.4.1...
[142arm64-default-job-10] `-- Installing gettext-runtime-0.23.1...
[142arm64-default-job-10] | `-- Installing indexinfo-0.3.1_1...
[142arm64-default-job-10] | `-- Extracting indexinfo-0.3.1_1: .... done
[142arm64-default-job-10] `-- Extracting gettext-runtime-0.23.1: .......... done
[142arm64-default-job-10] Extracting gmake-4.4.1: .......... done
===> gkl-0.8.11.9 depends on executable: gmake - found
===> Returning to build of gkl-0.8.11.9
===> gkl-0.8.11.9 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.31.7.pkg
[142arm64-default-job-10] Installing cmake-core-3.31.7...
[142arm64-default-job-10] `-- Installing expat-2.7.1...
[142arm64-default-job-10] `-- Extracting expat-2.7.1: .......... done
[142arm64-default-job-10] `-- Installing jsoncpp-1.9.6_1...
[142arm64-default-job-10] `-- Extracting jsoncpp-1.9.6_1: .......... done
[142arm64-default-job-10] `-- Installing libidn2-2.3.8...
[142arm64-default-job-10] | `-- Installing libunistring-1.3...
[142arm64-default-job-10] | `-- Extracting libunistring-1.3: .......... done
[142arm64-default-job-10] `-- Extracting libidn2-2.3.8: .......... done
[142arm64-default-job-10] `-- Installing libuv-1.51.0...
[142arm64-default-job-10] `-- Extracting libuv-1.51.0: .......... done
[142arm64-default-job-10] `-- Installing rhash-1.4.4_1...
[142arm64-default-job-10] `-- Extracting rhash-1.4.4_1: .......... done
<snip>
| ^
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/18/include/x86intrin.h:15:
/usr/lib/clang/18/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-0.8.11-9-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/18/include/x86intrin.h:15:
In file included from /usr/lib/clang/18/include/immintrin.h:17:
In file included from /usr/lib/clang/18/include/x86gprintrin.h:15:
/usr/lib/clang/18/include/hresetintrin.h:42:27: error: invalid input constraint 'a' in asm
42 | __asm__ ("hreset $0" :: "a"(__eax));
| ^
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/18/include/x86intrin.h:15:
In file included from /usr/lib/clang/18/include/immintrin.h:17:
In file included from /usr/lib/clang/18/include/x86gprintrin.h:30:
/usr/lib/clang/18/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 ---
Checking for strerror... Yes.
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
/usr/lib/clang/18/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/18/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/18/include/x86intrin.h:15:
In file included from /usr/lib/clang/18/include/immintrin.h:17:
In file included from /usr/lib/clang/18/include/x86gprintrin.h:30:
/usr/lib/clang/18/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/18/include/x86intrin.h:15:
In file included from /usr/lib/clang/18/include/immintrin.h:17:
In file included from /usr/lib/clang/18/include/x86gprintrin.h:40:
/usr/lib/clang/18/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/18/include/raointintrin.h:39:3: note: '__builtin_arm_addg' declared here
/usr/lib/clang/18/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/18/include/raointintrin.h:61:3: error: use of undeclared identifier '__builtin_ia32_aand32'
61 | __builtin_ia32_aand32((int *)__A, __B);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
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/18/include/x86intrin.h:13:
/usr/lib/clang/18/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/18/include/raointintrin.h:83:3: error: use of undeclared identifier '__builtin_ia32_aor32'
83 | __builtin_ia32_aor32((int *)__A, __B);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/18/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 ---
fatal error: too many errors emitted, stopping now [-ferror-limit=]
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/18/include/ia32intrin.h:408:10: error: use of undeclared identifier '__builtin_ia32_crc32qi'
408 | return __builtin_ia32_crc32qi(__C, __D);
| ^
/usr/lib/clang/18/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);
| ^
/usr/lib/clang/18/include/ia32intrin.h:428:10: note: '__builtin_arm_crc32h' declared here
/usr/lib/clang/18/include/ia32intrin.h:448:10: error: use of undeclared identifier '__builtin_ia32_crc32si'
448 | return __builtin_ia32_crc32si(__C, __D);
| ^
/usr/lib/clang/18/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/18/include/ia32intrin.h:487:10: note: '__builtin_arm_dmb' declared here
/usr/lib/clang/18/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/compression/CMakeFiles/otc_zlibExternal.dir/all ---
Checking for unistd.h... Yes.
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/18/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/18/include/ia32intrin.h:502:10: note: '__builtin_arm_rsrp' declared here
/usr/lib/clang/18/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);
| ^~~
/usr/lib/clang/18/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-0.8.11-9-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/18/include/x86intrin.h:15:
/usr/lib/clang/18/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 ---
Checking for stdarg.h... Yes.
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
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/18/include/x86intrin.h:15:
In file included from /usr/lib/clang/18/include/immintrin.h:17:
In file included from /usr/lib/clang/18/include/x86gprintrin.h:30:
/usr/lib/clang/18/include/crc32intrin.h:33:10: error: use of undeclared identifier '__builtin_ia32_crc32qi'
33 | return __builtin_ia32_crc32qi(__C, __D);
| ^
/usr/lib/clang/18/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/18/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/18/include/x86intrin.h:15:
In file included from /usr/lib/clang/18/include/immintrin.h:17:
In file included from /usr/lib/clang/18/include/x86gprintrin.h:30:
/usr/lib/clang/18/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/18/include/x86intrin.h:15:
In file included from /usr/lib/clang/18/include/immintrin.h:17:
In file included from /usr/lib/clang/18/include/x86gprintrin.h:40:
/usr/lib/clang/18/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/18/include/raointintrin.h:39:3: note: '__builtin_arm_addg' declared here
/usr/lib/clang/18/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/18/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 ---
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/usr/lib/clang/18/include/raointintrin.h:83:3: error: use of undeclared identifier '__builtin_ia32_aor32'
83 | __builtin_ia32_aor32((int *)__A, __B);
| ^
/usr/lib/clang/18/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 ---
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
--- 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 in /wrkdirs/usr/ports/biology/gkl/work/.build
1 error
make[2]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build
*** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all] Error code 2
make[1]: stopped in /wrkdirs/usr/ports/biology/gkl/work/.build
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
Checking for attribute(visibility) support... Yes.
--- 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 ---
cd /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/gkl/work/.build/src/main/native/compression/otc_zlibExternal-prefix/src/otc_zlibExternal-stamp/otc_zlibExternal-configure
*** [src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all] Error code 6
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