[*] c++ -v
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -v -I/home/pbulk/build/biology/hisat2/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:28:16 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA -I. -I third_party -o hisat2-build-s hisat2_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp -lpthread
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/hisat2/work/.buildlink/include -I/home/pbulk/build/biology/hisat2/work/.buildlink/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:28:16 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA -I. -Ithird_party -o hisat2-build-s hisat2_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp -lpthread
[*] c++ -v
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -v -I/home/pbulk/build/biology/hisat2/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:28:17 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall -I. -I third_party -o hisat2-build-l hisat2_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp -lpthread
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/hisat2/work/.buildlink/include -I/home/pbulk/build/biology/hisat2/work/.buildlink/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:28:17 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall -I. -Ithird_party -o hisat2-build-l hisat2_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp -lpthread
[*] c++ -v
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -v -I/home/pbulk/build/biology/hisat2/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:28:17 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -I. -I third_party -o hisat2-align-s hisat2.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp -lpthread
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/hisat2/work/.buildlink/include -I/home/pbulk/build/biology/hisat2/work/.buildlink/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:28:17 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall -I. -Ithird_party -o hisat2-align-s hisat2.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp -lpthread
[*] c++ -v
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -v -I/home/pbulk/build/biology/hisat2/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:28:17 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall -I. -I third_party -o hisat2-align-l hisat2.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp -lpthread
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/hisat2/work/.buildlink/include -I/home/pbulk/build/biology/hisat2/work/.buildlink/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:28:17 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall -I. -Ithird_party -o hisat2-align-l hisat2.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp -lpthread
[*] c++ -v
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -v -I/home/pbulk/build/biology/hisat2/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:29:41 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall -I. -I third_party -I . -o hisat2-inspect-s hisat2_inspect.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp -lpthread
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/hisat2/work/.buildlink/include -I/home/pbulk/build/biology/hisat2/work/.buildlink/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:29:41 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall -I. -Ithird_party -o hisat2-inspect-s hisat2_inspect.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp -lpthread
[*] c++ -v
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -v -I/home/pbulk/build/biology/hisat2/work/.buildlink/include
[*] c++ -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:29:42 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall -I. -I third_party -I . -o hisat2-inspect-l hisat2_inspect.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp -lpthread
<.> /home/pbulk/build/biology/hisat2/work/.gcc/bin/g++ -m64 -fstack-protector-strong -D_FORTIFY_SOURCE=2 -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/home/pbulk/build/biology/hisat2/work/.buildlink/include -I/home/pbulk/build/biology/hisat2/work/.buildlink/include/python3.12 '-DCOMPILER_OPTIONS="-pipe -O2 -msave-args -fno-aggressive-loop-optimizations -pthread -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.12 -std=c++11"' -std=c++11 -fno-strict-aliasing '-DHISAT2_VERSION="2.2.1"' '-DBUILD_HOST="pkgsrc-upstream-trunk"' '-DBUILD_TIME="Mon Aug 18 23:29:42 UTC 2025"' '-DCOMPILER_VERSION="gcc version 14.3.0 (GCC) "' -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall -I. -Ithird_party -o hisat2-inspect-l hisat2_inspect.cpp ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp -lpthread