=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Building for bowtie2-2.4.4nb2 clang++ -DCOMPILER_OPTIONS="\" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I/opt/pkg/include/python3.10 -I/opt/pkg/include -Ithird_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -L/opt/pkg/lib -lpthread -lz clang++ -DCOMPILER_OPTIONS="\" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I/opt/pkg/include/python3.10 -I/opt/pkg/include -Ithird_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -L/opt/pkg/lib -lpthread -lz clang++ -DCOMPILER_OPTIONS="\" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I/opt/pkg/include/python3.10 -I/opt/pkg/include -Ithird_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.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 bowtie_main.cpp \ -L/opt/pkg/lib -lpthread -lz In file included from bt2_search.cpp:41: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from bt2_build.cpp:28: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from bt2_build.cpp:28: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from bt2_search.cpp:54: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. 1 warning generated. 1 warning generated. In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. 1 warning generated. In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. 1 warning generated. In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. 1 warning generated. In file included from aligner_seed.cpp:23: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ clang++ -DCOMPILER_OPTIONS="\" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I/opt/pkg/include/python3.10 -I/opt/pkg/include -Ithird_party \ -o bowtie2-align-l bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.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 bowtie_main.cpp \ -L/opt/pkg/lib -lpthread -lz clang++ \ -DCOMPILER_OPTIONS="\" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \ -I/opt/pkg/include/python3.10 -I/opt/pkg/include -Ithird_party \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -L/opt/pkg/lib -lpthread -lz In file included from bt2_search.cpp:41: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_search.cpp:54: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. In file included from bt2_inspect.cpp:29: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. 1 warning generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:81: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. 1 warning generated. In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:31: In file included from ./sse_util.h:27: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from sse_util.cpp:20: In file included from ./sse_util.h:27: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_swsse.cpp:22: In file included from ./aligner_swsse.h:28: In file included from ./sse_util.h:27: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_seed.cpp:23: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. 1 warning generated. clang++ \ -DCOMPILER_OPTIONS="\" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -Os -I/opt/pkg/include/python3.10 -I/opt/pkg/include -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \ -I/opt/pkg/include/python3.10 -I/opt/pkg/include -Ithird_party \ -o bowtie2-inspect-l bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -L/opt/pkg/lib -lpthread -lz In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. 1 warning generated. In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ In file included from bt2_inspect.cpp:29: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 error generated. In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:81: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. 1 warning generated. gmake: *** [Makefile:343: bowtie2-align-s] Error 1 gmake: *** Waiting for unfinished jobs.... In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:31: In file included from ./sse_util.h:27: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. 1 warning generated. In file included from sse_util.cpp:20: In file included from ./sse_util.h:27: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_swsse.cpp:22: In file included from ./aligner_swsse.h:28: In file included from ./sse_util.h:27: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:73: ./sse_wrap.h:31:10: fatal error: 'simde/x86/sse2.h' file not found #include "simde/x86/sse2.h" ^~~~~~~~~~~~~~~~~~ 1 error generated. In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. gmake: *** [Makefile:351: bowtie2-align-l] Error 1 *** Error code 2 Stop. bmake[1]: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/bowtie2 *** Error code 1 Stop. bmake: stopped in /Volumes/data/jenkins/workspace/pkgsrc-macos11-trunk-arm64/biology/bowtie2