bowtie2-2.5.4
4078 | int thru = 0;
| ^
/build/source/aligner_bt.cpp:126:10: warning: variable 'neval' set but not used [-Wunused-but-set-variable]
126 | size_t neval = 0; // # cells evaluated in this diag
| ^
/build/source/aligner_bt.cpp:1171:9: warning: variable 'iters' set but not used [-Wunused-but-set-variable]
1171 | size_t iters = 0;
| ^
3 warnings generated.
[ 85%] Building CXX object CMakeFiles/bowtie2-align-l.dir/outq.cpp.o
In file included from /build/source/bowtie_main.cpp:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 86%] Building CXX object CMakeFiles/bowtie2-align-l.dir/aligner_swsse_loc_i16.cpp.o
In file included from /build/source/sse_util.cpp:20:
In file included from /build/source/sse_util.h:24:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 86%] Building CXX object CMakeFiles/bowtie2-align-l.dir/aligner_swsse_ee_i16.cpp.o
In file included from /build/source/aligner_swsse.cpp:21:
In file included from /build/source/aligner_sw_common.h:23:
In file included from /build/source/aligner_result.h:27:
In file included from /build/source/read.h:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 87%] Building CXX object CMakeFiles/bowtie2-align-l.dir/aligner_swsse_loc_u8.cpp.o
In file included from /build/source/aligner_driver.cpp:20:
In file included from /build/source/aligner_driver.h:78:
In file included from /build/source/aligner_seed2.h:101:
In file included from /build/source/random_util.h:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
In file included from /build/source/aligner_driver.cpp:20:
In file included from /build/source/aligner_driver.h:78:
In file included from /build/source/aligner_seed2.h:103:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
/build/source/diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
391 | size_t amapEnts = 1;
| ^
/build/source/diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
574 | TIndexOffU added = 0;
| ^
/build/source/diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
645 | TIndexOffU added = 0;
| ^
In file included from /build/source/aligner_driver.cpp:20:
In file included from /build/source/aligner_driver.h:78:
/build/source/aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable]
1264 | size_t nuninited = 0;
| ^
/build/source/aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
8 warnings generated.
[ 87%] Building CXX object CMakeFiles/bowtie2-align-l.dir/aligner_swsse_ee_u8.cpp.o
In file included from /build/source/outq.cpp:22:
In file included from /build/source/outq.h:24:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 88%] Building CXX object CMakeFiles/bowtie2-align-l.dir/aligner_driver.cpp.o
In file included from /build/source/aligner_swsse_loc_i16.cpp:56:
In file included from /build/source/aligner_sw.h:74:
In file included from /build/source/aligner_sw_common.h:23:
In file included from /build/source/aligner_result.h:27:
In file included from /build/source/read.h:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 89%] Building CXX object CMakeFiles/bowtie2-align-l.dir/bowtie_main.cpp.o
In file included from /build/source/aligner_swsse_ee_i16.cpp:56:
In file included from /build/source/aligner_sw.h:74:
In file included from /build/source/aligner_sw_common.h:23:
In file included from /build/source/aligner_result.h:27:
In file included from /build/source/read.h:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 89%] Building CXX object CMakeFiles/bowtie2-align-l.dir/bt2_search.cpp.o
In file included from /build/source/aligner_swsse_ee_u8.cpp:56:
In file included from /build/source/aligner_sw.h:74:
In file included from /build/source/aligner_sw_common.h:23:
In file included from /build/source/aligner_result.h:27:
In file included from /build/source/read.h:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 90%] Building CXX object CMakeFiles/bowtie2-align-l.dir/ccnt_lut.cpp.o
[ 90%] Building CXX object CMakeFiles/bowtie2-align-l.dir/ref_read.cpp.o
In file included from /build/source/ref_read.cpp:20:
In file included from /build/source/ref_read.h:33:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 91%] Building CXX object CMakeFiles/bowtie2-align-l.dir/alphabet.cpp.o
[ 92%] Building CXX object CMakeFiles/bowtie2-align-l.dir/shmem.cpp.o
[ 92%] Building CXX object CMakeFiles/bowtie2-align-l.dir/edit.cpp.o
In file included from /build/source/aligner_swsse_loc_u8.cpp:56:
In file included from /build/source/aligner_sw.h:74:
In file included from /build/source/aligner_sw_common.h:23:
In file included from /build/source/aligner_result.h:27:
In file included from /build/source/read.h:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
In file included from /build/source/edit.cpp:21:
In file included from /build/source/edit.h:29:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 93%] Building CXX object CMakeFiles/bowtie2-align-l.dir/bt2_idx.cpp.o
[ 94%] Building CXX object CMakeFiles/bowtie2-align-l.dir/bt2_io.cpp.o
In file included from /build/source/bt2_idx.cpp:25:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
In file included from /build/source/diff_sample.h:27:
In file included from /build/source/multikey_qsort.h:24:
In file included from /build/source/sequence_io.h:28:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
In file included from /build/source/bt2_idx.cpp:25:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
/build/source/diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
391 | size_t amapEnts = 1;
| ^
/build/source/diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
574 | TIndexOffU added = 0;
| ^
/build/source/diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
645 | TIndexOffU added = 0;
| ^
4 warnings generated.
In file included from /build/source/bt2_io.cpp:25:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
In file included from /build/source/diff_sample.h:27:
In file included from /build/source/multikey_qsort.h:24:
In file included from /build/source/sequence_io.h:28:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
In file included from /build/source/bt2_io.cpp:25:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
/build/source/diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
391 | size_t amapEnts = 1;
| ^
/build/source/diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
574 | TIndexOffU added = 0;
| ^
/build/source/diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
645 | TIndexOffU added = 0;
| ^
4 warnings generated.
[ 94%] Building CXX object CMakeFiles/bowtie2-align-l.dir/bt2_locks.cpp.o
[ 95%] Building CXX object CMakeFiles/bowtie2-align-l.dir/bt2_util.cpp.o
In file included from /build/source/bt2_util.cpp:26:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
In file included from /build/source/diff_sample.h:27:
In file included from /build/source/multikey_qsort.h:24:
In file included from /build/source/sequence_io.h:28:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
In file included from /build/source/bt2_util.cpp:26:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
/build/source/diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
391 | size_t amapEnts = 1;
| ^
/build/source/diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
574 | TIndexOffU added = 0;
| ^
/build/source/diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
645 | TIndexOffU added = 0;
| ^
/build/source/bt2_util.cpp:175:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable]
175 | TIndexOffU restOff = 0;
| ^
5 warnings generated.
[ 95%] Building CXX object CMakeFiles/bowtie2-align-l.dir/reference.cpp.o
[ 96%] Building CXX object CMakeFiles/bowtie2-align-l.dir/ds.cpp.o
In file included from /build/source/reference.cpp:22:
In file included from /build/source/reference.h:32:
In file included from /build/source/ref_read.h:33:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 97%] Building CXX object CMakeFiles/bowtie2-align-l.dir/multikey_qsort.cpp.o
In file included from /build/source/ds.cpp:20:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
[ 97%] Building CXX object CMakeFiles/bowtie2-align-l.dir/limit.cpp.o
[ 98%] Building CXX object CMakeFiles/bowtie2-align-l.dir/random_source.cpp.o
In file included from /build/source/random_source.cpp:21:
In file included from /build/source/random_util.h:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
In file included from /build/source/multikey_qsort.cpp:20:
In file included from /build/source/multikey_qsort.h:24:
In file included from /build/source/sequence_io.h:28:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
In file included from /build/source/multikey_qsort.cpp:20:
In file included from /build/source/multikey_qsort.h:27:
/build/source/diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
391 | size_t amapEnts = 1;
| ^
/build/source/diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
574 | TIndexOffU added = 0;
| ^
/build/source/diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
645 | TIndexOffU added = 0;
| ^
4 warnings generated.
In file included from /build/source/bowtie_main.cpp:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
1 warning generated.
In file included from /build/source/aligner_driver.cpp:20:
In file included from /build/source/aligner_driver.h:78:
In file included from /build/source/aligner_seed2.h:101:
In file included from /build/source/random_util.h:25:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
In file included from /build/source/aligner_driver.cpp:20:
In file included from /build/source/aligner_driver.h:78:
In file included from /build/source/aligner_seed2.h:103:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
/build/source/diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
391 | size_t amapEnts = 1;
| ^
/build/source/diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
574 | TIndexOffU added = 0;
| ^
/build/source/diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
645 | TIndexOffU added = 0;
| ^
In file included from /build/source/aligner_driver.cpp:20:
In file included from /build/source/aligner_driver.h:78:
/build/source/aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable]
1264 | size_t nuninited = 0;
| ^
/build/source/aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
8 warnings generated.
In file included from /build/source/bt2_search.cpp:41:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
In file included from /build/source/diff_sample.h:27:
In file included from /build/source/multikey_qsort.h:24:
In file included from /build/source/sequence_io.h:28:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
In file included from /build/source/bt2_search.cpp:41:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
/build/source/diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
391 | size_t amapEnts = 1;
| ^
/build/source/diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
574 | TIndexOffU added = 0;
| ^
/build/source/diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
645 | TIndexOffU added = 0;
| ^
In file included from /build/source/bt2_search.cpp:53:
In file included from /build/source/aligner_driver.h:78:
/build/source/aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable]
1264 | size_t nuninited = 0;
| ^
/build/source/aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/bt2_search.cpp:4663:6: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
4663 | int steal_ctr = 1;
| ^
9 warnings generated.
[ 99%] Linking CXX executable bowtie2-align-s
CMakeFiles/bowtie2-align-s.dir/sam.cpp.o:sam.cpp:function pizlonatedFI403_sqrt:(.text+0x410d1): error: undefined reference to 'pizlonated_sqrt'
CMakeFiles/bowtie2-align-s.dir/sam.cpp.o:sam.cpp:function pizlonatedFI403_log:(.text+0x411a1): error: undefined reference to 'pizlonated_log'
CMakeFiles/bowtie2-align-s.dir/aligner_seed.cpp.o:aligner_seed.cpp:function pizlonatedFI403_sqrt:(.text+0x28961): error: undefined reference to 'pizlonated_sqrt'
CMakeFiles/bowtie2-align-s.dir/aligner_seed.cpp.o:aligner_seed.cpp:function pizlonatedFI403_log:(.text+0x28a31): error: undefined reference to 'pizlonated_log'
CMakeFiles/bowtie2-align-s.dir/aligner_seed2.cpp.o:aligner_seed2.cpp:function pizlonatedFI4792_pow:(.text+0x1c046): error: undefined reference to 'pizlonated_pow'
CMakeFiles/bowtie2-align-s.dir/aligner_sw.cpp.o:aligner_sw.cpp:function pizlonatedFI403_sqrt:(.text+0xa761): error: undefined reference to 'pizlonated_sqrt'
CMakeFiles/bowtie2-align-s.dir/aligner_sw.cpp.o:aligner_sw.cpp:function pizlonatedFI403_log:(.text+0xa831): error: undefined reference to 'pizlonated_log'
CMakeFiles/bowtie2-align-s.dir/scoring.cpp.o:scoring.cpp:function pizlonatedFI403_sqrt:(.text+0x1501): error: undefined reference to 'pizlonated_sqrt'
CMakeFiles/bowtie2-align-s.dir/scoring.cpp.o:scoring.cpp:function pizlonatedFI403_log:(.text+0x15d1): error: undefined reference to 'pizlonated_log'
CMakeFiles/bowtie2-align-s.dir/bt2_search.cpp.o:bt2_search.cpp:function pizlonatedFI269_sqrtf:(.text+0xcc661): error: undefined reference to 'pizlonated_sqrtf'
clang-20: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [CMakeFiles/bowtie2-align-s.dir/build.make:821: bowtie2-align-s] Error 1
make[1]: *** [CMakeFiles/Makefile2:102: CMakeFiles/bowtie2-align-s.dir/all] Error 2
In file included from /build/source/bt2_search.cpp:41:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
In file included from /build/source/diff_sample.h:27:
In file included from /build/source/multikey_qsort.h:24:
In file included from /build/source/sequence_io.h:28:
/build/source/ds.h:4078:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
4078 | int thru = 0;
| ^
In file included from /build/source/bt2_search.cpp:41:
In file included from /build/source/bt2_idx.h:42:
In file included from /build/source/blockwise_sa.h:41:
/build/source/diff_sample.h:391:9: warning: variable 'amapEnts' set but not used [-Wunused-but-set-variable]
391 | size_t amapEnts = 1;
| ^
/build/source/diff_sample.h:574:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
574 | TIndexOffU added = 0;
| ^
/build/source/diff_sample.h:645:13: warning: variable 'added' set but not used [-Wunused-but-set-variable]
645 | TIndexOffU added = 0;
| ^
In file included from /build/source/bt2_search.cpp:53:
In file included from /build/source/aligner_driver.h:78:
/build/source/aligner_seed2.h:1264:10: warning: variable 'nuninited' set but not used [-Wunused-but-set-variable]
1264 | size_t nuninited = 0;
| ^
/build/source/aligner_seed2.h:2448:10: warning: variable 'ns' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable]
2448 | size_t ns = 0, ngap = 0, nrefn = 0;
| ^
/build/source/bt2_search.cpp:4663:6: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
4663 | int steal_ctr = 1;
| ^
9 warnings generated.
[100%] Linking CXX executable bowtie2-align-l
CMakeFiles/bowtie2-align-l.dir/sam.cpp.o:sam.cpp:function pizlonatedFI403_sqrt:(.text+0x410b1): error: undefined reference to 'pizlonated_sqrt'
CMakeFiles/bowtie2-align-l.dir/sam.cpp.o:sam.cpp:function pizlonatedFI403_log:(.text+0x41181): error: undefined reference to 'pizlonated_log'
CMakeFiles/bowtie2-align-l.dir/aligner_seed.cpp.o:aligner_seed.cpp:function pizlonatedFI403_sqrt:(.text+0x2aa21): error: undefined reference to 'pizlonated_sqrt'
CMakeFiles/bowtie2-align-l.dir/aligner_seed.cpp.o:aligner_seed.cpp:function pizlonatedFI403_log:(.text+0x2aaf1): error: undefined reference to 'pizlonated_log'
CMakeFiles/bowtie2-align-l.dir/aligner_seed2.cpp.o:aligner_seed2.cpp:function pizlonatedFI4792_pow:(.text+0x1c266): error: undefined reference to 'pizlonated_pow'
CMakeFiles/bowtie2-align-l.dir/aligner_sw.cpp.o:aligner_sw.cpp:function pizlonatedFI403_sqrt:(.text+0xa6b1): error: undefined reference to 'pizlonated_sqrt'
CMakeFiles/bowtie2-align-l.dir/aligner_sw.cpp.o:aligner_sw.cpp:function pizlonatedFI403_log:(.text+0xa781): error: undefined reference to 'pizlonated_log'
CMakeFiles/bowtie2-align-l.dir/scoring.cpp.o:scoring.cpp:function pizlonatedFI403_sqrt:(.text+0x1501): error: undefined reference to 'pizlonated_sqrt'
CMakeFiles/bowtie2-align-l.dir/scoring.cpp.o:scoring.cpp:function pizlonatedFI403_log:(.text+0x15d1): error: undefined reference to 'pizlonated_log'
CMakeFiles/bowtie2-align-l.dir/bt2_search.cpp.o:bt2_search.cpp:function pizlonatedFI269_sqrtf:(.text+0xcc3e1): error: undefined reference to 'pizlonated_sqrtf'
clang-20: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [CMakeFiles/bowtie2-align-l.dir/build.make:821: bowtie2-align-l] Error 1
make[1]: *** [CMakeFiles/Makefile2:134: CMakeFiles/bowtie2-align-l.dir/all] Error 2
make: *** [Makefile:146: all] Error 2
python3.12-basedmypy-2.10.0
error: building of '/nix/store/yazdvcyfgm2krisks0a9001lmcm1k9q8-python3.12-basedmypy-2.10.0-x86_64-unknown-linux-gnufilc0.drv' from in-memory derivation timed out after 900 seconds of silence
bees-0.10
error: Cannot build '/nix/store/6blh94h5znjizycn1fq4sqq3fhyylny6-bees-x86_64-unknown-linux-gnufilc0-0.10.drv'.
