[package - 150arm64-quarterly][biology/gkl] Failed for gkl-0.9.1 in build
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Date: Sat, 03 Jan 2026 01:13:23 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/ampere4/data/150arm64-quarterly/fce61163b43e/logs/gkl-0.9.1.log
Build URL: https://pkg-status.freebsd.org/ampere4/build.html?mastername=150arm64-quarterly&build=fce61163b43e
Log:
=>> Building biology/gkl
build started at Sat Jan 3 01:12:49 UTC 2026
port directory: /usr/ports/biology/gkl
package name: gkl-0.9.1
building for: FreeBSD 150arm64-quarterly-job-16 15.0-RELEASE-p1 FreeBSD 15.0-RELEASE-p1 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 464 Dec 25 01:01 /usr/ports/biology/gkl/Makefile
Ports top last git commit: fce61163b43eec25ce79a11257a6e9ee19056a7a
Ports top unclean checkout: no
Port dir last git commit: 0d8fad0cea6d8b6dae7fb6ba0da87e89f36f3720
Port dir unclean checkout: no
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Jail OSVERSION: 1500068
Job Id: 16
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#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
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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-2.4.2.pkg
[150arm64-quarterly-job-16] Installing pkg-2.4.2...
[150arm64-quarterly-job-16] Extracting pkg-2.4.2: .......... 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
[150arm64-quarterly-job-16] Installing gmake-4.4.1...
[150arm64-quarterly-job-16] `-- Installing gettext-runtime-0.23.1...
[150arm64-quarterly-job-16] | `-- Installing indexinfo-0.3.1_1...
[150arm64-quarterly-job-16] | `-- Extracting indexinfo-0.3.1_1: .... done
[150arm64-quarterly-job-16] `-- Extracting gettext-runtime-0.23.1: .......... done
[150arm64-quarterly-job-16] 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-3.31.9.pkg
[150arm64-quarterly-job-16] Installing cmake-core-3.31.9...
[150arm64-quarterly-job-16] `-- Installing expat-2.7.3...
[150arm64-quarterly-job-16] `-- Extracting expat-2.7.3: .......... done
[150arm64-quarterly-job-16] `-- Installing jsoncpp-1.9.6_1...
[150arm64-quarterly-job-16] `-- Extracting jsoncpp-1.9.6_1: .......... done
[150arm64-quarterly-job-16] `-- Installing libidn2-2.3.8...
[150arm64-quarterly-job-16] | `-- Installing libunistring-1.4.1...
[150arm64-quarterly-job-16] | `-- Extracting libunistring-1.4.1: .......... done
[150arm64-quarterly-job-16] `-- Extracting libidn2-2.3.8: .......... done
[150arm64-quarterly-job-16] `-- Installing libuv-1.51.0...
[150arm64-quarterly-job-16] `-- Extracting libuv-1.51.0: .......... done
[150arm64-quarterly-job-16] `-- Installing rhash-1.4.4_1...
[150arm64-quarterly-job-16] `-- Extracting rhash-1.4.4_1: .......... done
<snip>
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: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_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/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 ---
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/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/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/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/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:73:10: error: use of undeclared identifier '__builtin_ia32_crc32si'
73 | return __builtin_ia32_crc32si(__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/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: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);
| ^ ~~~
--- 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:73:10: error: use of undeclared identifier '__builtin_ia32_crc32si'
73 | return __builtin_ia32_crc32si(__C, __D);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
/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/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: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
--- 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'
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
39 | __builtin_ia32_aadd32((int *)__A, __B);
| ^ ~~~
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
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);
| ^
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
/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/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
fatal error: too many errors emitted, stopping now [-ferror-limit=]
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.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);
| ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
--- src/main/native/compression/CMakeFiles/otc_zlibExternal.dir/all ---
Building static library libz.a version 1.2.13 with cc.
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
1 warning and 20 errors generated.
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
1 warning and 20 errors generated.
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/all ---
*** [src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.dir/IntelPairHmm.cc.o] Error code 1
make[2]: stopped making "src/main/native/pairhmm/CMakeFiles/gkl_pairhmm_omp.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_omp.dir/build" in /wrkdirs/usr/ports/biology/gkl/work/.build
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
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_omp.dir/all ---
*** [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
--- src/main/native/pairhmm/CMakeFiles/gkl_pairhmm.dir/all ---
*** [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 ---
Checking for size_t... Yes.
Checking for off64_t... Yes.
Checking for fseeko... Yes.
Checking for strerror... Yes.
Checking for unistd.h... Yes.
Checking for stdarg.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf().
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for attribute(visibility) support... Yes.
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 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