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https://files.pythonhosted.org/packages/0d/f1/ec51368cfb9898c8cd30a29dbabb9585f22957280545561bd1e4bdbc1613/cyvcf2-0.30.4-cp39-cp39-manylinux2014_x86_64.whl#sha256=2a9c950e4e8370b0d8914ebd508fff15fc1ca2ea1b21d2cd787ba967d91615c4 (from https://pypi.org/simple/cyvcf2/) 2021-07-11T19:37:23,209 Found link https://files.pythonhosted.org/packages/63/2b/4313b604598a32075a649a45c3cbaff3c0136f49eb1c4da8dc45cd5b957c/cyvcf2-0.30.4.tar.gz#sha256=5088c1df2f1569392395c2e4c93e749149cd18e8e914257077581ee2fdb226a8 (from https://pypi.org/simple/cyvcf2/), version: 0.30.4 2021-07-11T19:37:23,209 Skipping link: not a file: https://pypi.org/simple/cyvcf2/ 2021-07-11T19:37:23,222 Given no hashes to check 1 links for project 'cyvcf2': discarding no candidates 2021-07-11T19:37:23,241 Collecting cyvcf2==0.5.5 2021-07-11T19:37:23,242 Created temporary directory: /tmp/pip-unpack-yzd1v_cs 2021-07-11T19:37:23,487 Downloading cyvcf2-0.5.5.tar.gz (963 kB) 2021-07-11T19:37:24,068 Added cyvcf2==0.5.5 from https://files.pythonhosted.org/packages/dd/12/433768e01c285407d1c294c8d3dd367ff44774b23620aa22b627ea799cc2/cyvcf2-0.5.5.tar.gz#sha256=79d75b115616bf4782cf452352e7e1d494c7ca38c452e65a80263996ced91594 to build tracker '/tmp/pip-req-tracker-f5x_aykg' 2021-07-11T19:37:24,069 Running setup.py (path:/tmp/pip-wheel-0dnxyhi6/cyvcf2_2e115abfe173476ba42332063d4189ba/setup.py) egg_info for package cyvcf2 2021-07-11T19:37:24,069 Created temporary directory: /tmp/pip-pip-egg-info-wr2xphwj 2021-07-11T19:37:24,070 Running command python setup.py egg_info 2021-07-11T19:37:25,342 running egg_info 2021-07-11T19:37:25,345 creating /tmp/pip-pip-egg-info-wr2xphwj/cyvcf2.egg-info 2021-07-11T19:37:25,345 writing /tmp/pip-pip-egg-info-wr2xphwj/cyvcf2.egg-info/PKG-INFO 2021-07-11T19:37:25,348 writing dependency_links to /tmp/pip-pip-egg-info-wr2xphwj/cyvcf2.egg-info/dependency_links.txt 2021-07-11T19:37:25,350 writing requirements to /tmp/pip-pip-egg-info-wr2xphwj/cyvcf2.egg-info/requires.txt 2021-07-11T19:37:25,351 writing top-level names to /tmp/pip-pip-egg-info-wr2xphwj/cyvcf2.egg-info/top_level.txt 2021-07-11T19:37:25,353 writing manifest file '/tmp/pip-pip-egg-info-wr2xphwj/cyvcf2.egg-info/SOURCES.txt' 2021-07-11T19:37:25,495 reading manifest file '/tmp/pip-pip-egg-info-wr2xphwj/cyvcf2.egg-info/SOURCES.txt' 2021-07-11T19:37:25,497 reading manifest template 'MANIFEST.in' 2021-07-11T19:37:25,507 adding license file 'LICENSE' 2021-07-11T19:37:25,513 writing manifest file '/tmp/pip-pip-egg-info-wr2xphwj/cyvcf2.egg-info/SOURCES.txt' 2021-07-11T19:37:25,607 Source in /tmp/pip-wheel-0dnxyhi6/cyvcf2_2e115abfe173476ba42332063d4189ba has version 0.5.5, which satisfies requirement cyvcf2==0.5.5 from https://files.pythonhosted.org/packages/dd/12/433768e01c285407d1c294c8d3dd367ff44774b23620aa22b627ea799cc2/cyvcf2-0.5.5.tar.gz#sha256=79d75b115616bf4782cf452352e7e1d494c7ca38c452e65a80263996ced91594 2021-07-11T19:37:25,608 Removed cyvcf2==0.5.5 from https://files.pythonhosted.org/packages/dd/12/433768e01c285407d1c294c8d3dd367ff44774b23620aa22b627ea799cc2/cyvcf2-0.5.5.tar.gz#sha256=79d75b115616bf4782cf452352e7e1d494c7ca38c452e65a80263996ced91594 from build tracker '/tmp/pip-req-tracker-f5x_aykg' 2021-07-11T19:37:25,612 Created temporary directory: /tmp/pip-unpack-a7w1zajk 2021-07-11T19:37:25,613 Building wheels for collected packages: cyvcf2 2021-07-11T19:37:25,617 Created temporary directory: /tmp/pip-wheel-ac4sl253 2021-07-11T19:37:25,617 Building wheel for cyvcf2 (setup.py): started 2021-07-11T19:37:25,617 Destination directory: /tmp/pip-wheel-ac4sl253 2021-07-11T19:37:25,618 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-0dnxyhi6/cyvcf2_2e115abfe173476ba42332063d4189ba/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-0dnxyhi6/cyvcf2_2e115abfe173476ba42332063d4189ba/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ac4sl253 2021-07-11T19:37:26,875 running bdist_wheel 2021-07-11T19:37:26,877 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2021-07-11T19:37:26,880 running build 2021-07-11T19:37:26,880 running build_py 2021-07-11T19:37:27,013 creating build 2021-07-11T19:37:27,014 creating build/lib.linux-armv7l-3.9 2021-07-11T19:37:27,014 creating build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T19:37:27,016 copying cyvcf2/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T19:37:27,018 creating build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,019 copying cyvcf2/tests/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,021 copying cyvcf2/tests/test_reader.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,023 copying cyvcf2/tests/test_hemi.