Reason: 1 dependency failed.
Output paths:
/nix/store/y6wsmllq45zmmjqh2ns5zhl1j47sq98c-bees-x86_64-unknown-linux-gnufilc0-0.10python3.12-behave-1.2.7.dev5
error: Cannot build '/nix/store/bk6zh0g3i39h64qg8x08wkccarrq2wn2-python3.12-behave-1.2.7.dev5-x86_64-unknown-linux-gnufilc0.drv'.
Reason: 2 dependencies failed.
Output paths:
/nix/store/g5pzr4rx5bj94cx8n0h3bjw49i5v0xvy-python3.12-behave-1.2.7.dev5-x86_64-unknown-linux-gnufilc0
/nix/store/h0cv2yphf7535cxr0lrlgf67x8bmr08g-python3.12-behave-1.2.7.dev5-x86_64-unknown-linux-gnufilc0-distpython3.12-black-25.1.0
error: Cannot build '/nix/store/n2jf6fpnawfinih71q3xrz29ps221p0d-python3.12-black-25.1.0-x86_64-unknown-linux-gnufilc0.drv'.
Reason: builder failed with exit code 1.
Output paths:
/nix/store/aj3cvsslh0cxg1yvh2k1cgd2i9f668zk-python3.12-black-25.1.0-x86_64-unknown-linux-gnufilc0-dist
/nix/store/xqrn9by415d3m8b3xbbw8pjcy7n3ra5v-python3.12-black-25.1.0-x86_64-unknown-linux-gnufilc0
Last 25 log lines:
> FAILED tests/test_black.py::BlackTestCase::test_required_version_matches_partial_version - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::BlackTestCase::test_required_version_matches_version - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::BlackTestCase::test_single_file_force_py36 - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::BlackTestCase::test_single_file_force_pyi - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::BlackTestCase::test_skip_magic_trailing_comma - AssertionError: 1 != 0
> FAILED tests/test_black.py::BlackTestCase::test_skip_source_first_line - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::BlackTestCase::test_works_in_mono_process_only_environment - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::TestCaching::test_cache_broken_file - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::TestCaching::test_cache_single_file_already_cached - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::TestCaching::test_cache_multiple_files - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::TestCaching::test_no_cache_when_writeback_diff[no-color] - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::TestCaching::test_no_cache_when_writeback_diff[with-color] - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::TestCaching::test_output_locking_when_writeback_diff[no-color] - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::TestCaching::test_output_locking_when_writeback_diff[with-color] - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::TestCaching::test_no_cache_when_stdin - assert not 1
> FAILED tests/test_black.py::TestCaching::test_failed_formatting_does_not_get_cached - AssertionError: Failed with args: ['--verbose', '--config', '/build/black-2...
> FAILED tests/test_black.py::TestFileCollection::test_invalid_gitignore - assert None
> FAILED tests/test_black.py::TestFileCollection::test_invalid_nested_gitignore - assert None
> FAILED tests/test_ipynb.py::test_ipynb_diff_with_change - assert '@@ -1,3 +1,3 @@\n %%time\n \n-print(\'foo\')\n+print("foo")\n' in "...
> FAILED tests/test_ipynb.py::test_ipynb_diff_with_no_change - assert '1 file would be left unchanged.' in "Python 3.12.5 has a memory saf...
> FAILED tests/test_ipynb.py::test_cache_isnt_written_if_no_jupyter_deps_single - assert 'No Python files are present to be formatted. Nothing to do' in "Pyt...
> FAILED tests/test_ipynb.py::test_cache_isnt_written_if_no_jupyter_deps_dir - assert 'No Python files are present to be formatted. Nothing to do' in "Pyt...
> FAILED tests/test_ipynb.py::test_ipynb_flag - assert '@@ -1,3 +1,3 @@\n %%time\n \n-print(\'foo\')\n+print("foo")\n' in "...
> FAILED tests/test_ipynb.py::test_ipynb_and_pyi_flags - AssertionError: assert 'Python 3.12....thon 3.12.4\n' == 'Cannot pass ...yn...
> ===== 54 failed, 395 passed, 2 skipped, 1 deselected in 174.17s (0:02:54) ======
For full logs, run:
nix log /nix/store/n2jf6fpnawfinih71q3xrz29ps221p0d-python3.12-black-25.1.0-x86_64-unknown-linux-gnufilc0.drvpython3.12-black-macchiato-1.3.0
error: Cannot build '/nix/store/2vv0awvfqmjqvxzrx2ggc3v06j1divi1-python3.12-black-macchiato-1.3.0-x86_64-unknown-linux-gnufilc0.drv'.
Reason: 1 dependency failed.
Output paths:
/nix/store/p8kfz7pjglx1plqcb7hkp2qvgfxmksrz-python3.12-black-macchiato-1.3.0-x86_64-unknown-linux-gnufilc0
/nix/store/zm2x7f1gb5fxj6lj3iy6vgfl8ypjy3p0-python3.12-black-macchiato-1.3.0-x86_64-unknown-linux-gnufilc0-distpython3.12-blacken-docs-1.19.1
error: Cannot build '/nix/store/1mm3jgjbi7x8mmg18svakf8bin8xvdhs-python3.12-blacken-docs-1.19.1-x86_64-unknown-linux-gnufilc0.drv'.
Reason: 1 dependency failed.
Output paths:
/nix/store/bfgnm0bi34nsn1dfrczhms47az5b15qn-python3.12-blacken-docs-1.19.1-x86_64-unknown-linux-gnufilc0
/nix/store/kbvw56gsg1blaag044i1k6d1rv28ps9i-python3.12-blacken-docs-1.19.1-x86_64-unknown-linux-gnufilc0-distboost-1.81.0
error: Cannot build '/nix/store/800xkr4dm9vyfpbzyq6gjhn12mvypcr7-boost-x86_64-unknown-linux-gnufilc0-1.81.0.drv'.
Reason: builder failed with exit code 1.
Output paths:
/nix/store/2igpzp687hmnzr2dbixhsxdcb9fsqdyl-boost-x86_64-unknown-linux-gnufilc0-1.81.0-dev
/nix/store/zgrhn7vgy3ihzi22wwymgz30cdc8k8b5-boost-x86_64-unknown-linux-gnufilc0-1.81.0
Last 25 log lines:
> In file included from ./boost/fiber/scheduler.hpp:17:
> ./boost/intrusive/list.hpp:1351:14: warning: variable 'node_count' set but not used [-Wunused-but-set-variable]
> 1351 | size_t node_count = 0;
> | ^
> In file included from libs/fiber/src/scheduler.cpp:7:
> In file included from ./boost/fiber/scheduler.hpp:20:
> ./boost/intrusive/slist.hpp:1939:14: warning: variable 'node_count' set but not used [-Wunused-but-set-variable]
> 1939 | size_t node_count = 0;
> | ^
> 2 warnings generated.
> ...skipped <pbin.v2/libs/fiber/build/gcc-cross/release/threading-multi/visibility-hidden>libboost_fiber.so.1.81.0 for lack of <pbin.v2/libs/context/build/gcc-cross/release/threading-multi/visibility-hidden>libboost_context.so.1.81.0...
> ...skipped <p/build/boost_1_81_0/stage/lib>libboost_fiber.so.1.81.0 for lack of <pbin.v2/libs/fiber/build/gcc-cross/release/threading-multi/visibility-hidden>libboost_fiber.so.1.81.0...
> ...skipped <p/build/boost_1_81_0/stage/lib>libboost_fiber.so for lack of <p/build/boost_1_81_0/stage/lib>libboost_fiber.so.1.81.0...
> ...skipped <pbin.v2/libs/fiber/build/gcc-cross/release/threading-multi/visibility-hidden>libboost_fiber-variant-shared.cmake for lack of <pbin.v2/libs/fiber/build/gcc-cross/release/threading-multi/visibility-hidden>libboost_fiber.so.1.81.0...
> ...skipped <p/build/boost_1_81_0/stage/lib/cmake/boost_fiber-1.81.0>libboost_fiber-variant-shared.cmake for lack of <pbin.v2/libs/fiber/build/gcc-cross/release/threading-multi/visibility-hidden>libboost_fiber-variant-shared.cmake...
> gcc.compile.c++ bin.v2/libs/wave/build/gcc-cross/release/threading-multi/visibility-hidden/instantiate_re2c_lexer_str.o
> gcc.compile.c++ bin.v2/libs/wave/build/gcc-cross/release/threading-multi/visibility-hidden/instantiate_re2c_lexer.o
> gcc.link.dll bin.v2/libs/wave/build/gcc-cross/release/threadapi-pthread/threading-multi/visibility-hidden/libboost_wave.so.1.81.0
> boost-install.generate-cmake-variant- bin.v2/libs/wave/build/gcc-cross/release/threadapi-pthread/threading-multi/visibility-hidden/libboost_wave-variant-shared.cmake
> common.copy /build/boost_1_81_0/stage/lib/cmake/boost_wave-1.81.0/libboost_wave-variant-shared.cmake
> common.copy /build/boost_1_81_0/stage/lib/libboost_wave.so.1.81.0
> ln-UNIX /build/boost_1_81_0/stage/lib/libboost_wave.so
> ...failed updating 3 targets...
> ...skipped 15 targets...
> ...updated 989 targets...
For full logs, run:
nix log /nix/store/800xkr4dm9vyfpbzyq6gjhn12mvypcr7-boost-x86_64-unknown-linux-gnufilc0-1.81.0.drvboost-1.82.0
error: Cannot build '/nix/store/dl2jiirdlm2hix5g4xj8y2b1qadx29hk-boost-x86_64-unknown-linux-gnufilc0-1.82.0.drv'.
Reason: builder failed with exit code 1.
Output paths:
/nix/store/4rq5vkpsldrzilhyvq6szvc3iavjxlci-boost-x86_64-unknown-linux-gnufilc0-1.82.0
/nix/store/kjaxw1cddcrbi88v9bw2a9zn7fqp0hln-boost-x86_64-unknown-linux-gnufilc0-1.82.0-dev
Last 25 log lines:
> ...skipped <p/build/boost_1_82_0/stage/lib>libboost_fiber.so for lack of <p/build/boost_1_82_0/stage/lib>libboost_fiber.so.1.82.0...
> ...skipped <pbin.v2/libs/fiber/build/gcc-cross/release/threading-multi/visibility-hidden>libboost_fiber-variant-shared.cmake for lack of <pbin.v2/libs/fiber/build/gcc-cross/release/threading-multi/visibility-hidden>libboost_fiber.so.1.82.0...
> ...skipped <p/build/boost_1_82_0/stage/lib/cmake/boost_fiber-1.82.0>libboost_fiber-variant-shared.cmake for lack of <pbin.v2/libs/fiber/build/gcc-cross/release/threading-multi/visibility-hidden>libboost_fiber-variant-shared.cmake...
> gcc.compile.c++ bin.v2/libs/url/build/gcc-cross/release/threading-multi/visibility-hidden/src.o
> gcc.link.dll bin.v2/libs/url/build/gcc-cross/release/threading-multi/visibility-hidden/libboost_url.so.1.82.0
> boost-install.generate-cmake-variant- bin.v2/libs/url/build/gcc-cross/release/threading-multi/visibility-hidden/libboost_url-variant-shared.cmake
> common.copy /build/boost_1_82_0/stage/lib/libboost_url.so.1.82.0
> common.copy /build/boost_1_82_0/stage/lib/cmake/boost_url-1.82.0/libboost_url-variant-shared.cmake
> ln-UNIX /build/boost_1_82_0/stage/lib/libboost_url.so
> gcc.compile.c++ bin.v2/libs/contract/build/gcc-cross/release/threading-multi/visibility-hidden/contract.o
> gcc.link.dll bin.v2/libs/contract/build/gcc-cross/release/threading-multi/visibility-hidden/libboost_contract.so.1.82.0
> boost-install.generate-cmake-variant- bin.v2/libs/contract/build/gcc-cross/release/threading-multi/visibility-hidden/libboost_contract-variant-shared.cmake
> common.copy /build/boost_1_82_0/stage/lib/libboost_contract.so.1.82.0
> ln-UNIX /build/boost_1_82_0/stage/lib/libboost_contract.so
> common.copy /build/boost_1_82_0/stage/lib/cmake/boost_contract-1.82.0/libboost_contract-variant-shared.cmake
> gcc.compile.c++ bin.v2/libs/wave/build/gcc-cross/release/threading-multi/visibility-hidden/instantiate_re2c_lexer.o
> gcc.compile.c++ bin.v2/libs/wave/build/gcc-cross/release/threading-multi/visibility-hidden/instantiate_re2c_lexer_str.o
> gcc.link.dll bin.v2/libs/wave/build/gcc-cross/release/threadapi-pthread/threading-multi/visibility-hidden/libboost_wave.so.1.82.0
> boost-install.generate-cmake-variant- bin.v2/libs/wave/build/gcc-cross/release/threadapi-pthread/threading-multi/visibility-hidden/libboost_wave-variant-shared.cmake
> common.copy /build/boost_1_82_0/stage/lib/cmake/boost_wave-1.82.0/libboost_wave-variant-shared.cmake
> common.copy /build/boost_1_82_0/stage/lib/libboost_wave.so.1.82.0
> ln-UNIX /build/boost_1_82_0/stage/lib/libboost_wave.so
> ...failed updating 3 targets...
> ...skipped 15 targets...
> ...updated 991 targets...
For full logs, run:
nix log /nix/store/dl2jiirdlm2hix5g4xj8y2b1qadx29hk-boost-x86_64-unknown-linux-gnufilc0-1.82.0.drvboost-1.86.0
error: Cannot build '/nix/store/m0cg5flpbw08682wgv9iigr6iyjmh0ki-boost-x86_64-unknown-linux-gnufilc0-1.86.0.drv'.
Reason: builder failed with exit code 1.
Output paths:
/nix/store/cmvy0zdpvx6lvqhzlp30lvx0fkh53qa9-boost-x86_64-unknown-linux-gnufilc0-1.86.0-dev
/nix/store/r9xrl39wwqdf28fghnjyy2f8gf04z5w5-boost-x86_64-unknown-linux-gnufilc0-1.86.0
Last 25 log lines:
> <p/build/boost_1_86_0/stage/lib/cmake/boost_fiber-1.86.0>boost_fiber-config.cmake
> <p/build/boost_1_86_0/stage/lib/cmake/boost_fiber-1.86.0>libboost_fiber-variant-shared.cmake
> <p/build/boost_1_86_0/stage/lib>libboost_context.so
> <p/build/boost_1_86_0/stage/lib>libboost_context.so.1.86.0
> <p/build/boost_1_86_0/stage/lib>libboost_coroutine.so
> <p/build/boost_1_86_0/stage/lib>libboost_coroutine.so.1.86.0
> <p/build/boost_1_86_0/stage/lib>libboost_fiber.so
> <p/build/boost_1_86_0/stage/lib>libboost_fiber.so.1.86.0
> <pbin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_context-variant-shared.cmake
> <pbin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_context.so.1.86.0
> <pbin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_context-config-version.cmake
> <pbin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_context-config.cmake
> <pbin.v2/libs/coroutine/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_coroutine-variant-shared.cmake
> <pbin.v2/libs/coroutine/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_coroutine.so.1.86.0
> <pbin.v2/libs/coroutine/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_coroutine-config-version.cmake
> <pbin.v2/libs/coroutine/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_coroutine-config.cmake
> <pbin.v2/libs/fiber/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_fiber-variant-shared.cmake
> <pbin.v2/libs/fiber/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_fiber.so.1.86.0
> <pbin.v2/libs/fiber/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_fiber-config-version.cmake
> <pbin.v2/libs/fiber/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_fiber-config.cmake
>
> ...failed updating 3 targets...
