[package - main-armv7-default][biology/btllib] Failed for btllib-1.6.2 in build
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Date: Sun, 20 Aug 2023 10:09:42 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-armv7-default/pd101ab5189f9_sb231322dbe/logs/btllib-1.6.2.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=pd101ab5189f9_sb231322dbe
Log:
=>> Building biology/btllib
build started at Sun Aug 20 10:07:47 UTC 2023
port directory: /usr/ports/biology/btllib
package name: btllib-1.6.2
building for: FreeBSD main-armv7-default-job-03 14.0-ALPHA1 FreeBSD 14.0-ALPHA1 1400094 arm
maintained by: yuri@FreeBSD.org
Makefile ident:
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Job Id: 03
!!! Jail is newer than host. (Jail: 1400094, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> btllib-1.6.2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.5.pkg
[main-armv7-default-job-03] Installing pkg-1.20.5...
[main-armv7-default-job-03] Extracting pkg-1.20.5: .......... done
===> btllib-1.6.2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of btllib-1.6.2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by btllib-1.6.2 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by btllib-1.6.2 for building
=> SHA256 Checksum OK for bcgsc-btllib-v1.6.2_GH0.tar.gz.
=> SHA256 Checksum OK for p-ranav-argparse-15d745f_GH0.tar.gz.
=> SHA256 Checksum OK for skystrife-cpptoml-fededad_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by btllib-1.6.2 for building
===> Extracting for btllib-1.6.2
=> SHA256 Checksum OK for bcgsc-btllib-v1.6.2_GH0.tar.gz.
=> SHA256 Checksum OK for p-ranav-argparse-15d745f_GH0.tar.gz.
=> SHA256 Checksum OK for skystrife-cpptoml-fededad_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for btllib-1.6.2
===> Applying FreeBSD patches for btllib-1.6.2 from /usr/ports/biology/btllib/files
===========================================================================
=======================<phase: build-depends >============================
===> btllib-1.6.2 depends on executable: bash - not found
<snip>
===> btllib-1.6.2 depends on shared library: libsdsl.so - found (/usr/local/lib/libsdsl.so)
===> Returning to build of btllib-1.6.2
===========================================================================
=======================<phase: configure >============================
===> Configuring for btllib-1.6.2
LLVM (http://llvm.org/):
LLVM version 16.0.6
Optimized build with assertions.
WARNING: Recommend using either -Dbuildtype or -Doptimization + -Ddebug. Using both is redundant since they override each other. See: https://mesonbuild.com/Builtin-options.html#build-type-options
The Meson build system
Version: 1.2.0
Source dir: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2
Build dir: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build
Build type: native build
Project name: btllib
Project version: 1.6.2
C++ compiler for the host machine: c++ (clang 16.0.6 "FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152)")
C++ linker for the host machine: c++ ld.lld 16.0.6
Host machine cpu family: arm
Host machine cpu: armv7
Configuring config.hpp using configuration
Run-time dependency threads found: YES
WARNING: OpenMP found but omp.h missing.
Run-time dependency OpenMP found: NO (tried system)
Executing subproject cpptoml method cmake
cpptoml| Found CMake: /usr/local/bin/cmake (3.26.1)
| Configuring the build directory with CMake version 3.26.1
| Running CMake with: -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local
| - build directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build/subprojects/cpptoml/__CMake_build
| - source directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/subprojects/cpptoml
| - toolchain file: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build/subprojects/cpptoml/__CMake_build/CMakeMesonToolchainFile.cmake
| - preload file: /usr/local/lib/python3.9/site-packages/mesonbuild/cmake/data/preload.cmake
| - trace args: --trace-expand --trace-format=json-v1 --no-warn-unused-cli --trace-redirect=cmake_trace.txt
| - disabled policy warnings: [CMP0025, CMP0047, CMP0056, CMP0060, CMP0065, CMP0066, CMP0067, CMP0082, CMP0089, CMP0102]
| Running with expanded trace output on.
| Not searching for unused variables given on the command line.
| Trace will be written to cmake_trace.txt
| -- The C compiler identification is Clang 16.0.6
| -- The CXX compiler identification is Clang 16.0.6
| -- Detecting C compiler ABI info
| -- Detecting C compiler ABI info - done
| -- Check for working C compiler: /usr/bin/cc - skipped
| -- Detecting C compile features
| -- Detecting C compile features - done
| -- Detecting CXX compiler ABI info
| -- Detecting CXX compiler ABI info - done
| -- Check for working CXX compiler: /usr/bin/c++ - skipped
| -- Detecting CXX compile features
| -- Detecting CXX compile features - done
| -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
| -- Configuring done (1.7s)
| -- Generating done (0.0s)
| -- Build files have been written to: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build/subprojects/cpptoml/__CMake_build
cpptoml| CMake configuration: SUCCEEDED
cpptoml| CMake project cpptoml has 1 build targets.
cmake-ast| Processing generated meson AST
cmake-ast| Build file: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build/subprojects/cpptoml/meson.build
cpptoml| Project name: cpptoml
cpptoml| Project version: undefined
cpptoml| Build targets in project: 0
cpptoml| Subproject cpptoml finished.
