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build_failure.osx-64.yaml
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build_failure.osx-64.yaml
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recipe_sha: 0b8f4f229432444fe063cced79c43374038dbe78fa551e1091a8e0288494d89a # The commit 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: |-
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/psl.c:1854:21: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
if (strlen(tString) != aliSize)
~~~~~~~~~~~~~~~ ^ ~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/psl.c:1979:21: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for (iBlk = 1; iBlk < psl->blockCount; iBlk)
~~~~ ^ ~~~~~~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/psl.c:2080:23: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (psl->blockCount == blocksAlloced)
~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/psl.c:2131:12: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for (i=0; i<psl->blockCount; i)
~^~~~~~~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/psl.c:2175:21: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for (iBlk = 0; iBlk < psl->blockCount; iBlk)
~~~~ ^ ~~~~~~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/psl.c:2255:16: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
for(ii = 0; ii < psl->blockCount; ii)
~~ ^ ~~~~~~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/psl.c:2260:18: warning: comparison of integers of different signs: 'int' and 'unsigned int' [-Wsign-compare]
if (diff > psl->blockSizes[ii])
~~~~ ^ ~~~~~~~~~~~~~~~~~~~
40 warnings generated.
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$SRC_DIR/kent/src/htslib -I$SRC_DIR/kent/src/inc -I$PREFIX/lib/python3.8/site-packages/numpy/core/include -I$PREFIX/lib/python3.8/site-packages/pysam -I$PREFIX/lib/python3.8/site-packages/pysam/include/htslib -I$PREFIX/lib/python3.8/site-packages/pysam/include/samtools -I$PREFIX/include/python3.8 -c $SRC_DIR/kent/src/lib/rangeTree.c -o build/temp.macosx-10.9-x86_64-cpython-38$SRC_DIR/kent/src/lib/rangeTree.o
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$SRC_DIR/kent/src/htslib -I$SRC_DIR/kent/src/inc -I$PREFIX/lib/python3.8/site-packages/numpy/core/include -I$PREFIX/lib/python3.8/site-packages/pysam -I$PREFIX/lib/python3.8/site-packages/pysam/include/htslib -I$PREFIX/lib/python3.8/site-packages/pysam/include/samtools -I$PREFIX/include/python3.8 -c $SRC_DIR/kent/src/lib/rbTree.c -o build/temp.macosx-10.9-x86_64-cpython-38$SRC_DIR/kent/src/lib/rbTree.o
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$SRC_DIR/kent/src/htslib -I$SRC_DIR/kent/src/inc -I$PREFIX/lib/python3.8/site-packages/numpy/core/include -I$PREFIX/lib/python3.8/site-packages/pysam -I$PREFIX/lib/python3.8/site-packages/pysam/include/htslib -I$PREFIX/lib/python3.8/site-packages/pysam/include/samtools -I$PREFIX/include/python3.8 -c $SRC_DIR/kent/src/lib/sqlList.c -o build/temp.macosx-10.9-x86_64-cpython-38$SRC_DIR/kent/src/lib/sqlList.o
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/sqlList.c:25:41: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (s == NULL || s[0] == 0 || count == arraySize)
~~~~~ ^ ~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/sqlList.c:105:41: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (s == NULL || s[0] == 0 || count == arraySize)
~~~~~ ^ ~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/sqlList.c:185:41: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (s == NULL || s[0] == 0 || count == arraySize)
~~~~~ ^ ~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/sqlList.c:275:41: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (s == NULL || s[0] == 0 || count == arraySize)
~~~~~ ^ ~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/sqlList.c:355:41: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (s == NULL || s[0] == 0 || count == arraySize)
~~~~~ ^ ~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/sqlList.c:434:41: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (s == NULL || s[0] == 0 || count == maxArraySize)
~~~~~ ^ ~~~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/sqlList.c:474:41: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (s == NULL || s[0] == 0 || count == maxArraySize)
~~~~~ ^ ~~~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/sqlList.c:613:41: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (s == NULL || s[0] == 0 || count == arraySize)
~~~~~ ^ ~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/sqlList.c:774:41: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare]
if (s == NULL || s[0] == 0 || count == arraySize)
~~~~~ ^ ~~~~~~~~~
9 warnings generated.