> gcc.compile.asm bin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden/asm/jump_x86_64_sysv_elf_gas.o
> gcc.compile.asm bin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden/asm/make_x86_64_sysv_elf_gas.o
> gcc.compile.asm bin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden/asm/ontop_x86_64_sysv_elf_gas.o
For full logs, run:
nix log /nix/store/m0cg5flpbw08682wgv9iigr6iyjmh0ki-boost-x86_64-unknown-linux-gnufilc0-1.86.0.drvboost-1.88.0
error: Cannot build '/nix/store/y98sm7fvm45940yslhz8pb9l19962gx7-boost-x86_64-unknown-linux-gnufilc0-1.88.0.drv'.
Reason: builder failed with exit code 1.
Output paths:
/nix/store/gqsl2zm5g6vmvjmcg0r2mhbk1fr0893s-boost-x86_64-unknown-linux-gnufilc0-1.88.0-dev
/nix/store/sdwspgjzbshq3nmw03k7n8mj6cp84lza-boost-x86_64-unknown-linux-gnufilc0-1.88.0
Last 25 log lines:
> <pbin.v2/libs/coroutine/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_coroutine-config.cmake
> <pbin.v2/libs/fiber/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_fiber.so.1.88.0
> <pbin.v2/libs/fiber/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_fiber-variant-shared.cmake
> <pbin.v2/libs/fiber/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_fiber-config-version.cmake
> <pbin.v2/libs/fiber/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_fiber-config.cmake
> <pbin.v2/libs/graph/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_graph-variant-shared.cmake
> <pbin.v2/libs/graph/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_graph.so.1.88.0
> <pbin.v2/libs/graph/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_graph-config-version.cmake
> <pbin.v2/libs/graph/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_graph-config.cmake
> <pbin.v2/libs/json/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_json.so.1.88.0
> <pbin.v2/libs/json/gcc-cross/release/x86_64/threading-multi/visibility-hidden>libboost_json-variant-shared.cmake
> <pbin.v2/libs/json/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_json-config-version.cmake
> <pbin.v2/libs/json/gcc-cross/release/x86_64/threading-multi/visibility-hidden>stage/boost_json-config.cmake
> <pbin.v2/libs/process/build/gcc-cross/release/x86_64/boost.process.fs-boost/threading-multi/visibility-hidden>libboost_process.so.1.88.0
> <pbin.v2/libs/process/gcc-cross/release/x86_64/boost.process.fs-boost/threading-multi/visibility-hidden>libboost_process-variant-shared.cmake
> <pbin.v2/libs/process/gcc-cross/release/x86_64/boost.process.fs-boost/threading-multi/visibility-hidden>stage/boost_process-config-version.cmake
> <pbin.v2/libs/process/gcc-cross/release/x86_64/boost.process.fs-boost/threading-multi/visibility-hidden>stage/boost_process-config.cmake
>
> ...failed updating 6 targets...
> gcc.compile.asm bin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden/asm/jump_x86_64_sysv_elf_gas.o
> gcc.compile.asm bin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden/asm/make_x86_64_sysv_elf_gas.o
> gcc.compile.asm bin.v2/libs/context/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden/asm/ontop_x86_64_sysv_elf_gas.o
> gcc.compile.c++ bin.v2/libs/graph/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden/graphml.o
> gcc.compile.c++ bin.v2/libs/graph/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden/read_graphviz_new.o
> gcc.compile.c++ bin.v2/libs/json/build/gcc-cross/release/x86_64/threading-multi/visibility-hidden/src.o
For full logs, run:
nix log /nix/store/y98sm7fvm45940yslhz8pb9l19962gx7-boost-x86_64-unknown-linux-gnufilc0-1.88.0.drvbootil-unstable-2019-11-18
error: Cannot build '/nix/store/bbarw42hbb670b32776whhni2ks9m0yv-bootil-x86_64-unknown-linux-gnufilc0-unstable-2019-11-18.drv'.
Reason: builder failed with exit code 2.
Output paths:
/nix/store/x98z70zw7hai8kpl03z3nbjr3fm8m4r3-bootil-x86_64-unknown-linux-gnufilc0-unstable-2019-11-18
Last 25 log lines:
> src/3rdParty/xzip/unzip.cc:3802:43: note: remove extraneous parentheses around the comparison to silence this warning
> 3802 | if ((pfile_in_zip_read_info->read_buffer == NULL)) return UNZ_END_OF_LIST_OF_FILE;
> | ~ ^ ~
> src/3rdParty/xzip/unzip.cc:3802:43: note: use '=' to turn this equality comparison into an assignment
> 3802 | if ((pfile_in_zip_read_info->read_buffer == NULL)) return UNZ_END_OF_LIST_OF_FILE;
> | ^~
> | =
> src/3rdParty/xzip/unzip.cc:4280:2: warning: expression result unused [-Wunused-value]
> 4280 | readonly;
> | ^~~~~~~~
> src/3rdParty/xzip/unzip.cc:4281:2: warning: expression result unused [-Wunused-value]
> 4281 | hidden;
> | ^~~~~~
> src/3rdParty/xzip/unzip.cc:4282:2: warning: expression result unused [-Wunused-value]
> 4282 | system;
> | ^~~~~~
> src/3rdParty/xzip/unzip.cc:4283:2: warning: expression result unused [-Wunused-value]
> 4283 | isdir;
> | ^~~~~
> src/3rdParty/xzip/unzip.cc:4284:2: warning: expression result unused [-Wunused-value]
> 4284 | archive;
> | ^~~~~~~
> 12 warnings and 5 errors generated.
> make[1]: *** [bootil_static.make:339: obj/Release/unzip.o] Error 1
> make: *** [Makefile:17: bootil_static] Error 2
For full logs, run:
nix log /nix/store/bbarw42hbb670b32776whhni2ks9m0yv-bootil-x86_64-unknown-linux-gnufilc0-unstable-2019-11-18.drvbootloadhid-0-unstable-2012-12-08
error: Cannot build '/nix/store/62x1zars41202xh0n8srra1scy54rw89-bootloadhid-x86_64-unknown-linux-gnufilc0-0-unstable-2012-12-08.drv'.
Reason: builder failed with exit code 2.
Output paths:
/nix/store/yhar9y3sfhpwg5ql0w7jnm4gim8d7sj8-bootloadhid-x86_64-unknown-linux-gnufilc0-0-unstable-2012-12-08
Last 25 log lines:
> Running phase: configurePhase
> no configure script, doing nothing
> Running phase: buildPhase
> build flags: SHELL=/nix/store/cfqbabpc7xwg8akbcchqbq3cai6qq2vs-bash-5.2p37/bin/bash CC=cc
> cc -O2 -Wall `libusb-config --cflags` -c main.c -o main.o
> cc -O2 -Wall `libusb-config --cflags` -c usbcalls.c -o usbcalls.o
> In file included from usbcalls.c:19:
> ./usb-libusb.c:196:9: warning: expression result unused [-Wunused-value]
> 196 | *len++;
> | ^~~~~~
> 1 warning generated.
> cc -O2 -Wall `libusb-config --cflags` -o bootloadHID main.o usbcalls.o `libusb-config --libs`
> usbcalls.o:usbcalls.c:function pizlonatedFI1_usb_init:(.text+0x2047): error: undefined reference to 'pizlonated_usb_init'
> usbcalls.o:usbcalls.c:function pizlonatedFI2_usb_find_busses:(.text+0x20b7): error: undefined reference to 'pizlonated_usb_find_busses'
> usbcalls.o:usbcalls.c:function pizlonatedFI2_usb_find_devices:(.text+0x2147): error: undefined reference to 'pizlonated_usb_find_devices'
> usbcalls.o:usbcalls.c:function pizlonatedFI9_usb_get_busses:(.text+0x21d7): error: undefined reference to 'pizlonated_usb_get_busses'
> usbcalls.o:usbcalls.c:function pizlonatedFI1073_usb_open:(.text+0x2271): error: undefined reference to 'pizlonated_usb_open'
> usbcalls.o:usbcalls.c:function pizlonatedFI9_usb_strerror:(.text+0x2327): error: undefined reference to 'pizlonated_usb_strerror'
> usbcalls.o:usbcalls.c:function pizlonatedFI3000912518_usb_control_msg:(.text+0x24cd): error: undefined reference to 'pizlonated_usb_control_msg'
> usbcalls.o:usbcalls.c:function pizlonatedFI1066_usb_close:(.text+0x2701): error: undefined reference to 'pizlonated_usb_close'
> usbcalls.o:usbcalls.c:function pizlonatedFI2529_usb_set_configuration:(.text+0x27c7): error: undefined reference to 'pizlonated_usb_set_configuration'
> usbcalls.o:usbcalls.c:function pizlonatedFI2529_usb_claim_interface:(.text+0x28b7): error: undefined reference to 'pizlonated_usb_claim_interface'
> usbcalls.o:usbcalls.c:function pizlonatedFI2529_usb_detach_kernel_driver_np:(.text+0x29a7): error: undefined reference to 'pizlonated_usb_detach_kernel_driver_np'
> clang-20: error: linker command failed with exit code 1 (use -v to see invocation)
> make: *** [Makefile:36: bootloadHID] Error 1
For full logs, run:
nix log /nix/store/62x1zars41202xh0n8srra1scy54rw89-bootloadhid-x86_64-unknown-linux-gnufilc0-0-unstable-2012-12-08.drvboron-2.1.0
error: Cannot build '/nix/store/9shc4fqx8rcdjn0yg20jfj5x2b21p861-boron-x86_64-unknown-linux-gnufilc0-2.1.0.drv'.
Reason: builder failed with exit code 1.
Output paths:
/nix/store/ffk6kz3vz469ngb2aqqpb5p4419bmq7d-boron-x86_64-unknown-linux-gnufilc0-2.1.0
Last 13 log lines:
> Running phase: unpackPhase
> unpacking source archive /nix/store/1y7jki9j99z52p3klqj1ka9010shv3sk-boron-2.1.0.tar.gz
> source root is boron-2.1.0
> setting SOURCE_DATE_EPOCH to timestamp 1702357240 of file "boron-2.1.0/urlan/string.c"
> Running phase: patchPhase
> Running phase: updateAutotoolsGnuConfigScriptsPhase
> Running phase: updateAutotoolsGnuConfigScriptsPhase
> Running phase: configurePhase
> patching script interpreter paths in configure
> configure: interpreter directive changed from "#!/bin/bash" to "/nix/store/cfqbabpc7xwg8akbcchqbq3cai6qq2vs-bash-5.2p37/bin/bash"
> patching script interpreter paths in ./configure
> configure flags: --thread --build=x86_64-unknown-linux-gnu --host=x86_64-unknown-linux-gnufilc0
> Invalid option
For full logs, run:
nix log /nix/store/9shc4fqx8rcdjn0yg20jfj5x2b21p861-boron-x86_64-unknown-linux-gnufilc0-2.1.0.drvbotan-2.19.5
error: Cannot build '/nix/store/xrblv8i1axckf97a9qljvb6h41xszggk-botan-x86_64-unknown-linux-gnufilc0-2.19.5.drv'.
Reason: builder failed with exit code 2.