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,025 running egg_info 2021-07-11T19:37:27,038 writing cyvcf2.egg-info/PKG-INFO 2021-07-11T19:37:27,040 writing dependency_links to cyvcf2.egg-info/dependency_links.txt 2021-07-11T19:37:27,042 writing requirements to cyvcf2.egg-info/requires.txt 2021-07-11T19:37:27,043 writing top-level names to cyvcf2.egg-info/top_level.txt 2021-07-11T19:37:27,050 reading manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-11T19:37:27,054 reading manifest template 'MANIFEST.in' 2021-07-11T19:37:27,065 adding license file 'LICENSE' 2021-07-11T19:37:27,074 writing manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-11T19:37:27,080 copying cyvcf2/cyvcf2.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T19:37:27,132 copying cyvcf2/cyvcf2.pxd -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T19:37:27,135 copying cyvcf2/cyvcf2.pyx -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T19:37:27,138 copying cyvcf2/helpers.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T19:37:27,140 copying cyvcf2/helpers.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T19:37:27,142 copying cyvcf2/relatedness.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T19:37:27,144 copying cyvcf2/tests/__init__.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,147 copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,149 copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,154 copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,156 copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,174 copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,177 copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,180 copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,184 copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,186 copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,189 copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,197 copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,199 copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,202 copying cyvcf2/tests/test_hemi.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,204 copying cyvcf2/tests/test_reader.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T19:37:27,209 running build_ext 2021-07-11T19:37:27,273 cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c 2021-07-11T19:37:27,897 /usr/local/lib/python3.9/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-wheel-0dnxyhi6/cyvcf2_2e115abfe173476ba42332063d4189ba/cyvcf2/cyvcf2.pxd 2021-07-11T19:37:27,897 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-11T19:37:29,277 warning: cyvcf2/cyvcf2.pxd:24:16: Declarations should not be declared inline. 2021-07-11T19:37:38,943 building 'cyvcf2.cyvcf2' extension 2021-07-11T19:37:38,945 creating build/temp.linux-armv7l-3.9 2021-07-11T19:37:38,945 creating build/temp.linux-armv7l-3.9/cyvcf2 2021-07-11T19:37:38,946 creating build/temp.linux-armv7l-3.9/htslib 2021-07-11T19:37:38,947 creating build/temp.linux-armv7l-3.9/htslib/cram 2021-07-11T19:37:38,949 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c cyvcf2/cyvcf2.c -o build/temp.linux-armv7l-3.9/cyvcf2/cyvcf2.o 2021-07-11T19:37:39,383 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-11T19:37:39,383 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-11T19:37:39,383 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-11T19:37:39,383 from cyvcf2/cyvcf2.c:613: 2021-07-11T19:37:39,383 /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2021-07-11T19:37:39,384 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-11T19:37:39,384 | ^~~~~~~ 2021-07-11T19:37:39,611 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_2add_to_header’: 2021-07-11T19:37:39,617 cyvcf2/cyvcf2.c:7494:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:39,617 7494 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); 2021-07-11T19:37:39,617 | ~~~~~~~~~~~~^~~~~ 2021-07-11T19:37:39,617 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T19:37:39,617 htslib/htslib/vcf.h:441:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T19:37:39,618 441 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-11T19:37:39,618 | ~~~~~~~~~~~^ 2021-07-11T19:37:39,623 cyvcf2/cyvcf2.c:7536:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:39,624 7536 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-11T19:37:39,624 | ~~~~~~~~~~~~^~~~~ 2021-07-11T19:37:39,624 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T19:37:39,624 htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T19:37:39,624 477 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-11T19:37:39,624 | ~~~~~~~~~~~^ 2021-07-11T19:37:39,633 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10set_samples’: 2021-07-11T19:37:39,639 cyvcf2/cyvcf2.c:8044:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:39,639 8044 | __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); 2021-07-11T19:37:39,639 | ~~~~~~~~~~~~^~~~~ 2021-07-11T19:37:39,639 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T19:37:39,640 htslib/htslib/vcf.h:313:40: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T19:37:39,640 313 | int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); 2021-07-11T19:37:39,640 | ~~~~~~~~~~~^~~ 2021-07-11T19:37:39,649 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12update’: 2021-07-11T19:37:39,655 cyvcf2/cyvcf2.c:8335:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:39,655 8335 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); 2021-07-11T19:37:39,655 | ~~~~~~~~~~~~^~~~~ 2021-07-11T19:37:39,656 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T19:37:39,656 htslib/htslib/vcf.h:441:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T19:37:39,656 441 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-11T19:37:39,656 | ~~~~~~~~~~~^ 2021-07-11T19:37:39,663 cyvcf2/cyvcf2.c:8388:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:39,663 8388 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-11T19:37:39,663 | ~~~~~~~~~~~~^~~~~ 2021-07-11T19:37:39,663 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T19:37:39,664 htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T19:37:39,664 477 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-11T19:37:39,664 | ~~~~~~~~~~~^ 2021-07-11T19:37:39,667 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_16generator’: 2021-07-11T19:37:39,670 cyvcf2/cyvcf2.c:8602:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:39,670 8602 | __pyx_cur_scope->__pyx_v_itr = bcf_itr_querys(__pyx_cur_scope->__pyx_v_self->hidx, __pyx_cur_scope->__pyx_v_self->hdr, __pyx_t_2); 2021-07-11T19:37:39,670 htslib/htslib/vcf.h:762:103: note: in definition of macro ‘bcf_itr_querys’ 2021-07-11T19:37:39,671 762 | #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) 2021-07-11T19:37:39,671 | ^~~ 2021-07-11T19:37:39,671 In file included from cyvcf2/cyvcf2.c:624: 2021-07-11T19:37:39,671 htslib/htslib/hts.h:534:97: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T19:37:39,671 534 | hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec); 2021-07-11T19:37:39,671 | ~~~~~~^~~ 2021-07-11T19:37:39,694 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_22generator2’: 2021-07-11T19:37:39,701 cyvcf2/cyvcf2.c:9789:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:39,701 9789 | __pyx_t_4 = ((PyObject *)__pyx_f_6cyvcf2_6cyvcf2_newHREC((__pyx_cur_scope->__pyx_v_self->hdr->hrec[__pyx_cur_scope->__pyx_v_i]), __pyx_cur_scope->__pyx_v_self->hdr)); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 284, __pyx_L1_error) 2021-07-11T19:37:39,701 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-11T19:37:39,703 cyvcf2/cyvcf2.c:2913:107: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T19:37:39,704 2913 | static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ 2021-07-11T19:37:39,704 | ^~~~~~~~~~~ 2021-07-11T19:37:39,766 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_29__dealloc__’: 2021-07-11T19:37:39,773 cyvcf2/cyvcf2.c:11063:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:39,774 11063 | bcf_hdr_destroy(__pyx_v_self->hdr); 2021-07-11T19:37:39,774 | ~~~~~~~~~~~~^~~~~ 2021-07-11T19:37:39,774 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T19:37:39,774 htslib/htslib/vcf.h:259:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T19:37:39,774 259 | void bcf_hdr_destroy(bcf_hdr_t *h); 2021-07-11T19:37:39,775 | ~~~~~~~~~~~^ 2021-07-11T19:37:39,778 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: 2021-07-11T19:37:39,786 cyvcf2/cyvcf2.c:11524:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 2021-07-11T19:37:39,786 11524 | __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); 2021-07-11T19:37:39,786 | ^~~~~~~~~ 2021-07-11T19:37:39,786 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T19:37:39,786 htslib/htslib/vcf.h:437:11: note: declared here 2021-07-11T19:37:39,787 437 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) 2021-07-11T19:37:39,787 | ^~~~~~~~~~~~~~~~ 2021-07-11T19:37:39,791 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: 2021-07-11T19:37:39,794 cyvcf2/cyvcf2.c:11735:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:39,795 11735 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-11T19:37:39,795 