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$SRC_DIR/kent/src/htslib -I$SRC_DIR/kent/src/inc -I$PREFIX/lib/python3.8/site-packages/numpy/core/include -I$PREFIX/lib/python3.8/site-packages/pysam -I$PREFIX/lib/python3.8/site-packages/pysam/include/htslib -I$PREFIX/lib/python3.8/site-packages/pysam/include/samtools -I$PREFIX/include/python3.8 -c $SRC_DIR/kent/src/lib/sqlNum.c -o build/temp.macosx-10.9-x86_64-cpython-38$SRC_DIR/kent/src/lib/sqlNum.o
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$SRC_DIR/kent/src/htslib -I$SRC_DIR/kent/src/inc -I$PREFIX/lib/python3.8/site-packages/numpy/core/include -I$PREFIX/lib/python3.8/site-packages/pysam -I$PREFIX/lib/python3.8/site-packages/pysam/include/htslib -I$PREFIX/lib/python3.8/site-packages/pysam/include/samtools -I$PREFIX/include/python3.8 -c $SRC_DIR/kent/src/lib/tokenizer.c -o build/temp.macosx-10.9-x86_64-cpython-38$SRC_DIR/kent/src/lib/tokenizer.o
x86_64-apple-darwin13.4.0-clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -I$PREFIX/include -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$SRC_DIR/kent/src/htslib -I$SRC_DIR/kent/src/inc -I$PREFIX/lib/python3.8/site-packages/numpy/core/include -I$PREFIX/lib/python3.8/site-packages/pysam -I$PREFIX/lib/python3.8/site-packages/pysam/include/htslib -I$PREFIX/lib/python3.8/site-packages/pysam/include/samtools -I$PREFIX/include/python3.8 -c $SRC_DIR/kent/src/lib/udc.c -o build/temp.macosx-10.9-x86_64-cpython-38$SRC_DIR/kent/src/lib/udc.o
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/udc.c:282:5: error: incompatible pointer to integer conversion assigning to 'int' from 'void *' [-Wint-conversion]
sd = NULL; //netUrlOpen(rangeUrl);
^ ~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/udc.c:288:18: error: incompatible pointer to integer conversion assigning to 'int' from 'void *' [-Wint-conversion]
sd = ci->socket = NULL; //netUrlOpenSockets(rangeUrl, &(ci->ctrlSocket));
^ ~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/udc.c:909:28: warning: comparison of integers of different signs: 'unsigned long long' and 'time_t' (aka 'long') [-Wsign-compare]
if (bits->remoteUpdate != file->updateTime || bits->fileSize != file->size ||
~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/udc.c:1054:18: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
if (strlen(name) > maxLen)
~~~~~~~~~~~~ ^ ~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/udc.c:1197:52: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare]
useCacheInfo = (udcCacheAge(url, cacheDir) < udcCacheTimeout());
~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/udc.c:1442:19: warning: comparison of integers of different signs: 'time_t' (aka 'long') and 'unsigned long' [-Wsign-compare]
oldestTime = min(fileModTime(sl->name), oldestTime);
^ ~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/inc/common.h:1302:24: note: expanded from macro 'min'
#define min(a,b) ( (a) < (b) ? (a) : (b) )
~ ^ ~
/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/kent/src/lib/udc.c:1514:20: warning: comparison of integers of different signs: 'int' and 'unsigned long long' [-Wsign-compare]
if (actualSize != readSize)
~~~~~~~~~~ ^ ~~~~~~~~
5 warnings and 2 errors generated.
error: command '/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/_build_env/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 1
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in <module>
sys.exit(main())
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
call_conda_build(action, config)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
result = api.build(
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
return build_tree(
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
packages_from_this = build(metadata, stats,
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build
utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env,
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/plastid_1685547601950/work/conda_build.sh']' returned non-zero exit status 1.
# Last 100 lines of the build log.