Output paths:
/nix/store/30mf3vnh5bxb7xkklwpn9k3i2dnnlf0g-botan-x86_64-unknown-linux-gnufilc0-2.19.5-dev
/nix/store/76y69anzc5cfsc3lzy7kn8cd0jlb4yf6-botan-x86_64-unknown-linux-gnufilc0-2.19.5
/nix/store/8mvn515c1lln8v631df9vlb2ybifcl1k-botan-x86_64-unknown-linux-gnufilc0-2.19.5-man
/nix/store/f8agswhdc97qjicnz2wf3bv7yzjz82na-botan-x86_64-unknown-linux-gnufilc0-2.19.5-bin
/nix/store/j8dmc3gzsxlw7w95r7gnphadp35w24bb-botan-x86_64-unknown-linux-gnufilc0-2.19.5-doc
Last 25 log lines:
> clang++ -fstack-protector -m64 -pthread -std=c++11 -D_REENTRANT -O3 -DBOTAN_IS_BEING_BUILT -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Ibuild/include -Ibuild/include/external -c src/tests/unit_asio_stream.cpp -o build/obj/test/unit_asio_stream.o
> clang++ -fstack-protector -m64 -pthread -std=c++11 -D_REENTRANT -O3 -DBOTAN_IS_BEING_BUILT -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Ibuild/include -Ibuild/include/external -c src/tests/unit_ecc.cpp -o build/obj/test/unit_ecc.o
> clang++ -fstack-protector -m64 -pthread -std=c++11 -D_REENTRANT -O3 -DBOTAN_IS_BEING_BUILT -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Ibuild/include -Ibuild/include/external -c src/tests/unit_ecdh.cpp -o build/obj/test/unit_ecdh.o
> clang++ -fstack-protector -m64 -pthread -std=c++11 -D_REENTRANT -O3 -DBOTAN_IS_BEING_BUILT -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Ibuild/include -Ibuild/include/external -c src/tests/unit_ecdsa.cpp -o build/obj/test/unit_ecdsa.o
> clang++ -fstack-protector -m64 -pthread -std=c++11 -D_REENTRANT -O3 -DBOTAN_IS_BEING_BUILT -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Ibuild/include -Ibuild/include/external -c src/tests/unit_tls.cpp -o build/obj/test/unit_tls.o
> clang++ -fstack-protector -m64 -pthread -std=c++11 -D_REENTRANT -O3 -DBOTAN_IS_BEING_BUILT -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Ibuild/include -Ibuild/include/external -c src/tests/unit_tls_policy.cpp -o build/obj/test/unit_tls_policy.o
> clang++ -fstack-protector -m64 -pthread -std=c++11 -D_REENTRANT -O3 -DBOTAN_IS_BEING_BUILT -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Ibuild/include -Ibuild/include/external -c src/tests/unit_x509.cpp -o build/obj/test/unit_x509.o
> "/nix/store/vxl8pzgkkw8vdb4agzwm58imrfclmfrx-python3-3.12.11/bin/python" "src/scripts/build_docs.py" --build-dir="build"
> INFO: Starting rst2man build/botan.rst build/botan.1
> clang++ -shared -fPIC -Wl,-soname,libbotan-2.so.19 -fstack-protector -m64 -pthread build/obj/lib/asn1_alg_id.o build/obj/lib/asn1_obj.o build/obj/lib/asn1_oid.o build/obj/lib/asn1_print.o build/obj/lib/asn1_str.o build/obj/lib/asn1_time.o build/obj/lib/asn1_ber_dec.o build/obj/lib/asn1_der_enc.o build/obj/lib/asn1_oid_maps.o build/obj/lib/asn1_oids.o build/obj/lib/base_buf_comp.o build/obj/lib/base_scan_name.o build/obj/lib/base_sym_algo.o build/obj/lib/base_symkey.o build/obj/lib/block_aes.o build/obj/lib/block_aes_ni.o build/obj/lib/block_aes_vperm.o build/obj/lib/block_aria.o build/obj/lib/block_cipher.o build/obj/lib/block_blowfish.o build/obj/lib/block_camellia.o build/obj/lib/block_cascade.o build/obj/lib/block_cast128.o build/obj/lib/block_cast256.o build/obj/lib/block_des.o build/obj/lib/block_des_tab.o build/obj/lib/block_des_desx.o build/obj/lib/block_gost_28147.o build/obj/lib/block_idea.o build/obj/lib/block_idea_sse2.o build/obj/lib/block_kasumi.o build/obj/lib/block_lion.o build/obj/lib/block_misty1.o build/obj/lib/block_noekeon.o build/obj/lib/block_noekeon_simd.o build/obj/lib/block_seed.o build/obj/lib/block_serpent.o build/obj/lib/block_serpent_avx2.o build/obj/lib/block_serpent_simd.o build/obj/lib/block_shacal2.o build/obj/lib/block_shacal2_avx2.o build/obj/lib/block_shacal2_simd.o build/obj/lib/block_shacal2_x86.o build/obj/lib/block_sm4.o build/obj/lib/block_threefish_512.o build/obj/lib/block_threefish_512_threefish_512_avx2.o build/obj/lib/block_twofish.o build/obj/lib/block_twofish_tab.o build/obj/lib/block_xtea.o build/obj/lib/codec_base32.o build/obj/lib/codec_base58.o build/obj/lib/codec_base64.o build/obj/lib/codec_hex.o build/obj/lib/compat_sodium_25519.o build/obj/lib/compat_sodium_aead.o build/obj/lib/compat_sodium_auth.o build/obj/lib/compat_sodium_box.o build/obj/lib/compat_sodium_chacha.o build/obj/lib/compat_sodium_salsa.o build/obj/lib/compat_sodium_secretbox.o build/obj/lib/compat_sodium_utils.o build/obj/lib/compression_bzip2.o build/obj/lib/compression_compress_utils.o build/obj/lib/compression.o build/obj/lib/compression_zlib.o build/obj/lib/entropy_dev_random.o build/obj/lib/entropy_srcs.o build/obj/lib/entropy_proc_walk.o build/obj/lib/entropy_rdseed.o build/obj/lib/ffi.o build/obj/lib/ffi_block.o build/obj/lib/ffi_cert.o build/obj/lib/ffi_cipher.o build/obj/lib/ffi_fpe.o build/obj/lib/ffi_hash.o build/obj/lib/ffi_hotp.o build/obj/lib/ffi_kdf.o build/obj/lib/ffi_keywrap.o build/obj/lib/ffi_mac.o build/obj/lib/ffi_mp.o build/obj/lib/ffi_pk_op.o build/obj/lib/ffi_pkey.o build/obj/lib/ffi_pkey_algs.o build/obj/lib/ffi_rng.o build/obj/lib/ffi_totp.o build/obj/lib/filters_algo_filt.o build/obj/lib/filters_b64_filt.o build/obj/lib/filters_basefilt.o build/obj/lib/filters_buf_filt.o build/obj/lib/filters_cipher_filter.o build/obj/lib/filters_comp_filter.o build/obj/lib/filters_data_snk.o build/obj/lib/filters_fd_unix.o build/obj/lib/filters_filter.o build/obj/lib/filters_hex_filt.o build/obj/lib/filters_out_buf.o build/obj/lib/filters_pipe.o build/obj/lib/filters_pipe_io.o build/obj/lib/filters_pipe_rw.o build/obj/lib/filters_secqueue.o build/obj/lib/filters_threaded_fork.o build/obj/lib/hash_blake2_blake2b.o build/obj/lib/hash_checksum_adler32.o build/obj/lib/hash_checksum_crc24.o build/obj/lib/hash_checksum_crc32.o build/obj/lib/hash_comb4p.o build/obj/lib/hash_gost_3411.o build/obj/lib/hash.o build/obj/lib/hash_keccak.o build/obj/lib/hash_md4.o build/obj/lib/hash_md5.o build/obj/lib/hash_mdx_hash.o build/obj/lib/hash_par_hash.o build/obj/lib/hash_rmd160.o build/obj/lib/hash_sha1_sha160.o build/obj/lib/hash_sha1_sse2.o build/obj/lib/hash_sha1_x86.o build/obj/lib/hash_sha2_32.o build/obj/lib/hash_sha2_32_sha2_32_bmi2.o build/obj/lib/hash_sha2_32_sha2_32_x86.o build/obj/lib/hash_sha2_64.o build/obj/lib/hash_sha2_64_sha2_64_bmi2.o build/obj/lib/hash_sha3.o build/obj/lib/hash_sha3_bmi2.o build/obj/lib/hash_shake.o build/obj/lib/hash_skein_512.o build/obj/lib/hash_sm3.o build/obj/lib/hash_streebog.o build/obj/lib/hash_streebog_precalc.o build/obj/lib/hash_tiger_tig_tab.o build/obj/lib/hash_tiger.o build/obj/lib/hash_whirlpool.o build/obj/lib/hash_whirlpool_whrl_tab.o build/obj/lib/kdf_hkdf.o build/obj/lib/kdf.o build/obj/lib/kdf_kdf1.o build/obj/lib/kdf_kdf1_iso18033.o build/obj/lib/kdf_kdf2.o build/obj/lib/kdf_prf_tls.o build/obj/lib/kdf_prf_x942.o build/obj/lib/kdf_sp800_108.o build/obj/lib/kdf_sp800_56a.o build/obj/lib/kdf_sp800_56c.o build/obj/lib/mac_cbc_mac.o build/obj/lib/mac_cmac.o build/obj/lib/mac_gmac.o build/obj/lib/mac_hmac.o build/obj/lib/mac.o build/obj/lib/mac_poly1305.o build/obj/lib/mac_siphash.o build/obj/lib/mac_x919_mac.o build/obj/lib/math_bigint_big_code.o build/obj/lib/math_bigint_big_io.o build/obj/lib/math_bigint_big_ops2.o build/obj/lib/math_bigint_big_ops3.o build/obj/lib/math_bigint_big_rand.o build/obj/lib/math_bigint.o build/obj/lib/math_bigint_divide.o build/obj/lib/math_mp_comba.o build/obj/lib/math_mp_karat.o build/obj/lib/math_mp_monty.o build/obj/lib/math_mp_monty_n.o build/obj/lib/math_numbertheory_dsa_gen.o build/obj/lib/math_numbertheory_jacobi.o build/obj/lib/math_numbertheory_make_prm.o build/obj/lib/math_numbertheory_mod_inv.o build/obj/lib/math_numbertheory_monty.o build/obj/lib/math_numbertheory_monty_exp.o build/obj/lib/math_numbertheory_mp_numth.o build/obj/lib/math_numbertheory_nistp_redc.o build/obj/lib/math_numbertheory_numthry.o build/obj/lib/math_numbertheory_pow_mod.o build/obj/lib/math_numbertheory_primality.o build/obj/lib/math_numbertheory_primes.o build/obj/lib/math_numbertheory_reducer.o build/obj/lib/math_numbertheory_ressol.o build/obj/lib/misc_aont_package.o build/obj/lib/misc_cryptobox.o build/obj/lib/misc_fpe_fe1.o build/obj/lib/misc_hotp.o build/obj/lib/misc_hotp_totp.o build/obj/lib/misc_nist_keywrap.o build/obj/lib/misc_rfc3394.o build/obj/lib/misc_roughtime.o build/obj/lib/misc_srp6.o build/obj/lib/misc_tss.o build/obj/lib/misc_zfec.o build/obj/lib/misc_zfec_sse2.o build/obj/lib/misc_zfec_vperm.o build/obj/lib/modes_aead.o build/obj/lib/modes_aead_ccm.o build/obj/lib/modes_aead_chacha20poly1305.o build/obj/lib/modes_aead_eax.o build/obj/lib/modes_aead_gcm.o build/obj/lib/modes_aead_ocb.o build/obj/lib/modes_aead_siv.o build/obj/lib/modes_cbc.o build/obj/lib/modes_cfb.o build/obj/lib/modes_cipher_mode.o build/obj/lib/modes_mode_pad.o build/obj/lib/modes_xts.o build/obj/lib/passhash_bcrypt.o build/obj/lib/passhash_passhash9.o build/obj/lib/pbkdf_argon2.o build/obj/lib/pbkdf_argon2_ssse3.o build/obj/lib/pbkdf_argon2_argon2fmt.o build/obj/lib/pbkdf_argon2_argon2pwhash.o build/obj/lib/pbkdf_bcrypt_pbkdf.o build/obj/lib/pbkdf.o build/obj/lib/pbkdf_pbkdf1.o build/obj/lib/pbkdf_pbkdf2.o build/obj/lib/pbkdf_pgp_s2k.o build/obj/lib/pbkdf_pwdhash.o build/obj/lib/pbkdf_scrypt.o build/obj/lib/pk_pad_eme.o build/obj/lib/pk_pad_eme_oaep_oaep.o build/obj/lib/pk_pad_eme_pkcs1_eme_pkcs.o build/obj/lib/pk_pad_eme_raw.o build/obj/lib/pk_pad_emsa.o build/obj/lib/pk_pad_emsa1.o build/obj/lib/pk_pad_emsa_pkcs1.o build/obj/lib/pk_pad_emsa_pssr_pssr.o build/obj/lib/pk_pad_emsa_raw.o build/obj/lib/pk_pad_emsa_x931.o build/obj/lib/pk_pad_hash_id.o build/obj/lib/pk_pad_iso9796.o build/obj/lib/pk_pad_mgf1.o build/obj/lib/pk_pad_padding.o build/obj/lib/prov_pkcs11_p11.o build/obj/lib/prov_pkcs11_p11_ecc_key.o build/obj/lib/prov_pkcs11_p11_ecdh.o build/obj/lib/prov_pkcs11_p11_ecdsa.o build/obj/lib/prov_pkcs11_p11_mechanism.o build/obj/lib/prov_pkcs11_p11_module.o build/obj/lib/prov_pkcs11_p11_object.o build/obj/lib/prov_pkcs11_p11_randomgenerator.o build/obj/lib/prov_pkcs11_p11_rsa.o build/obj/lib/prov_pkcs11_p11_session.o build/obj/lib/prov_pkcs11_p11_slot.o build/obj/lib/prov_pkcs11_p11_x509.o build/obj/lib/psk_db.o build/obj/lib/psk_db_psk_db_sql.o build/obj/lib/pubkey_blinding.o build/obj/lib/pubkey_cecpq1.o build/obj/lib/pubkey_curve25519.o build/obj/lib/pubkey_curve25519_donna.o build/obj/lib/pubkey_dh.o build/obj/lib/pubkey_dl_algo.o build/obj/lib/pubkey_dl_group.o build/obj/lib/pubkey_dl_group_dl_named.o build/obj/lib/pubkey_dlies.o build/obj/lib/pubkey_dsa.o build/obj/lib/pubkey_ec_group_curve_gfp.o build/obj/lib/pubkey_ec_group.o build/obj/lib/pubkey_ec_group_ec_named.o build/obj/lib/pubkey_ec_group_point_gfp.o build/obj/lib/pubkey_ec_group_point_mul.o build/obj/lib/pubkey_ecc_key.o build/obj/lib/pubkey_ecdh.o build/obj/lib/pubkey_ecdsa.o build/obj/lib/pubkey_ecgdsa.o build/obj/lib/pubkey_ecies.o build/obj/lib/pubkey_eckcdsa.o build/obj/lib/pubkey_ed25519.o build/obj/lib/pubkey_ed25519_fe.o build/obj/lib/pubkey_ed25519_key.o build/obj/lib/pubkey_ed25519_ge.o build/obj/lib/pubkey_ed25519_sc_muladd.o build/obj/lib/pubkey_ed25519_sc_reduce.o build/obj/lib/pubkey_elgamal.o build/obj/lib/pubkey_gost_3410.o build/obj/lib/pubkey_keypair.o build/obj/lib/pubkey_mce_code_based_key_gen.o build/obj/lib/pubkey_mce_gf2m_rootfind_dcmp.o build/obj/lib/pubkey_mce_gf2m_small_m.o build/obj/lib/pubkey_mce_goppa_code.o build/obj/lib/pubkey_mce_workfactor.o build/obj/lib/pubkey_mce_mceliece.o build/obj/lib/pubkey_mce_mceliece_key.o build/obj/lib/pubkey_mce_polyn_gf2m.o build/obj/lib/pubkey_mceies.o build/obj/lib/pubkey_newhope.o build/obj/lib/pubkey_pbes2.o build/obj/lib/pubkey_pem.o build/obj/lib/pubkey_pk_algs.o build/obj/lib/pubkey_pk_keys.o build/obj/lib/pubkey_pk_ops.o build/obj/lib/pubkey_pkcs8.o build/obj/lib/pubkey.o build/obj/lib/pubkey_rfc6979.o build/obj/lib/pubkey_rsa.o build/obj/lib/pubkey_sm2.o build/obj/lib/pubkey_sm2_enc.o build/obj/lib/pubkey_workfactor.o build/obj/lib/pubkey_x509_key.o