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build_failure.linux-64.yaml
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recipe_sha: a4138472bb3ac3a509f98d73a55851e2f8f7512d60fa05872d3a579decd87550 # The hash of the recipe's meta.yaml at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
log: |-
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strremovews_s.o safeclib/strremovews_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memmove32_s.o safeclib/memmove32_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strcpyfld_s.o safeclib/strcpyfld_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strspn_s.o safeclib/strspn_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memmove_s.o safeclib/memmove_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strcpy_s.o safeclib/strcpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strstr_s.o safeclib/strstr_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/mem_primitives_lib.o safeclib/mem_primitives_lib.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strcspn_s.o safeclib/strcspn_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strtok_s.o safeclib/strtok_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strfirstchar_s.o safeclib/strfirstchar_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strtolowercase_s.o safeclib/strtolowercase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memset16_s.o safeclib/memset16_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strfirstdiff_s.o safeclib/strfirstdiff_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strtouppercase_s.o safeclib/strtouppercase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memset32_s.o safeclib/memset32_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strfirstsame_s.o safeclib/strfirstsame_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strzero_s.o safeclib/strzero_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memset_s.o safeclib/memset_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strisalphanumeric_s.o safeclib/strisalphanumeric_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcpcpy_s.o safeclib/wcpcpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memzero16_s.o safeclib/memzero16_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strisascii_s.o safeclib/strisascii_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcscat_s.o safeclib/wcscat_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memzero32_s.o safeclib/memzero32_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strisdigit_s.o safeclib/strisdigit_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcscpy_s.o safeclib/wcscpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
src/bwtindex.cpp: In function 'void bwt_bwtupdate_core(bwt_t*)':
src/bwtindex.cpp:185:95: warning: ISO C forbids converting a string constant to 'char*' [-Wwrite-strings]
185 | memcpy_bwamem(buf k, sizeof(bwtint_t) * 4, c, sizeof(bwtint_t) * 4, __FILE__, __LINE__);
| ^~~~~~~~
src/bwtindex.cpp:192:79: warning: ISO C forbids converting a string constant to 'char*' [-Wwrite-strings]
192 | memcpy_bwamem(buf k, sizeof(bwtint_t) * 4, c, sizeof(bwtint_t) * 4, __FILE__, __LINE__);
| ^~~~~~~~
src/bwtindex.cpp: In function 'int bwa_index(int, char**)':
src/bwtindex.cpp:276:32: warning: invalid conversion from 'void*' to 'char*' [-fpermissive]
276 | prefix = malloc(strnlen_s(argv[optind], PATH_MAX) 4);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| void*
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/memzero_s.o safeclib/memzero_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
src/bwtindex.cpp: In function 'int bwa_idx_build_Learned_index(const char*, const char*, int)':
src/bwtindex.cpp:371:31: warning: invalid conversion from 'const char*' to 'char*' [-fpermissive]
371 | buildSAandLEP(prefix, num_threads);
| ^~~~~~
| |
| const char*
In file included from src/bwtindex.cpp:43:
src/Learnedindex.h:35:27: note: initializing argument 1 of 'void buildSAandLEP(char*, int)'
35 | void buildSAandLEP( char* prefix, int num_threads);
| ~~~~~~^~~~~~