Found pkg-config: /usr/local/bin/pkgconf (1.8.1)
Run-time dependency sdsl-lite found: YES 2.1.0
Executing subproject argparse method cmake
| Configuring the build directory with CMake version 3.26.1
| Running CMake with: -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local
| - build directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build/subprojects/argparse/__CMake_build
| - source directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/subprojects/argparse
| - toolchain file: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build/subprojects/argparse/__CMake_build/CMakeMesonToolchainFile.cmake
| - preload file: /usr/local/lib/python3.9/site-packages/mesonbuild/cmake/data/preload.cmake
| - trace args: --trace-expand --trace-format=json-v1 --no-warn-unused-cli --trace-redirect=cmake_trace.txt
| - disabled policy warnings: [CMP0025, CMP0047, CMP0056, CMP0060, CMP0065, CMP0066, CMP0067, CMP0082, CMP0089, CMP0102]
| Running with expanded trace output on.
| Not searching for unused variables given on the command line.
| Trace will be written to cmake_trace.txt
| -- The CXX compiler identification is Clang 16.0.6
| -- Detecting CXX compiler ABI info
| -- Detecting CXX compiler ABI info - done
| -- Check for working CXX compiler: /usr/bin/c++ - skipped
| -- Detecting CXX compile features
| -- Detecting CXX compile features - done
| -- Configuring done (1.1s)
| -- Generating done (0.0s)
| -- Build files have been written to: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build/subprojects/argparse/__CMake_build
argparse| CMake configuration: SUCCEEDED
argparse| CMake project argparse has 1 build targets.
cmake-ast| Processing generated meson AST
cmake-ast| Build file: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build/subprojects/argparse/meson.build
argparse| Project name: argparse
argparse| Project version: undefined
argparse| Build targets in project: 0
argparse| Subproject argparse finished.
Program samtools found: YES (/usr/local/bin/samtools)
Program gzip found: YES (/usr/bin/gzip)
Program xz found: YES (/usr/bin/xz)
Program bzip2 found: YES (/usr/bin/bzip2)
Program tar found: YES (/usr/bin/tar)
Program gcovr found: NO
Program swig found: NO
Program doxygen found: NO
WARNING: You should add the boolean check kwarg to the run_command call.
It currently defaults to false,
but it will default to true in future releases of meson.
See also: https://github.com/mesonbuild/meson/issues/9300
Program python3 found: YES (/wrkdirs/usr/ports/biology/btllib/work/.bin/python3)
Program python3-config found: NO
Message: python3-config not found, skipping Python wrappers.
Build targets in project: 11
btllib 1.6.2
Subprojects
argparse : YES
cpptoml : YES
User defined options
auto_features : enabled
buildtype : release
infodir : share/info
mandir : man
optimization : plain
prefix : /usr/local
strip : True
python.bytecompile: -1
b_colorout : never
Found ninja-1.11.1 at /usr/local/bin/ninja
WARNING: Need gcovr or lcov/genhtml to generate any coverage reports
WARNING: Running the setup command as `meson [options]` instead of `meson setup [options]` is ambiguous and deprecated.
===========================================================================
=======================<phase: build >============================
===> Building for btllib-1.6.2
[ 4% 2/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_multiline_fasta_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_multiline_fasta_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_multiline_fasta_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/seq_reader_multiline_fasta_module.cpp
[ 8% 3/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_fasta_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_fasta_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_fasta_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/seq_reader_fasta_module.cpp
[ 12% 4/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/seq.cpp
[ 16% 5/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_sam_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_sam_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_sam_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/seq_reader_sam_module.cpp
[ 20% 6/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_aahash.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_aahash.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_aahash.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/aahash.cpp
[ 24% 7/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/seq_reader.cpp
[ 28% 8/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_data_stream.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_data_stream.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_data_stream.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/data_stream.cpp
[ 32% 9/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_writer.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_writer.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_writer.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/seq_writer.cpp
[ 36% 10/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_randseq.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_randseq.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_randseq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/randseq.cpp
[ 40% 11/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_multiline_fastq_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_multiline_fastq_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_multiline_fastq_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/seq_reader_multiline_fastq_module.cpp
[ 44% 12/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_process_pipeline.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_process_pipeline.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_process_pipeline.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/process_pipeline.cpp
[ 48% 13/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_nthash.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_nthash.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_nthash.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/nthash.cpp
[ 52% 14/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_util.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_util.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_util.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/util.cpp
[ 56% 15/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_fastq_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_fastq_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_fastq_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/seq_reader_fastq_module.cpp