build/obj/lib/pubkey_xmss_common_ops.o build/obj/lib/pubkey_xmss_hash.o build/obj/lib/pubkey_xmss_index_registry.o build/obj/lib/pubkey_xmss_parameters.o build/obj/lib/pubkey_xmss_privatekey.o build/obj/lib/pubkey_xmss_publickey.o build/obj/lib/pubkey_xmss_signature.o build/obj/lib/pubkey_xmss_signature_operation.o build/obj/lib/pubkey_xmss_verification_operation.o build/obj/lib/pubkey_xmss_wots_parameters.o build/obj/lib/pubkey_xmss_wots_privatekey.o build/obj/lib/pubkey_xmss_wots_publickey.o build/obj/lib/rng_auto_rng.o build/obj/lib/rng_chacha_rng.o build/obj/lib/rng_hmac_drbg.o build/obj/lib/rng_processor_rng.o build/obj/lib/rng_rdrand_rng.o build/obj/lib/rng.o build/obj/lib/rng_stateful_rng.o build/obj/lib/rng_system_rng.o build/obj/lib/stream_chacha.o build/obj/lib/stream_chacha_avx2.o build/obj/lib/stream_chacha_simd32.o build/obj/lib/stream_ctr.o build/obj/lib/stream_ofb.o build/obj/lib/stream_rc4.o build/obj/lib/stream_salsa20.o build/obj/lib/stream_shake_cipher.o build/obj/lib/stream_cipher.o build/obj/lib/tls_credentials_manager.o build/obj/lib/tls_msg_cert_req.o build/obj/lib/tls_msg_cert_status.o build/obj/lib/tls_msg_cert_verify.o build/obj/lib/tls_msg_certificate.o build/obj/lib/tls_msg_client_hello.o build/obj/lib/tls_msg_client_kex.o build/obj/lib/tls_msg_finished.o build/obj/lib/tls_msg_hello_verify.o build/obj/lib/tls_msg_server_hello.o build/obj/lib/tls_msg_server_kex.o build/obj/lib/tls_msg_session_ticket.o build/obj/lib/tls_sessions_sql_tls_session_manager_sql.o build/obj/lib/tls_alert.o build/obj/lib/tls_algos.o build/obj/lib/tls_blocking.o build/obj/lib/tls_callbacks.o build/obj/lib/tls_cbc.o build/obj/lib/tls_channel.o build/obj/lib/tls_ciphersuite.o build/obj/lib/tls_client.o build/obj/lib/tls_extensions.o build/obj/lib/tls_handshake_hash.o build/obj/lib/tls_handshake_io.o build/obj/lib/tls_handshake_state.o build/obj/lib/tls_policy.o build/obj/lib/tls_record.o build/obj/lib/tls_server.o build/obj/lib/tls_session.o build/obj/lib/tls_session_key.o build/obj/lib/tls_session_manager_memory.o build/obj/lib/tls_suite_info.o build/obj/lib/tls_text_policy.o build/obj/lib/tls_version.o build/obj/lib/utils_assert.o build/obj/lib/utils_calendar.o build/obj/lib/utils_charset.o build/obj/lib/utils_cpuid.o build/obj/lib/utils_cpuid_arm.o build/obj/lib/utils_cpuid_ppc.o build/obj/lib/utils_cpuid_x86.o build/obj/lib/utils_ct_utils.o build/obj/lib/utils_data_src.o build/obj/lib/utils_dyn_load.o build/obj/lib/utils_exceptn.o build/obj/lib/utils_filesystem.o build/obj/lib/utils_ghash.o build/obj/lib/utils_ghash_cpu.o build/obj/lib/utils_ghash_vperm.o build/obj/lib/utils_http_util.o build/obj/lib/utils_locking_allocator.o build/obj/lib/utils_mem_ops.o build/obj/lib/utils_mem_pool.o build/obj/lib/utils_os_utils.o build/obj/lib/utils_parsing.o build/obj/lib/utils_poly_dbl.o build/obj/lib/utils_read_cfg.o build/obj/lib/utils_read_kv.o build/obj/lib/utils_socket.o build/obj/lib/utils_socket_udp.o build/obj/lib/utils_socket_uri.o build/obj/lib/utils_thread_utils_barrier.o build/obj/lib/utils_thread_utils_rwlock.o build/obj/lib/utils_thread_utils_semaphore.o build/obj/lib/utils_thread_utils_thread_pool.o build/obj/lib/utils_timer.o build/obj/lib/utils_uuid.o build/obj/lib/utils_version.o build/obj/lib/x509_asn1_alt_name.o build/obj/lib/x509_cert_status.o build/obj/lib/x509_certstor.o build/obj/lib/x509_certstor_flatfile.o build/obj/lib/x509_certstor_sql.o build/obj/lib/x509_certstor_system.o build/obj/lib/x509_crl_ent.o build/obj/lib/x509_datastor.o build/obj/lib/x509_key_constraint.o build/obj/lib/x509_name_constraint.o build/obj/lib/x509_ocsp.o build/obj/lib/x509_ocsp_types.o build/obj/lib/x509_pkcs10.o build/obj/lib/x509_attribute.o build/obj/lib/x509_ca.o build/obj/lib/x509_crl.o build/obj/lib/x509_dn.o build/obj/lib/x509_dn_ub.o build/obj/lib/x509_ext.o build/obj/lib/x509_obj.o build/obj/lib/x509_x509cert.o build/obj/lib/x509_x509opt.o build/obj/lib/x509_x509path.o build/obj/lib/x509_x509self.o -lbz2 -ldl -lrt -lz -o libbotan-2.so.19
> cd . && ln -fs libbotan-2.so.19 libbotan-2.so
> cd . && ln -fs libbotan-2.so.19 libbotan-2.so.19.19.5
> clang++ -fstack-protector -m64 -pthread build/obj/cli/argon2.o build/obj/cli/asn1.o build/obj/cli/bcrypt.o build/obj/cli/cc_enc.o build/obj/cli/cli.o build/obj/cli/cli_rng.o build/obj/cli/codec.o build/obj/cli/compress.o build/obj/cli/encryption.o build/obj/cli/entropy.o build/obj/cli/hash.o build/obj/cli/hmac.o build/obj/cli/main.o build/obj/cli/math.o build/obj/cli/pbkdf.o build/obj/cli/pk_crypt.o build/obj/cli/psk.o build/obj/cli/pubkey.o build/obj/cli/roughtime.o build/obj/cli/sandbox.o build/obj/cli/speed.o build/obj/cli/timing_tests.o build/obj/cli/tls_client.o build/obj/cli/tls_http_server.o build/obj/cli/tls_proxy.o build/obj/cli/tls_server.o build/obj/cli/tls_utils.o build/obj/cli/tss.o build/obj/cli/utils.o build/obj/cli/x509.o build/obj/cli/zfec.o -L. -lbotan-2 -lbz2 -ldl -lrt -lz -o botan
> clang++ -fstack-protector -m64 -pthread build/obj/test/main.o build/obj/test/test_aead.o build/obj/test/test_asn1.o build/obj/test/test_bigint.o build/obj/test/test_block.o build/obj/test/test_blowfish.o build/obj/test/test_c25519.o build/obj/test/test_certstor.o build/obj/test/test_certstor_flatfile.o build/obj/test/test_certstor_system.o build/obj/test/test_certstor_utils.o build/obj/test/test_clang_bug.o build/obj/test/test_compression.o build/obj/test/test_cryptobox.o build/obj/test/test_datastore.o build/obj/test/test_dh.o build/obj/test/test_dl_group.o build/obj/test/test_dlies.o build/obj/test/test_dsa.o build/obj/test/test_ecc_pointmul.o build/obj/test/test_ecdh.o build/obj/test/test_ecdsa.o build/obj/test/test_ecgdsa.o build/obj/test/test_ecies.o build/obj/test/test_eckcdsa.o build/obj/test/test_ed25519.o build/obj/test/test_elgamal.o build/obj/test/test_entropy.o build/obj/test/test_ffi.o build/obj/test/test_filters.o build/obj/test/test_fpe.o build/obj/test/test_gf2m.o build/obj/test/test_gost_3410.o build/obj/test/test_hash.o build/obj/test/test_hash_id.o build/obj/test/test_kdf.o build/obj/test/test_keywrap.o build/obj/test/test_mac.o build/obj/test/test_mceliece.o build/obj/test/test_modes.o build/obj/test/test_mp.o build/obj/test/test_name_constraint.o build/obj/test/test_newhope.o build/obj/test/test_ocb.o build/obj/test/test_ocsp.o build/obj/test/test_octetstring.o build/obj/test/test_oid.o build/obj/test/test_os_utils.o build/obj/test/test_otp.o build/obj/test/test_package_transform.o build/obj/test/test_pad.o build/obj/test/test_passhash.o build/obj/test/test_pbkdf.o build/obj/test/test_pem.o build/obj/test/test_pk_pad.o build/obj/test/test_pkcs11_high_level.o build/obj/test/test_pkcs11_low_level.o build/obj/test/test_psk_db.o build/obj/test/test_pubkey.o build/obj/test/test_rfc6979.o build/obj/test/test_rng.o build/obj/test/test_rng_kat.o build/obj/test/test_roughtime.o build/obj/test/test_rsa.o build/obj/test/test_runner.o build/obj/test/test_simd.o build/obj/test/test_siv.o build/obj/test/test_sm2.o build/obj/test/test_sodium.o build/obj/test/test_srp6.o build/obj/test/test_stream.o build/obj/test/test_tests.o build/obj/test/test_thread_utils.o build/obj/test/test_tls.o build/obj/test/test_tls_messages.o build/obj/test/test_tls_stream_integration.o build/obj/test/test_tpm.o build/obj/test/test_tss.o build/obj/test/test_uri.o build/obj/test/test_utils.o build/obj/test/test_workfactor.o build/obj/test/test_x509_dn.o build/obj/test/test_x509_path.o build/obj/test/test_xmss.o build/obj/test/test_zfec.o build/obj/test/tests.o build/obj/test/unit_asio_stream.o build/obj/test/unit_ecc.o build/obj/test/unit_ecdh.o build/obj/test/unit_ecdsa.o build/obj/test/unit_tls.o build/obj/test/unit_tls_policy.o build/obj/test/unit_x509.o -L. -lbotan-2 -lbz2 -ldl -lrt -lz -o botan-test
> ./libbotan-2.so: error: undefined reference to 'pizlonated_log'
> ./libbotan-2.so: error: undefined reference to 'pizlonated_pow'
> ./libbotan-2.so: error: undefined reference to 'pizlonated_log2'
> clang-20: error: linker command failed with exit code 1 (use -v to see invocation)
> make: *** [Makefile:74: botan] Error 1
> make: *** Waiting for unfinished jobs....
> ./libbotan-2.so: error: undefined reference to 'pizlonated_log'
> ./libbotan-2.so: error: undefined reference to 'pizlonated_pow'
> ./libbotan-2.so: error: undefined reference to 'pizlonated_log2'
> clang-20: error: linker command failed with exit code 1 (use -v to see invocation)
> make: *** [Makefile:77: botan-test] Error 1
For full logs, run:
nix log /nix/store/xrblv8i1axckf97a9qljvb6h41xszggk-botan-x86_64-unknown-linux-gnufilc0-2.19.5.drvbotan-3.8.1
error: Cannot build '/nix/store/19lw0nifgy05y0cs7l17cw9fhyrkhp87-botan-x86_64-unknown-linux-gnufilc0-3.8.1.drv'.
Reason: builder failed with exit code 2.
Output paths:
/nix/store/0l690395ss5sa064czfn6dgyn1x2kynm-botan-x86_64-unknown-linux-gnufilc0-3.8.1-dev
/nix/store/180f7nvhw0vl9dwbz7kp8pw978rjv5mb-botan-x86_64-unknown-linux-gnufilc0-3.8.1-bin
/nix/store/ag0s175bwcsxqj2mj53hxnbnwd2zf39c-botan-x86_64-unknown-linux-gnufilc0-3.8.1-doc
/nix/store/f63r3hmwy3fn8nf94pylmr7gwz4pjiqp-botan-x86_64-unknown-linux-gnufilc0-3.8.1
/nix/store/xdqbakcxvq0cnxqa8h3pjl2hgddic1gi-botan-x86_64-unknown-linux-gnufilc0-3.8.1-man
Last 25 log lines:
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/test_utils_buffer.cpp -o build/obj/test/test_utils_buffer.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/test_workfactor.cpp -o build/obj/test/test_workfactor.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/test_x25519.cpp -o build/obj/test/test_x25519.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/test_x448.cpp -o build/obj/test/test_x448.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/test_x509_dn.cpp -o build/obj/test/test_x509_dn.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/test_x509_path.cpp -o build/obj/test/test_x509_path.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/test_xmss.cpp -o build/obj/test/test_xmss.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/test_xof.cpp -o build/obj/test/test_xof.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/test_zfec.cpp -o build/obj/test/test_zfec.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/tests.cpp -o build/obj/test/tests.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/unit_asio_stream.cpp -o build/obj/test/unit_asio_stream.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/unit_ecdsa.cpp -o build/obj/test/unit_ecdsa.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/unit_tls.cpp -o build/obj/test/unit_tls.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/unit_tls_policy.cpp -o build/obj/test/unit_tls_policy.o
> clang++ -fstack-protector -m64 -pthread -std=c++20 -D_REENTRANT -O3 -Wall -Wextra -Wpedantic -Wshadow -Wstrict-aliasing -Wstrict-overflow=5 -Wcast-align -Wmissing-declarations -Wpointer-arith -Wcast-qual -Wshorten-64-to-32 -Wcomma -Wdocumentation -DBOTAN_IS_BEING_BUILT -I build/include/public -I build/include/internal -isystem build/include/external -c src/tests/unit_x509.cpp -o build/obj/test/unit_x509.o
