=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Building for bowtie2-2.5.2 clang++ -DCOMPILER_OPTIONS="\" -pipe -Os -I/opt/pkg/include/python3.11 -I/opt/pkg/include -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -pipe -Os -I/opt/pkg/include/python3.11 -I/opt/pkg/include -std=c++11 -DPOPCNT_CAPABILITY -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/python3.11 -I/opt/pkg/include -I third_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 In file included from bt2_build.cpp:28: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:41: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_build.cpp:28: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:41: ./diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_build.cpp:28: In file included from ./bt2_idx.h:60: In file included from ./processor_support.h:17: third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:130:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:15: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:19: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:22: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:26: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:19: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:22: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:133:15: note: use constraint modifier "w" "push{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:136:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:162:3: error: invalid output constraint '=a' in asm __cpuid (__ext, __eax, __ebx, __ecx, __edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ third_party/cpuid.h:185:3: error: invalid output constraint '=a' in asm __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ 13 warnings and 2 errors generated. In file included from ref_read.cpp:20: In file included from ./ref_read.h:33: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from edit.cpp:21: In file included from ./edit.h:29: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:41: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:41: ./diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_idx.cpp:25: In file included from ./bt2_idx.h:60: In file included from ./processor_support.h:17: third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:130:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:15: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:19: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:22: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:26: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:19: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:22: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:133:15: note: use constraint modifier "w" "push{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:136:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:162:3: error: invalid output constraint '=a' in asm __cpuid (__ext, __eax, __ebx, __ecx, __edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ third_party/cpuid.h:185:3: error: invalid output constraint '=a' in asm __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ 13 warnings and 2 errors generated. In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:41: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:41: ./diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_io.cpp:25: In file included from ./bt2_idx.h:60: In file included from ./processor_support.h:17: third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:130:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:15: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:19: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:22: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:26: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:19: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:22: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:133:15: note: use constraint modifier "w" "push{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:136:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:162:3: error: invalid output constraint '=a' in asm __cpuid (__ext, __eax, __ebx, __ecx, __edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ third_party/cpuid.h:185:3: error: invalid output constraint '=a' in asm __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ 13 warnings and 2 errors generated. In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:41: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:42: In file included from ./blockwise_sa.h:41: ./diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ In file included from bt2_util.cpp:26: In file included from ./bt2_idx.h:60: In file included from ./processor_support.h:17: third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:130:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:15: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:19: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:29: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:22: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w1 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:131:26: note: use constraint modifier "w" "mov{l}\t{%0, %1|%1, %0}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:19: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:132:22: note: use constraint modifier "w" "xor{l}\t{%2, %0|%0, %2}\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:133:15: note: use constraint modifier "w" "push{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:138:14: warning: value size does not match register size specified by the constraint and modifier [-Wasm-operand-widths] : "=&r" (__eax), "=&r" (__ebx) ^ third_party/cpuid.h:136:14: note: use constraint modifier "w" "pop{l}\t%0\n\t" ^~ %w0 third_party/cpuid.h:162:3: error: invalid output constraint '=a' in asm __cpuid (__ext, __eax, __ebx, __ecx, __edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ third_party/cpuid.h:185:3: error: invalid output constraint '=a' in asm __cpuid (__level, *__eax, *__ebx, *__ecx, *__edx); ^ third_party/cpuid.h:104:7: note: expanded from macro '__cpuid' : "=a" (a), "=b" (b), "=c" (c), "=d" (d) \ ^ bt2_util.cpp:175:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable] TIndexOffU restOff = 0; ^ 14 warnings and 2 errors generated. In file included from reference.cpp:22: In file included from ./reference.h:32: In file included from ./ref_read.h:33: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from ds.cpp:20: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from multikey_qsort.cpp:20: In file included from ./multikey_qsort.h:27: ./diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from random_source.cpp:21: In file included from ./random_util.h:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. In file included from diff_sample.cpp:20: In file included from ./diff_sample.h:27: In file included from ./multikey_qsort.h:24: In file included from ./sequence_io.h:28: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ In file included from diff_sample.cpp:20: ./diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable] size_t amapEnts = 1; ^ ./diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ ./diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable] TIndexOffU added = 0; ^ 4 warnings generated. In file included from bowtie_build_main.cpp:25: ./ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] int thru = 0; ^ 1 warning generated. gmake: *** [Makefile:329: bowtie2-build-s] 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