[ 60% 16/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_status.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_status.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_status.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/status.cpp
[ 64% 17/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_cstring.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_cstring.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_cstring.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/cstring.cpp
[ 68% 18/25] c++ -Irecipes/indexlr.p -Irecipes -I../recipes -Iinclude -I../include -I. -I.. -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -MD -MQ recipes/indexlr.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_indexlr.cpp.o -MF recipes/indexlr.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_indexlr.cpp.o.d -o recipes/indexlr.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_indexlr.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/recipes/indexlr.cpp
[ 72% 19/25] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_bloom_filter.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_bloom_filter.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_bloom_filter.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/src/btllib/bloom_filter.cpp
[ 76% 20/25] c++ -o libbtllib.so libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_fasta_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_multiline_fasta_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_sam_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_aahash.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_data_stream.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_writer.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_randseq.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2
_src_btllib_process_pipeline.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_multiline_fastq_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_nthash.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_util.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_bloom_filter.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_seq_reader_fastq_module.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_status.cpp.o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_src_btllib_cstring.cpp.o --coverage -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,libbtllib.so -ldl -lstdc++ -lm -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wl,-rpath,/usr/local/lib -Wl,-rpath-link,/usr/local/lib -
pthread /usr/local/lib/libsdsl.so /usr/local/lib/libdivsufsort.so /usr/local/lib/libdivsufsort64.so -Wl,--end-group
[ 80% 21/25] /usr/local/bin/meson --internal symbolextractor /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build libbtllib.so libbtllib.so libbtllib.so.p/libbtllib.so.symbols
[ 84% 22/25] c++ -o recipes/indexlr recipes/indexlr.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_indexlr.cpp.o --coverage -Wl,--as-needed -Wl,--no-undefined -Wl,-O1 -Wl,--start-group -ldl -lstdc++ -lm -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing '-Wl,-rpath,$ORIGIN/..:/usr/local/lib' -Wl,-rpath-link,/wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/_build/ -Wl,-rpath-link,/usr/local/lib libbtllib.so -pthread /usr/local/lib/libsdsl.so /usr/local/lib/libdivsufsort.so /usr/local/lib/libdivsufsort64.so -Wl,--end-group
[ 88% 23/25] c++ -Irecipes/randseq.p -Irecipes -I../recipes -Iinclude -I../include -I. -I.. -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I../subprojects/argparse/include -Isubprojects/argparse/__CMake_build -I../subprojects/argparse/__CMake_build -Isubprojects/argparse -I../subprojects/argparse -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -MD -MQ recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_randseq.cpp.o -MF recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_randseq.cpp.o.d -o recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_randseq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/recipes/randseq.cpp
FAILED: recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_randseq.cpp.o
c++ -Irecipes/randseq.p -Irecipes -I../recipes -Iinclude -I../include -I. -I.. -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I../subprojects/argparse/include -Isubprojects/argparse/__CMake_build -I../subprojects/argparse/__CMake_build -Isubprojects/argparse -I../subprojects/argparse -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -MD -MQ recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_randseq.cpp.o -MF recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_randseq.cpp.o.d -o recipes/randseq.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_randseq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/recipes/randseq.cpp
/wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/recipes/randseq.cpp:9:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 error generated.
[ 92% 23/25] c++ -Irecipes/mi_bf_generate.p -Irecipes -I../recipes -Iinclude -I../include -I. -I.. -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -MD -MQ recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_mi_bloom_filter.cpp.o -MF recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_mi_bloom_filter.cpp.o.d -o recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_mi_bloom_filter.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/recipes/mi_bloom_filter.cpp
FAILED: recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_mi_bloom_filter.cpp.o
c++ -Irecipes/mi_bf_generate.p -Irecipes -I../recipes -Iinclude -I../include -I. -I.. -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fno-color-diagnostics --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -pthread -MD -MQ recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_mi_bloom_filter.cpp.o -MF recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_mi_bloom_filter.cpp.o.d -o recipes/mi_bf_generate.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.6.2_recipes_mi_bloom_filter.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/recipes/mi_bloom_filter.cpp
In file included from /wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/recipes/mi_bloom_filter.cpp:1:
In file included from ../include/btllib/mi_bloom_filter.hpp:12:
In file included from /usr/local/include/sdsl/bit_vector_il.hpp:25:
In file included from /usr/local/include/sdsl/int_vector.hpp:26:
/usr/local/include/sdsl/util.hpp:492:19: warning: variable 'vals' set but not used [-Wunused-but-set-variable]
uint64_t n=0, vals=0;
^
/wrkdirs/usr/ports/biology/btllib/work/btllib-1.6.2/recipes/mi_bloom_filter.cpp:8:10: fatal error: 'omp.h' file not found
#include <omp.h>
^~~~~~~
1 warning and 1 error generated.
ninja: build stopped: subcommand failed.
===> 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/btllib