> clang++ -shared -fPIC -Wl,-soname,libbotan-3.so.8 -fstack-protector -m64 -pthread build/obj/lib/asn1_alg_id.o build/obj/lib/asn1_obj.o build/obj/lib/asn1_oid.o build/obj/lib/asn1_print.o build/obj/lib/asn1_str.o build/obj/lib/asn1_time.o build/obj/lib/asn1_ber_dec.o build/obj/lib/asn1_der_enc.o build/obj/lib/asn1_oid_map.o build/obj/lib/asn1_oid_maps.o build/obj/lib/asn1_oids.o build/obj/lib/asn1_pss_params.o build/obj/lib/base_buf_comp.o build/obj/lib/base_sym_algo.o build/obj/lib/base_symkey.o build/obj/lib/block_aes.o build/obj/lib/block_aes_ni.o build/obj/lib/block_aes_vaes.o build/obj/lib/block_aes_vperm.o build/obj/lib/block_aria.o build/obj/lib/block_cipher.o build/obj/lib/block_blowfish.o build/obj/lib/block_camellia.o build/obj/lib/block_cascade.o build/obj/lib/block_cast128.o build/obj/lib/block_des.o build/obj/lib/block_gost_28147.o build/obj/lib/block_idea.o build/obj/lib/block_idea_sse2.o build/obj/lib/block_kuznyechik.o build/obj/lib/block_lion.o build/obj/lib/block_noekeon.o build/obj/lib/block_noekeon_simd.o build/obj/lib/block_seed.o build/obj/lib/block_serpent.o build/obj/lib/block_serpent_avx2.o build/obj/lib/block_serpent_avx512.o build/obj/lib/block_serpent_simd.o build/obj/lib/block_shacal2.o build/obj/lib/block_shacal2_avx2.o build/obj/lib/block_shacal2_simd.o build/obj/lib/block_shacal2_x86.o build/obj/lib/block_sm4.o build/obj/lib/block_sm4_gfni.o build/obj/lib/block_sm4_x86.o build/obj/lib/block_threefish_512.o build/obj/lib/block_twofish.o build/obj/lib/block_twofish_tab.o build/obj/lib/codec_base32.o build/obj/lib/codec_base58.o build/obj/lib/codec_base64.o build/obj/lib/codec_hex.o build/obj/lib/compat_sodium_25519.o build/obj/lib/compat_sodium_aead.o build/obj/lib/compat_sodium_auth.o build/obj/lib/compat_sodium_box.o build/obj/lib/compat_sodium_chacha.o build/obj/lib/compat_sodium_salsa.o build/obj/lib/compat_sodium_secretbox.o build/obj/lib/compat_sodium_utils.o build/obj/lib/compression_bzip2.o build/obj/lib/compression_compress_utils.o build/obj/lib/compression.o build/obj/lib/compression_zlib.o build/obj/lib/entropy_srcs.o build/obj/lib/entropy_getentropy.o build/obj/lib/entropy_rdseed.o build/obj/lib/ffi.o build/obj/lib/ffi_block.o build/obj/lib/ffi_cert.o build/obj/lib/ffi_cipher.o build/obj/lib/ffi_ec.o build/obj/lib/ffi_fpe.o build/obj/lib/ffi_hash.o build/obj/lib/ffi_hotp.o build/obj/lib/ffi_kdf.o build/obj/lib/ffi_keywrap.o build/obj/lib/ffi_mac.o build/obj/lib/ffi_mp.o build/obj/lib/ffi_oid.o build/obj/lib/ffi_pk_op.o build/obj/lib/ffi_pkey.o build/obj/lib/ffi_pkey_algs.o build/obj/lib/ffi_rng.o build/obj/lib/ffi_srp6.o build/obj/lib/ffi_totp.o build/obj/lib/ffi_tpm2.o build/obj/lib/ffi_zfec.o build/obj/lib/filters_algo_filt.o build/obj/lib/filters_b64_filt.o build/obj/lib/filters_basefilt.o build/obj/lib/filters_buf_filt.o build/obj/lib/filters_cipher_filter.o build/obj/lib/filters_comp_filter.o build/obj/lib/filters_data_snk.o build/obj/lib/filters_fd_unix.o build/obj/lib/filters_filter.o build/obj/lib/filters_hex_filt.o build/obj/lib/filters_out_buf.o build/obj/lib/filters_pipe.o build/obj/lib/filters_pipe_io.o build/obj/lib/filters_pipe_rw.o build/obj/lib/filters_secqueue.o build/obj/lib/filters_threaded_fork.o build/obj/lib/hash_blake2_blake2b.o build/obj/lib/hash_blake2s.o build/obj/lib/hash_checksum_adler32.o build/obj/lib/hash_checksum_crc24.o build/obj/lib/hash_checksum_crc32.o build/obj/lib/hash_comb4p.o build/obj/lib/hash_gost_3411.o build/obj/lib/hash.o build/obj/lib/hash_keccak.o build/obj/lib/hash_md4.o build/obj/lib/hash_md5.o build/obj/lib/hash_par_hash.o build/obj/lib/hash_rmd160.o build/obj/lib/hash_sha1.o build/obj/lib/hash_sha1_simd.o build/obj/lib/hash_sha1_x86.o build/obj/lib/hash_sha2_32.o build/obj/lib/hash_sha2_32_sha2_32_avx2.o build/obj/lib/hash_sha2_32_sha2_32_simd.o build/obj/lib/hash_sha2_32_sha2_32_x86.o build/obj/lib/hash_sha2_64.o build/obj/lib/hash_sha2_64_sha2_64_avx2.o build/obj/lib/hash_sha2_64_sha2_64_avx512.o build/obj/lib/hash_sha2_64_sha2_64_x86.o build/obj/lib/hash_sha3.o build/obj/lib/hash_shake.o build/obj/lib/hash_skein_512.o build/obj/lib/hash_sm3.o build/obj/lib/hash_streebog.o build/obj/lib/hash_streebog_precalc.o build/obj/lib/hash_trunc_hash.o build/obj/lib/hash_whirlpool.o build/obj/lib/kdf_hkdf.o build/obj/lib/kdf.o build/obj/lib/kdf_kdf1.o build/obj/lib/kdf_kdf1_iso18033.o build/obj/lib/kdf_kdf2.o build/obj/lib/kdf_prf_tls.o build/obj/lib/kdf_prf_x942.o build/obj/lib/kdf_sp800_108.o build/obj/lib/kdf_sp800_56a_sp800_56c_one_step.o build/obj/lib/kdf_sp800_56c_sp800_56c_two_step.o build/obj/lib/kdf_xmd.o build/obj/lib/mac_blake2mac_blake2bmac.o build/obj/lib/mac_cmac.o build/obj/lib/mac_gmac.o build/obj/lib/mac_hmac.o build/obj/lib/mac_kmac.o build/obj/lib/mac.o build/obj/lib/mac_poly1305.o build/obj/lib/mac_siphash.o build/obj/lib/mac_x919_mac.o build/obj/lib/math_bigint_big_code.o build/obj/lib/math_bigint_big_io.o build/obj/lib/math_bigint_big_ops2.o build/obj/lib/math_bigint_big_ops3.o build/obj/lib/math_bigint_big_rand.o build/obj/lib/math_bigint.o build/obj/lib/math_bigint_divide.o build/obj/lib/math_mp_comba.o build/obj/lib/math_mp_karat.o build/obj/lib/math_mp_monty.o build/obj/lib/math_mp_monty_n.o build/obj/lib/math_numbertheory_barrett.o build/obj/lib/math_numbertheory_dsa_gen.o build/obj/lib/math_numbertheory_make_prm.o build/obj/lib/math_numbertheory_mod_inv.o build/obj/lib/math_numbertheory_monty.o build/obj/lib/math_numbertheory_monty_exp.o build/obj/lib/math_numbertheory_numthry.o build/obj/lib/math_numbertheory_primality.o build/obj/lib/math_numbertheory_primes.o build/obj/lib/math_numbertheory_reducer.o build/obj/lib/math_pcurves.o build/obj/lib/math_pcurves_brainpool256r1.o build/obj/lib/math_pcurves_brainpool384r1.o build/obj/lib/math_pcurves_brainpool512r1.o build/obj/lib/math_pcurves_frp256v1.o build/obj/lib/math_pcurves_generic.o build/obj/lib/math_pcurves_numsp512d1.o build/obj/lib/math_pcurves_secp192r1.o build/obj/lib/math_pcurves_secp224r1.o build/obj/lib/math_pcurves_secp256k1.o build/obj/lib/math_pcurves_secp256r1.o build/obj/lib/math_pcurves_secp384r1.o build/obj/lib/math_pcurves_secp521r1.o build/obj/lib/math_pcurves_sm2p256v1.o build/obj/lib/misc_cryptobox.o build/obj/lib/misc_fpe_fe1.o build/obj/lib/misc_hotp.o build/obj/lib/misc_hotp_totp.o build/obj/lib/misc_nist_keywrap.o build/obj/lib/misc_rfc3394.o build/obj/lib/misc_roughtime.o build/obj/lib/misc_srp6.o build/obj/lib/misc_tss.o build/obj/lib/misc_zfec.o build/obj/lib/misc_zfec_sse2.o build/obj/lib/misc_zfec_vperm.o build/obj/lib/modes_aead.o build/obj/lib/modes_aead_ccm.o build/obj/lib/modes_aead_chacha20poly1305.o build/obj/lib/modes_aead_eax.o build/obj/lib/modes_aead_gcm.o build/obj/lib/modes_aead_ocb.o build/obj/lib/modes_aead_siv.o build/obj/lib/modes_cbc.o build/obj/lib/modes_cfb.o build/obj/lib/modes_cipher_mode.o build/obj/lib/modes_mode_pad.o build/obj/lib/modes_xts.o build/obj/lib/passhash_argon2fmt.o build/obj/lib/passhash_bcrypt.o build/obj/lib/passhash_passhash9.o build/obj/lib/pbkdf_argon2.o build/obj/lib/pbkdf_argon2_avx2.o build/obj/lib/pbkdf_argon2_ssse3.o build/obj/lib/pbkdf_argon2_argon2pwhash.o build/obj/lib/pbkdf_bcrypt_pbkdf.o build/obj/lib/pbkdf.o build/obj/lib/pbkdf_pbkdf2.o build/obj/lib/pbkdf_pgp_s2k.o build/obj/lib/pbkdf_pgp_s2k_rfc4880.o build/obj/lib/pbkdf_pwdhash.o build/obj/lib/pbkdf_scrypt.o build/obj/lib/permutations_keccak_perm_keccak_helpers.o build/obj/lib/permutations_keccak_perm.o build/obj/lib/permutations_keccak_perm_keccak_perm_bmi2.o build/obj/lib/pk_pad_eme.o build/obj/lib/pk_pad_eme_oaep_oaep.o build/obj/lib/pk_pad_eme_pkcs1_eme_pkcs.o build/obj/lib/pk_pad_eme_raw.o build/obj/lib/pk_pad_emsa.o build/obj/lib/pk_pad_emsa_pkcs1.o build/obj/lib/pk_pad_emsa_pssr_pssr.o build/obj/lib/pk_pad_emsa_raw.o build/obj/lib/pk_pad_emsa_x931.o build/obj/lib/pk_pad_hash_id.o build/obj/lib/pk_pad_iso9796.o build/obj/lib/pk_pad_mgf1.o build/obj/lib/pk_pad_raw_hash.o build/obj/lib/prov_pkcs11_p11.o build/obj/lib/prov_pkcs11_p11_ecc_key.o build/obj/lib/prov_pkcs11_p11_ecdh.o build/obj/lib/prov_pkcs11_p11_ecdsa.o build/obj/lib/prov_pkcs11_p11_mechanism.o build/obj/lib/prov_pkcs11_p11_module.o build/obj/lib/prov_pkcs11_p11_object.o build/obj/lib/prov_pkcs11_p11_randomgenerator.o build/obj/lib/prov_pkcs11_p11_rsa.o build/obj/lib/prov_pkcs11_p11_session.o build/obj/lib/prov_pkcs11_p11_slot.o build/obj/lib/prov_pkcs11_p11_x509.o build/obj/lib/psk_db.o build/obj/lib/psk_db_psk_db_sql.o build/obj/lib/pubkey_blinding.o build/obj/lib/pubkey_classic_mceliece_cmce.o build/obj/lib/pubkey_classic_mceliece_cmce_decaps.o build/obj/lib/pubkey_classic_mceliece_cmce_encaps.o build/obj/lib/pubkey_classic_mceliece_cmce_field_ordering.o build/obj/lib/pubkey_classic_mceliece_cmce_gf.o build/obj/lib/pubkey_classic_mceliece_cmce_keys_internal.o build/obj/lib/pubkey_classic_mceliece_cmce_matrix.o build/obj/lib/pubkey_classic_mceliece_cmce_parameter_set.o build/obj/lib/pubkey_classic_mceliece_cmce_parameters.o build/obj/lib/pubkey_classic_mceliece_cmce_poly.o build/obj/lib/pubkey_curve448_gf.o build/obj/lib/pubkey_curve448_scalar.o build/obj/lib/pubkey_curve448_ed448.o build/obj/lib/pubkey_curve448_ed448_internal.o build/obj/lib/pubkey_curve448_x448.o build/obj/lib/pubkey_curve448_x448_internal.o build/obj/lib/pubkey_dh.o build/obj/lib/pubkey_dilithium_common_dilithium.o build/obj/lib/pubkey_dilithium_common_dilithium_algos.o build/obj/lib/pubkey_dilithium_common_dilithium_constants.o build/obj/lib/pubkey_dilithium_common_dilithium_keys.o build/obj/lib/pubkey_dilithium_common_dilithium_symmetric_primitives.o build/obj/lib/pubkey_dilithium_round3_dilithium_aes.o build/obj/lib/pubkey_dilithium_round3_dilithium_round3_symmetric_primitives.o build/obj/lib/pubkey_dilithium_ml_dsa_ml_dsa_impl.o build/obj/lib/pubkey_dl_algo_dl_scheme.o build/obj/lib/pubkey_dl_group.o build/obj/lib/pubkey_dl_group_dl_named.o build/obj/lib/pubkey_dlies.o build/obj/lib/pubkey_dsa.o build/obj/lib/pubkey_ec_group_ec_apoint.o build/obj/lib/pubkey_ec_group.o build/obj/lib/pubkey_ec_group_ec_inner_data.o build/obj/lib/pubkey_ec_group_ec_inner_pc.o build/obj/lib/pubkey_ec_group_ec_named.o build/obj/lib/pubkey_ec_group_ec_scalar.o build/obj/lib/pubkey_ec_group_legacy_ec_point_ec_inner_bn.o build/obj/lib/pubkey_ec_group_legacy_ec_point_ec_point.o build/obj/lib/pubkey_ec_group_legacy_ec_point_mul.o build/obj/lib/pubkey_ecc_key_ec_key_data.o build/obj/lib/pubkey_ecc_key.o build/obj/lib/pubkey_ecdh.o build/obj/lib/pubkey_ecdsa.o build/obj/lib/pubkey_ecgdsa.o build/obj/lib/pubkey_ecies.o build/obj/lib/pubkey_eckcdsa.o build/obj/lib/pubkey_ed25519.o build/obj/lib/pubkey_ed25519_fe.o build/obj/lib/pubkey_ed25519_key.o build/obj/lib/pubkey_ed25519_ge.o build/obj/lib/pubkey_ed25519_sc_muladd.o build/obj/lib/pubkey_ed25519_sc_reduce.o build/obj/lib/pubkey_elgamal.o build/obj/lib/pubkey_frodokem_common_frodo_constants.o build/obj/lib/pubkey_frodokem_common_frodo_matrix.o build/obj/lib/pubkey_frodokem_common_frodo_mode.o build/obj/lib/pubkey_frodokem_common_frodokem.o build/obj/lib/pubkey_gost_3410.o build/obj/lib/pubkey_hss_lms_hss.o build/obj/lib/pubkey_hss_lms.o build/obj/lib/pubkey_hss_lms_hss_lms_utils.o build/obj/lib/pubkey_hss_lms_lm_ots.o build/obj/lib/pubkey_hss_lms_lms.o build/obj/lib/pubkey_hybrid_kem.o build/obj/lib/pubkey_hybrid_kem_hybrid_kem_ops.o build/obj/lib/pubkey_kex_to_kem_adapter.o build/obj/lib/pubkey_keypair.o build/obj/lib/pubkey_kyber_common_kyber.o build/obj/lib/pubkey_kyber_common_kyber_algos.o build/obj/lib/pubkey_kyber_common_kyber_constants.o build/obj/lib/pubkey_kyber_common_kyber_keys.o build/obj/lib/pubkey_kyber_round3_kyber_round3_impl.o build/obj/lib/pubkey_kyber_ml_kem_ml_kem_impl.o build/obj/lib/pubkey_mce_code_based_key_gen.o build/obj/lib/pubkey_mce_gf2m_rootfind_dcmp.o build/obj/lib/pubkey_mce_gf2m_small_m.o build/obj/lib/pubkey_mce_goppa_code.o build/obj/lib/pubkey_mce_workfactor.o build/obj/lib/pubkey_mce_mceliece.o build/obj/lib/pubkey_mce_mceliece_key.o build/obj/lib/pubkey_mce_polyn_gf2m.o build/obj/lib/pubkey_pbes2.o build/obj/lib/pubkey_pem.o build/obj/lib/pubkey_pk_algs.o build/obj/lib/pubkey_pk_keys.o build/obj/lib/pubkey_pk_ops.o build/obj/lib/pubkey_pkcs8.o build/obj/lib/pubkey.o build/obj/lib/pubkey_rfc6979.o build/obj/lib/pubkey_rsa.o build/obj/lib/pubkey_sm2.o build/obj/lib/pubkey_sm2_enc.o build/obj/lib/pubkey_sphincsplus_common_sp_fors.o build/obj/lib/pubkey_sphincsplus_common_sp_hash.o build/obj/lib/pubkey_sphincsplus_common_sp_hypertree.o build/obj/lib/pubkey_sphincsplus_common_sp_parameters.o build/obj/lib/pubkey_sphincsplus_common_sp_treehash.o build/obj/lib/pubkey_sphincsplus_common_sp_wots.o build/obj/lib/pubkey_sphincsplus_common_sp_xmss.o build/obj/lib/pubkey_sphincsplus_common_sphincsplus.o build/obj/lib/pubkey_workfactor.o build/obj/lib/pubkey_x25519_donna.o build/obj/lib/pubkey_x25519.o