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strishex_s.o safeclib/strishex_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcsncat_s.o safeclib/wcsncat_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strislowercase_s.o safeclib/strislowercase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcsncpy_s.o safeclib/wcsncpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/safe_mem_constraint.o safeclib/safe_mem_constraint.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strismixedcase_s.o safeclib/strismixedcase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wcsnlen_s.o safeclib/wcsnlen_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strispassword_s.o safeclib/strispassword_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wmemcmp_s.o safeclib/wmemcmp_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/safe_str_constraint.o safeclib/safe_str_constraint.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strisuppercase_s.o safeclib/strisuppercase_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wmemcpy_s.o safeclib/wmemcpy_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strlastchar_s.o safeclib/strlastchar_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wmemmove_s.o safeclib/wmemmove_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/snprintf_support.o safeclib/snprintf_support.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/strlastdiff_s.o safeclib/strlastdiff_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
ar rcs libbwa.a src/fastmap.o src/main.o src/utils.o src/memcpy_bwamem.o src/kthread.o src/kstring.o src/ksw.o src/bwt.o src/ertindex.o src/Learnedindex.o src/bntseq.o src/bwamem.o src/ertseeding.o src/LearnedIndex_seeding.o src/profiling.o src/bandedSWA.o src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o src/bwamem_extra.o src/bwtbuild.o src/QSufSort.o src/bwt_gen.o src/rope.o src/rle.o src/is.o src/kopen.o src/bwtindex.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -z noexecstack -z relo -z now -c -o obj/wmemset_s.o safeclib/wmemset_s.c -Iinclude -fstack-protector-strong -fPIE -fPIC -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security
ar rcs libsafestring.a obj/abort_handler_s.o obj/stpcpy_s.o obj/strlastsame_s.o obj/ignore_handler_s.o obj/stpncpy_s.o obj/strljustify_s.o obj/memcmp16_s.o obj/strcasecmp_s.o obj/strncat_s.o obj/memcmp32_s.o obj/strcasestr_s.o obj/strncpy_s.o obj/memcmp_s.o obj/strcat_s.o obj/strnlen_s.o obj/memcpy16_s.o obj/strcmpfld_s.o obj/strnterminate_s.o obj/memcpy32_s.o obj/strcmp_s.o obj/strpbrk_s.o obj/memcpy_s.o obj/strcpyfldin_s.o obj/strprefix_s.o obj/memmove16_s.o obj/strcpyfldout_s.o obj/strremovews_s.o obj/memmove32_s.o obj/strcpyfld_s.o obj/strspn_s.o obj/memmove_s.o obj/strcpy_s.o obj/strstr_s.o obj/mem_primitives_lib.o obj/strcspn_s.o obj/strtok_s.o obj/strfirstchar_s.o obj/strtolowercase_s.o obj/memset16_s.o obj/strfirstdiff_s.o obj/strtouppercase_s.o obj/memset32_s.o obj/strfirstsame_s.o obj/strzero_s.o obj/memset_s.o obj/strisalphanumeric_s.o obj/wcpcpy_s.o obj/memzero16_s.o obj/strisascii_s.o obj/wcscat_s.o obj/memzero32_s.o obj/strisdigit_s.o obj/wcscpy_s.o obj/memzero_s.o obj/strishex_s.o obj/wcsncat_s.o obj/strislowercase_s.o obj/wcsncpy_s.o obj/safe_mem_constraint.o obj/strismixedcase_s.o obj/wcsnlen_s.o obj/strispassword_s.o obj/wmemcmp_s.o obj/safe_str_constraint.o obj/strisuppercase_s.o obj/wmemcpy_s.o obj/strlastchar_s.o obj/wmemmove_s.o obj/snprintf_support.o obj/strlastdiff_s.o obj/wmemset_s.o
make[2]: Leaving directory '$SRC_DIR/ext/safestringlib'
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bwa-meme-1.0.6 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -g -O3 -fpermissive -fopenmp -msse -msse2 -msse3 -mssse3 -msse4.1 -g -O3 -fpermissive -fopenmp -msse -msse2 -msse3 -mssse3 -msse4.1 src/main.o libbwa.a -DMODE=1 -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring -Imimalloc/include -Wl,-whole-archive build/mimalloc/libmimalloc.a -Wl,-no-whole-archive -lrt -o bwa-meme_mode1.sse41
/opt/conda/conda-bld/bwa-meme_1734150155172/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory
collect2: error: ld returned 1 exit status
make[1]: *** [Makefile:162: bwa-meme_mode1.sse41] Error 1
make[1]: Leaving directory '$SRC_DIR'
make: *** [Makefile:123: multi] Error 2
Traceback (most recent call last):
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build
utils.check_call_env(
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bwa-meme_1734150155172/work/conda_build.sh']' returned non-zero exit status 2.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute
api.build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build
return build_tree(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree
packages_from_this = build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build
raise BuildScriptException(str(exc), caused_by=exc) from exc
conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bwa-meme_1734150155172/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.