build/obj/lib/pubkey_x509_key.o build/obj/lib/pubkey_xmss_common_ops.o build/obj/lib/pubkey_xmss_hash.o build/obj/lib/pubkey_xmss_index_registry.o build/obj/lib/pubkey_xmss_parameters.o build/obj/lib/pubkey_xmss_privatekey.o build/obj/lib/pubkey_xmss_publickey.o build/obj/lib/pubkey_xmss_signature.o build/obj/lib/pubkey_xmss_signature_operation.o build/obj/lib/pubkey_xmss_verification_operation.o build/obj/lib/pubkey_xmss_wots.o build/obj/lib/pubkey_xmss_wots_parameters.o build/obj/lib/rng_auto_rng.o build/obj/lib/rng_chacha_rng.o build/obj/lib/rng_hmac_drbg.o build/obj/lib/rng_jitter_rng.o build/obj/lib/rng_processor_rng.o build/obj/lib/rng.o build/obj/lib/rng_stateful_rng.o build/obj/lib/rng_system_rng.o build/obj/lib/stream_chacha.o build/obj/lib/stream_chacha_avx2.o build/obj/lib/stream_chacha_avx512.o build/obj/lib/stream_chacha_simd32.o build/obj/lib/stream_ctr.o build/obj/lib/stream_ofb.o build/obj/lib/stream_rc4.o build/obj/lib/stream_salsa20.o build/obj/lib/stream_shake_cipher.o build/obj/lib/stream_cipher.o build/obj/lib/tls_credentials_manager.o build/obj/lib/tls_msg_cert_req.o build/obj/lib/tls_msg_cert_verify.o build/obj/lib/tls_msg_client_hello.o build/obj/lib/tls_msg_finished.o build/obj/lib/tls_msg_server_hello.o build/obj/lib/tls_msg_session_ticket.o build/obj/lib/tls_sessions_sql_tls_session_manager_sql.o build/obj/lib/tls_tls12_msg_cert_status.o build/obj/lib/tls_tls12_msg_certificate_12.o build/obj/lib/tls_tls12_msg_client_kex.o build/obj/lib/tls_tls12_msg_hello_verify.o build/obj/lib/tls_tls12_msg_server_kex.o build/obj/lib/tls_tls12_tls_cbc.o build/obj/lib/tls_tls12_tls_channel_impl_12.o build/obj/lib/tls_tls12_tls_client_impl_12.o build/obj/lib/tls_tls12_tls_handshake_hash.o build/obj/lib/tls_tls12_tls_handshake_io.o build/obj/lib/tls_tls12_tls_handshake_state.o build/obj/lib/tls_tls12_tls_record.o build/obj/lib/tls_tls12_tls_server_impl_12.o build/obj/lib/tls_tls12_tls_session_key.o build/obj/lib/tls_tls13_msg_certificate_13.o build/obj/lib/tls_tls13_msg_certificate_req_13.o build/obj/lib/tls_tls13_msg_encrypted_extensions.o build/obj/lib/tls_tls13_msg_key_update.o build/obj/lib/tls_tls13_tls_channel_impl_13.o build/obj/lib/tls_tls13_tls_cipher_state.o build/obj/lib/tls_tls13_tls_client_impl_13.o build/obj/lib/tls_tls13_tls_extensions_key_share.o build/obj/lib/tls_tls13_tls_extensions_psk.o build/obj/lib/tls_tls13_tls_handshake_layer_13.o build/obj/lib/tls_tls13_tls_handshake_state_13.o build/obj/lib/tls_tls13_tls_psk_identity_13.o build/obj/lib/tls_tls13_tls_record_layer_13.o build/obj/lib/tls_tls13_tls_server_impl_13.o build/obj/lib/tls_tls13_tls_transcript_hash_13.o build/obj/lib/tls_tls13_pqc_hybrid_public_key.o build/obj/lib/tls_alert.o build/obj/lib/tls_algos.o build/obj/lib/tls_callbacks.o build/obj/lib/tls_ciphersuite.o build/obj/lib/tls_client.o build/obj/lib/tls_extensions.o build/obj/lib/tls_extensions_cert_status_req.o build/obj/lib/tls_external_psk.o build/obj/lib/tls_handshake_transitions.o build/obj/lib/tls_policy.o build/obj/lib/tls_server.o build/obj/lib/tls_session.o build/obj/lib/tls_session_manager.o build/obj/lib/tls_session_manager_hybrid.o build/obj/lib/tls_session_manager_memory.o build/obj/lib/tls_session_manager_noop.o build/obj/lib/tls_session_manager_stateless.o build/obj/lib/tls_signature_scheme.o build/obj/lib/tls_suite_info.o build/obj/lib/tls_text_policy.o build/obj/lib/tls_version.o build/obj/lib/utils_allocator.o build/obj/lib/utils_assert.o build/obj/lib/utils_calendar.o build/obj/lib/utils_charset.o build/obj/lib/utils_cpuid.o build/obj/lib/utils_cpuid_x86_cpuid_features.o build/obj/lib/utils_cpuid_x86.o build/obj/lib/utils_ct_utils.o build/obj/lib/utils_data_src.o build/obj/lib/utils_dyn_load.o build/obj/lib/utils_exceptn.o build/obj/lib/utils_filesystem.o build/obj/lib/utils_ghash.o build/obj/lib/utils_ghash_cpu.o build/obj/lib/utils_ghash_vperm.o build/obj/lib/utils_http_util.o build/obj/lib/utils_locking_allocator.o build/obj/lib/utils_mem_ops.o build/obj/lib/utils_mem_pool.o build/obj/lib/utils_mem_utils.o build/obj/lib/utils_os_utils.o build/obj/lib/utils_parsing.o build/obj/lib/utils_poly_dbl.o build/obj/lib/utils_prefetch.o build/obj/lib/utils_read_cfg.o build/obj/lib/utils_read_kv.o build/obj/lib/utils_scan_name.o build/obj/lib/utils_socket.o build/obj/lib/utils_socket_udp.o build/obj/lib/utils_socket_uri.o build/obj/lib/utils_thread_utils_barrier.o build/obj/lib/utils_thread_utils_rwlock.o build/obj/lib/utils_thread_utils_semaphore.o build/obj/lib/utils_thread_utils_thread_pool.o build/obj/lib/utils_uuid.o build/obj/lib/utils_version.o build/obj/lib/x509_alt_name.o build/obj/lib/x509_asn1_alt_name.o build/obj/lib/x509_cert_status.o build/obj/lib/x509_certstor.o build/obj/lib/x509_certstor_flatfile.o build/obj/lib/x509_certstor_sql.o build/obj/lib/x509_certstor_system.o build/obj/lib/x509_crl_ent.o build/obj/lib/x509_key_constraint.o build/obj/lib/x509_name_constraint.o build/obj/lib/x509_ocsp.o build/obj/lib/x509_ocsp_types.o build/obj/lib/x509_pkcs10.o build/obj/lib/x509_attribute.o build/obj/lib/x509_ca.o build/obj/lib/x509_crl.o build/obj/lib/x509_dn.o build/obj/lib/x509_dn_ub.o build/obj/lib/x509_ext.o build/obj/lib/x509_obj.o build/obj/lib/x509_x509cert.o build/obj/lib/x509_x509opt.o build/obj/lib/x509_x509path.o build/obj/lib/x509_x509self.o build/obj/lib/xof_aes_crystals_xof.o build/obj/lib/xof_cshake_xof.o build/obj/lib/xof_shake_xof.o build/obj/lib/xof.o -lbz2 -ldl -ljitterentropy -lrt -lz -o libbotan-3.so.8
> cd . && ln -fs libbotan-3.so.8 libbotan-3.so
> cd . && ln -fs libbotan-3.so.8 libbotan-3.so.8.8.1
> clang++ -fstack-protector -m64 -pthread build/obj/cli/argon2.o build/obj/cli/asn1.o build/obj/cli/bcrypt.o build/obj/cli/cc_enc.o build/obj/cli/cipher.o build/obj/cli/cli.o build/obj/cli/cli_rng.o build/obj/cli/codec.o build/obj/cli/compress.o build/obj/cli/entropy.o build/obj/cli/hash.o build/obj/cli/hmac.o build/obj/cli/main.o build/obj/cli/math.o build/obj/cli/pbkdf.o build/obj/cli/perf.o build/obj/cli/perf_ec.o build/obj/cli/perf_math.o build/obj/cli/perf_misc.o build/obj/cli/perf_pk_enc.o build/obj/cli/perf_pk_ka.o build/obj/cli/perf_pk_kem.o build/obj/cli/perf_pk_misc.o build/obj/cli/perf_pk_sig.o build/obj/cli/perf_pwdhash.o build/obj/cli/perf_rng.o build/obj/cli/perf_sym.o build/obj/cli/perf_x509.o build/obj/cli/pk_crypt.o build/obj/cli/psk.o build/obj/cli/pubkey.o build/obj/cli/roughtime.o build/obj/cli/sandbox.o build/obj/cli/speed.o build/obj/cli/timer.o build/obj/cli/timing_tests.o build/obj/cli/tls_client.o build/obj/cli/tls_http_server.o build/obj/cli/tls_proxy.o build/obj/cli/tls_server.o build/obj/cli/tls_utils.o build/obj/cli/tss.o build/obj/cli/utils.o build/obj/cli/x509.o build/obj/cli/zfec.o -L. -lbotan-3 -lbz2 -ldl -ljitterentropy -lrt -lz -o botan
> ./libbotan-3.so: error: undefined reference to 'pizlonated_log'
> ./libbotan-3.so: error: undefined reference to 'pizlonated_pow'
> ./libbotan-3.so: error: undefined reference to 'pizlonated_log2'
> clang-20: error: linker command failed with exit code 1 (use -v to see invocation)
> make: *** [Makefile:83: botan] Error 1
> make: *** Waiting for unfinished jobs....
For full logs, run:
nix log /nix/store/19lw0nifgy05y0cs7l17cw9fhyrkhp87-botan-x86_64-unknown-linux-gnufilc0-3.8.1.drvbowtie-1.3.1
error: Cannot build '/nix/store/fraap7c44ql7g0mcqyaz10nal2387xsk-bowtie-x86_64-unknown-linux-gnufilc0-1.3.1.drv'.
Reason: builder failed with exit code 2.
Output paths:
/nix/store/q4yv1yik0k21vb0r9nxcclllc4b2clnq-bowtie-x86_64-unknown-linux-gnufilc0-1.3.1
Last 25 log lines:
> In file included from ebwt_build.cpp:10:
> ./ebwt.h:2791:13: warning: variable 'restOff' set but not used [-Wunused-but-set-variable]
> 2791 | TIndexOffU restOff = 0;
> | ^
> ./ebwt.h:3890:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
> 3890 | TIndexOffU patoff = 0;
> | ^
> ./ebwt.h:3882:13: warning: variable 'seqsRead' set but not used [-Wunused-but-set-variable]
> 3882 | TIndexOffU seqsRead = 0;
> | ^
> 12 warnings generated.
> In file included from ref_read.cpp:2:
> In file included from ./ref_read.h:13:
> ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
> 4077 | int thru = 0;
> | ^
> 1 warning generated.
> In file included from bowtie_build_main.cpp:13:
> ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable]
> 4077 | int thru = 0;
> | ^
> 1 warning generated.
> /build/ebwt_build-eaa1b0.o:ebwt_build.cpp:function pizlonatedFI403_sqrt:(.text+0x57a31): error: undefined reference to 'pizlonated_sqrt'
> clang-20: error: linker command failed with exit code 1 (use -v to see invocation)
> make: *** [Makefile:240: bowtie-build-s] Error 1
For full logs, run:
nix log /nix/store/fraap7c44ql7g0mcqyaz10nal2387xsk-bowtie-x86_64-unknown-linux-gnufilc0-1.3.1.drvbowtie2-2.5.4
error: Cannot build '/nix/store/w1fqjphiqn7whd0nzv8zv6y8jn4pz325-bowtie2-x86_64-unknown-linux-gnufilc0-2.5.4.drv'.
Reason: builder failed with exit code 2.
Output paths:
/nix/store/w7lhzmh2kbk2dzvkkzj94a0kgh1c0p10-bowtie2-x86_64-unknown-linux-gnufilc0-2.5.4
Last 25 log lines:
> /build/source/aligner_seed2.h:2448:18: warning: variable 'ngap' set but not used [-Wunused-but-set-variable]
> 2448 | size_t ns = 0, ngap = 0, nrefn = 0;
> | ^
> /build/source/aligner_seed2.h:2448:28: warning: variable 'nrefn' set but not used [-Wunused-but-set-variable]
> 2448 | size_t ns = 0, ngap = 0, nrefn = 0;
> | ^
> /build/source/bt2_search.cpp:4663:6: warning: variable 'steal_ctr' set but not used [-Wunused-but-set-variable]
> 4663 | int steal_ctr = 1;
> | ^
> 9 warnings generated.
> [100%] Linking CXX executable bowtie2-align-l
> CMakeFiles/bowtie2-align-l.dir/sam.cpp.o:sam.cpp:function pizlonatedFI403_sqrt:(.text+0x410b1): error: undefined reference to 'pizlonated_sqrt'
> CMakeFiles/bowtie2-align-l.dir/sam.cpp.o:sam.cpp:function pizlonatedFI403_log:(.text+0x41181): error: undefined reference to 'pizlonated_log'
> CMakeFiles/bowtie2-align-l.dir/aligner_seed.cpp.o:aligner_seed.cpp:function pizlonatedFI403_sqrt:(.text+0x2aa21): error: undefined reference to 'pizlonated_sqrt'
> CMakeFiles/bowtie2-align-l.dir/aligner_seed.cpp.o:aligner_seed.cpp:function pizlonatedFI403_log:(.text+0x2aaf1): error: undefined reference to 'pizlonated_log'
> CMakeFiles/bowtie2-align-l.dir/aligner_seed2.cpp.o:aligner_seed2.cpp:function pizlonatedFI4792_pow:(.text+0x1c266): error: undefined reference to 'pizlonated_pow'
> CMakeFiles/bowtie2-align-l.dir/aligner_sw.cpp.o:aligner_sw.cpp:function pizlonatedFI403_sqrt:(.text+0xa6b1): error: undefined reference to 'pizlonated_sqrt'
> CMakeFiles/bowtie2-align-l.dir/aligner_sw.cpp.o:aligner_sw.cpp:function pizlonatedFI403_log:(.text+0xa781): error: undefined reference to 'pizlonated_log'
> CMakeFiles/bowtie2-align-l.dir/scoring.cpp.o:scoring.cpp:function pizlonatedFI403_sqrt:(.text+0x1501): error: undefined reference to 'pizlonated_sqrt'
> CMakeFiles/bowtie2-align-l.dir/scoring.cpp.o:scoring.cpp:function pizlonatedFI403_log:(.text+0x15d1): error: undefined reference to 'pizlonated_log'
> CMakeFiles/bowtie2-align-l.dir/bt2_search.cpp.o:bt2_search.cpp:function pizlonatedFI269_sqrtf:(.text+0xcc3e1): error: undefined reference to 'pizlonated_sqrtf'
> clang-20: error: linker command failed with exit code 1 (use -v to see invocation)
> make[2]: *** [CMakeFiles/bowtie2-align-l.dir/build.make:821: bowtie2-align-l] Error 1
> make[1]: *** [CMakeFiles/Makefile2:134: CMakeFiles/bowtie2-align-l.dir/all] Error 2
> make: *** [Makefile:146: all] Error 2
For full logs, run:
nix log /nix/store/w1fqjphiqn7whd0nzv8zv6y8jn4pz325-bowtie2-x86_64-unknown-linux-gnufilc0-2.5.4.drvbox64-0.3.4
error: Cannot build '/nix/store/nijihvdx4rm44jkcxq7rl7ykrjjyvk3q-box64-x86_64-unknown-linux-gnufilc0-0.3.4.drv'.
Reason: builder failed with exit code 2.
Output paths:
/nix/store/vbz27kb847g2vk3rzigp3pmcbjx6gsyl-box64-x86_64-unknown-linux-gnufilc0-0.3.4
Last 25 log lines:
> 237 | h->DynStr+sym->st_name, (void*)sym->st_value, sym->st_size,
> | ^~~~~~~~~~~~
> 244 warnings generated.
> [ 19%] Building C object CMakeFiles/box64.dir/src/emu/x64run_private.c.o
> [ 19%] Building C object CMakeFiles/box64.dir/src/emu/x64shaext.c.o
> [ 19%] Building C object CMakeFiles/box64.dir/src/emu/x64syscall.c.o
> [ 20%] Building C object CMakeFiles/box64.dir/src/emu/x64tls.c.o
> [ 20%] Building C object CMakeFiles/box64.dir/src/emu/x64trace.c.o
> [ 20%] Building C object CMakeFiles/box64.dir/src/librarian/librarian.c.o
> [ 20%] Building C object CMakeFiles/box64.dir/src/librarian/library.c.o
> [ 21%] Building C object CMakeFiles/box64.dir/src/librarian/dictionnary.c.o
> [ 21%] Building C object CMakeFiles/box64.dir/src/librarian/symbols.c.o
> [ 21%] Building C object CMakeFiles/box64.dir/src/libtools/auxval.c.o
> [ 22%] Building C object CMakeFiles/box64.dir/src/libtools/myalign.c.o
> [ 22%] Building C object CMakeFiles/box64.dir/src/libtools/signals.c.o
> [ 22%] Building C object CMakeFiles/box64.dir/src/libtools/decopcode.c.o
> /build/source/src/libtools/signals.c:1864:21: error: call to undeclared library function 'vfork' with type 'int (void)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
> 1864 | int v = vfork(); // is this ok in a signal handler???
> | ^
> /build/source/src/libtools/signals.c:1864:21: note: include the header <unistd.h> or explicitly provide a declaration for 'vfork'
> 1 error generated.
> make[2]: *** [CMakeFiles/box64.dir/build.make:825: CMakeFiles/box64.dir/src/libtools/signals.c.o] Error 1
> make[2]: *** Waiting for unfinished jobs....
> make[1]: *** [CMakeFiles/Makefile2:157: CMakeFiles/box64.dir/all] Error 2
> make: *** [Makefile:121: all] Error 2
For full logs, run:
nix log /nix/store/nijihvdx4rm44jkcxq7rl7ykrjjyvk3q-box64-x86_64-unknown-linux-gnufilc0-0.3.4.drvboxfort-0.1.4
error: Cannot build '/nix/store/fbwiifmdsla5sdrsk2kr1br1953f5bgf-boxfort-x86_64-unknown-linux-gnufilc0-0.1.4.drv'.
Reason: builder failed with exit code 1.
Output paths:
/nix/store/5pk50hxp0q43laxmrk76sn9jp43sml0m-boxfort-x86_64-unknown-linux-gnufilc0-0.1.4
/nix/store/f290szwx93axqp1zvqm6l17sk2scp34p-boxfort-x86_64-unknown-linux-gnufilc0-0.1.4-dev
Last 25 log lines:
> sbindir : /nix/store/5pk50hxp0q43laxmrk76sn9jp43sml0m-boxfort-x86_64-unknown-linux-gnufilc0-0.1.4/sbin
> wrap_mode : nodownload
>
> Found ninja-1.12.1 at /nix/store/0gk4i8rv9vppwwbig525k1fkhkph6vwx-ninja-1.12.1/bin/ninja
> mesonConfigurePhase: enabled\ parallel\ building
> Running phase: buildPhase
> build flags: -j6
> [1/19] Compiling C object src/libboxfort.a.p/exe-trampoline-fixup.c.o
> [2/19] Compiling C object src/libboxfort.a.p/addr.c.o
> [3/19] Compiling C object src/libboxfort.a.p/sandbox.c.o
> [4/19] Compiling C object src/libboxfort.a.p/timestamp.c.o
> [5/19] Compiling C object src/libboxfort.a.p/exe-elf.c.o
> [6/19] Compiling C object src/libboxfort.a.p/timeout-posix.c.o
> [7/19] Compiling C object src/libboxfort.a.p/arena.c.o
> [8/19] Compiling C object src/libboxfort.a.p/asm_trampoline-x86_64.S.o
> FAILED: src/libboxfort.a.p/asm_trampoline-x86_64.S.o
> clang -Isrc/libboxfort.a.p -Isrc -I../src -I../include -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c99 -Wno-unused-parameter -Wno-unused-value -fvisibility=hidden -DBXF_BUILDING_LIB -D_GNU_SOURCE -fPIC -pthread -MD -MQ src/libboxfort.a.p/asm_trampoline-x86_64.S.o -MF src/libboxfort.a.p/asm_trampoline-x86_64.S.o.d -o src/libboxfort.a.p/asm_trampoline-x86_64.S.o -c ../src/asm/trampoline-x86_64.S
> clang-20: error: sarcasm assembler command failed with exit code 1 (use -v to see invocation)
> sarcasm: /build/trampoline-x86_64-14f14a.s: label 'bxfi_trampoline' outside any function is not supported (globals cannot be made memory-safe automatically)
> [9/19] Compiling C object src/libboxfort.a.p/context.c.o
> [10/19] Compiling C object sample/callback.c.bin.p/callback.c.o
> [11/19] Compiling C object src/libboxfort.a.p/sandbox-posix.c.o
> [12/19] Compiling C object sample/timeout.c.bin.p/timeout.c.o
> [13/19] Compiling C object sample/nested.c.bin.p/nested.c.o
> ninja: build stopped: subcommand failed.
For full logs, run:
nix log /nix/store/fbwiifmdsla5sdrsk2kr1br1953f5bgf-boxfort-x86_64-unknown-linux-gnufilc0-0.1.4.drvboxfs-2-20150109
error: Cannot build '/nix/store/50blkfwqxrd1c83n7vn7i4qlnkv2s22k-boxfs-x86_64-unknown-linux-gnufilc0-2-20150109.drv'.
Reason: builder failed with exit code 2.
Output paths:
/nix/store/bbwyxam1cpgiynb05mnlvgj7m2kv19md-boxfs-x86_64-unknown-linux-gnufilc0-2-20150109
Last 17 log lines:
> Running phase: unpackPhase
> unpacking source archive /nix/store/ahrvnm5nbsqx4zr60qrdq3m8zl34yymd-source
> source root is source
> Running phase: patchPhase
> substituteStream() in derivation boxfs-x86_64-unknown-linux-gnufilc0-2-20150109: WARNING: '--replace' is deprecated, use --replace-{fail,warn,quiet}. (file 'Makefile')
> applying patch /nix/store/95ih7gvi8594cnvc663q5plzk0m4mfb9-work-around-API-borkage.patch
> patching file boxapi.c
> applying patch /nix/store/bvxrcxvwmlck13bnz7cjcq9s5axb3ng1-libapp-include-ctype.diff
> patching file libapp/libapp/app.c
> Running phase: updateAutotoolsGnuConfigScriptsPhase
> Running phase: updateAutotoolsGnuConfigScriptsPhase
> Running phase: configurePhase
> no configure script, doing nothing
> Running phase: buildPhase
> build flags: SHELL=/nix/store/cfqbabpc7xwg8akbcchqbq3cai6qq2vs-bash-5.2p37/bin/bash static CC=cc
> *** Please install pkg-config
> make: *** [Makefile:47: check_pkg] Error 1
For full logs, run:
nix log /nix/store/50blkfwqxrd1c83n7vn7i4qlnkv2s22k-boxfs-x86_64-unknown-linux-gnufilc0-2-20150109.drvbpfmon-2.53
error: Cannot build '/nix/store/5mx78w6szgdhhbs237q8s25nv6i3aqps-bpfmon-x86_64-unknown-linux-gnufilc0-2.53.drv'.
Reason: 1 dependency failed.
Output paths:
/nix/store/977kp0hfz0gdqq9cq6wwnm4hb07srm1n-bpfmon-x86_64-unknown-linux-gnufilc0-2.53bpp-core-2.4.1
error: Cannot build '/nix/store/ih9rq5j7vmjzgvjbx2jzclf1j4jcmzjb-bpp-core-x86_64-unknown-linux-gnufilc0-2.4.1.drv'.
Reason: builder failed with exit code 2.
Output paths:
/nix/store/zjq734ac2gw4fr5sham7dddd10nfxx4r-bpp-core-x86_64-unknown-linux-gnufilc0-2.4.1
Last 25 log lines:
> [ 83%] Building CXX object src/CMakeFiles/bpp-core-static.dir/Bpp/Text/StringTokenizer.cpp.o
> [ 84%] Building CXX object src/CMakeFiles/bpp-core-static.dir/Bpp/Text/TextTools.cpp.o
> [ 84%] Building CXX object src/CMakeFiles/bpp-core-static.dir/Bpp/Utils/AttributesTools.cpp.o
> [ 85%] Linking CXX static library libbpp-core.a
> [ 85%] Built target bpp-core-static
> [ 86%] Linking CXX executable test_dAGraphObs
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_log1p'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_lgamma'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_cosh'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_atan'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_tanh'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_tan'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_atanh'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_log10'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_sqrtf'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_hypot'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_exp2'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_log'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_exp'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_sqrt'
> ../src/libbpp-core.so.4.1.0: error: undefined reference to 'pizlonated_pow'
> clang-20: error: linker command failed with exit code 1 (use -v to see invocation)
> make[2]: *** [test/CMakeFiles/test_dAGraphObs.dir/build.make:101: test/test_dAGraphObs] Error 1
> make[1]: *** [CMakeFiles/Makefile2:1272: test/CMakeFiles/test_dAGraphObs.dir/all] Error 2
> make: *** [Makefile:166: all] Error 2
For full logs, run:
nix log /nix/store/ih9rq5j7vmjzgvjbx2jzclf1j4jcmzjb-bpp-core-x86_64-unknown-linux-gnufilc0-2.4.1.drvbpp-phyl-2.4.1
error: Cannot build '/nix/store/3mka5hzhwda9dmy6b9gh33cl7rwbj3ni-bpp-phyl-x86_64-unknown-linux-gnufilc0-2.4.1.drv'.
Reason: 2 dependencies failed.
Output paths:
/nix/store/23fv8dmk623dbyi3iqa5s4k22cyvi6vs-bpp-phyl-x86_64-unknown-linux-gnufilc0-2.4.1bpp-popgen-2.4.1
error: Cannot build '/nix/store/qwmzmv1s6ns0w45xbhdj1078hw07rmnv-bpp-popgen-x86_64-unknown-linux-gnufilc0-2.4.1.drv'.
Reason: 2 dependencies failed.
Output paths:
/nix/store/66yk8qdjf0fvbc9n2h21yc36lppzsdw3-bpp-popgen-x86_64-unknown-linux-gnufilc0-2.4.1bpp-seq-2.4.1
error: Cannot build '/nix/store/44bmr6gqgx7zv36mcbl0qa775rafia3f-bpp-seq-x86_64-unknown-linux-gnufilc0-2.4.1.drv'.
Reason: 1 dependency failed.
Output paths:
/nix/store/xvn63zdkz2f8rw10hbgsq7gxyylq8ddc-bpp-seq-x86_64-unknown-linux-gnufilc0-2.4.1bppsuite-2.4.1
error: Cannot build '/nix/store/r05cgds18p38w5mqwjpsm2wdzrgkrqfn-bppsuite-x86_64-unknown-linux-gnufilc0-2.4.1.drv'.
Reason: 4 dependencies failed.
Output paths:
/nix/store/5z6rlghnpff03q8jqwqakm9x1jbv3p79-bppsuite-x86_64-unknown-linux-gnufilc0-2.4.1botan-3.8.1
error: build of '/nix/store/19lw0nifgy05y0cs7l17cw9fhyrkhp87-botan-x86_64-unknown-linux-gnufilc0-3.8.1.drv^*', '/nix/store/1mm3jgjbi7x8mmg18svakf8bin8xvdhs-python3.12-blacken-docs-1.19.1-x86_64-unknown-linux-gnufilc0.drv^*', '/nix/store/2vv0awvfqmjqvxzrx2ggc3v06j1divi1-python3.12-black-macchiato-1.3.0-x86_64-unknown-linux-gnufilc0.drv^*', '/nix/store/3mka5hzhwda9dmy6b9gh33cl7rwbj3ni-bpp-phyl-x86_64-unknown-linux-gnufilc0-2.4.1.drv^*', '/nix/store/44bmr6gqgx7zv36mcbl0qa775rafia3f-bpp-seq-x86_64-unknown-linux-gnufilc0-2.4.1.drv^*', '/nix/store/50blkfwqxrd1c83n7vn7i4qlnkv2s22k-boxfs-x86_64-unknown-linux-gnufilc0-2-20150109.drv^*', '/nix/store/5mx78w6szgdhhbs237q8s25nv6i3aqps-bpfmon-x86_64-unknown-linux-gnufilc0-2.53.drv^*', '/nix/store/62x1zars41202xh0n8srra1scy54rw89-bootloadhid-x86_64-unknown-linux-gnufilc0-0-unstable-2012-12-08.drv^*', '/nix/store/6blh94h5znjizycn1fq4sqq3fhyylny6-bees-x86_64-unknown-linux-gnufilc0-0.10.drv^*', '/nix/store/800xkr4dm9vyfpbzyq6gjhn12mvypcr7-boost-x86_64-unknown-linux-gnufilc0-1.81.0.drv^*', '/nix/store/9shc4fqx8rcdjn0yg20jfj5x2b21p861-boron-x86_64-unknown-linux-gnufilc0-2.1.0.drv^*', '/nix/store/bbarw42hbb670b32776whhni2ks9m0yv-bootil-x86_64-unknown-linux-gnufilc0-unstable-2019-11-18.drv^*', '/nix/store/bk6zh0g3i39h64qg8x08wkccarrq2wn2-python3.12-behave-1.2.7.dev5-x86_64-unknown-linux-gnufilc0.drv^*', '/nix/store/dl2jiirdlm2hix5g4xj8y2b1qadx29hk-boost-x86_64-unknown-linux-gnufilc0-1.82.0.drv^*', '/nix/store/fbwiifmdsla5sdrsk2kr1br1953f5bgf-boxfort-x86_64-unknown-linux-gnufilc0-0.1.4.drv^*', '/nix/store/fraap7c44ql7g0mcqyaz10nal2387xsk-bowtie-x86_64-unknown-linux-gnufilc0-1.3.1.drv^*', '/nix/store/ih9rq5j7vmjzgvjbx2jzclf1j4jcmzjb-bpp-core-x86_64-unknown-linux-gnufilc0-2.4.1.drv^*', '/nix/store/m0cg5flpbw08682wgv9iigr6iyjmh0ki-boost-x86_64-unknown-linux-gnufilc0-1.86.0.drv^*', '/nix/store/n2jf6fpnawfinih71q3xrz29ps221p0d-python3.12-black-25.1.0-x86_64-unknown-linux-gnufilc0.drv^*', '/nix/store/nijihvdx4rm44jkcxq7rl7ykrjjyvk3q-box64-x86_64-unknown-linux-gnufilc0-0.3.4.drv^*', '/nix/store/qwmzmv1s6ns0w45xbhdj1078hw07rmnv-bpp-popgen-x86_64-unknown-linux-gnufilc0-2.4.1.drv^*', '/nix/store/r05cgds18p38w5mqwjpsm2wdzrgkrqfn-bppsuite-x86_64-unknown-linux-gnufilc0-2.4.1.drv^*', '/nix/store/w1fqjphiqn7whd0nzv8zv6y8jn4pz325-bowtie2-x86_64-unknown-linux-gnufilc0-2.5.4.drv^*', '/nix/store/xrblv8i1axckf97a9qljvb6h41xszggk-botan-x86_64-unknown-linux-gnufilc0-2.19.5.drv^*', '/nix/store/y98sm7fvm45940yslhz8pb9l19962gx7-boost-x86_64-unknown-linux-gnufilc0-1.88.0.drv^*', '/nix/store/yazdvcyfgm2krisks0a9001lmcm1k9q8-python3.12-basedmypy-2.10.0-x86_64-unknown-linux-gnufilc0.drv^*' failed
End of log