htslib/htslib/vcf.h:765:112: note: in definition of macro ‘bcf_index_seqnames’ 2021-07-11T19:37:39,795 765 | #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) 2021-07-11T19:37:39,795 | ^~~ 2021-07-11T19:37:39,795 In file included from cyvcf2/cyvcf2.c:624: 2021-07-11T19:37:39,795 htslib/htslib/hts.h:536:92: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T19:37:39,796 536 | const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values 2021-07-11T19:37:39,796 | ~~~~~~^~~ 2021-07-11T19:37:39,805 cyvcf2/cyvcf2.c:11735:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-11T19:37:39,805 11735 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-11T19:37:39,806 | ^ 2021-07-11T19:37:39,818 cyvcf2/cyvcf2.c:11899:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-11T19:37:39,818 11899 | __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); 2021-07-11T19:37:39,818 | ^ 2021-07-11T19:37:39,826 cyvcf2/cyvcf2.c:11929:20: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-11T19:37:39,827 11929 | __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-11T19:37:39,827 | ^ 2021-07-11T19:37:40,453 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’: 2021-07-11T19:37:40,468 cyvcf2/cyvcf2.c:21235:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:37:40,468 21235 | for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) { 2021-07-11T19:37:40,469 | ^ 2021-07-11T19:37:40,759 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’: 2021-07-11T19:37:40,780 cyvcf2/cyvcf2.c:28201:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:37:40,780 28201 | for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-07-11T19:37:40,780 | ^ 2021-07-11T19:37:40,782 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’: 2021-07-11T19:37:40,802 cyvcf2/cyvcf2.c:28296:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:37:40,802 28296 | for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2021-07-11T19:37:40,802 | ^ 2021-07-11T19:37:40,810 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’: 2021-07-11T19:37:40,830 cyvcf2/cyvcf2.c:28511:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:37:40,830 28511 | for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2021-07-11T19:37:40,830 | ^ 2021-07-11T19:37:40,852 cyvcf2/cyvcf2.c:28569:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:37:40,852 28569 | __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0); 2021-07-11T19:37:40,852 | ^~ 2021-07-11T19:37:40,875 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: 2021-07-11T19:37:40,897 cyvcf2/cyvcf2.c:30546:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:40,897 30546 | __pyx_v_h = __pyx_t_6; 2021-07-11T19:37:40,898 | ^ 2021-07-11T19:37:40,983 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_10__next__’: 2021-07-11T19:37:41,006 cyvcf2/cyvcf2.c:33205:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:41,006 33205 | __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); 2021-07-11T19:37:41,007 | ^ 2021-07-11T19:37:41,015 cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: 2021-07-11T19:37:41,039 cyvcf2/cyvcf2.c:34198:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:41,039 34198 | __pyx_v_i->hdr = __pyx_t_4; 2021-07-11T19:37:41,040 | ^ 2021-07-11T19:37:41,056 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: 2021-07-11T19:37:41,080 cyvcf2/cyvcf2.c:34591:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T19:37:41,080 34591 | __pyx_v_h = __pyx_t_3; 2021-07-11T19:37:41,080 | ^ 2021-07-11T19:37:45,313 At top level: 2021-07-11T19:37:45,318 cyvcf2/cyvcf2.c:6453:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] 2021-07-11T19:37:45,318 6453 | static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { 2021-07-11T19:37:45,319 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T19:38:09,754 cyvcf2/cyvcf2.c: In function ‘__pyx_getprop_6cyvcf2_6cyvcf2_3VCF_seqnames’: 2021-07-11T19:38:09,762 cyvcf2/cyvcf2.c:11581:10: warning: ‘__pyx_v_cnames’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-11T19:38:09,763 11581 | char **__pyx_v_cnames; 2021-07-11T19:38:09,763 | ^~~~~~~~~~~~~~ 2021-07-11T19:38:35,111 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c cyvcf2/helpers.c -o build/temp.linux-armv7l-3.9/cyvcf2/helpers.o 2021-07-11T19:38:35,404 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/bgzf.c -o build/temp.linux-armv7l-3.9/htslib/bgzf.o 2021-07-11T19:38:35,607 htslib/bgzf.c: In function ‘bgzf_read’: 2021-07-11T19:38:35,608 htslib/bgzf.c:691:23: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:35,608 691 | while (bytes_read < length) { 2021-07-11T19:38:35,608 | ^ 2021-07-11T19:38:35,608 htslib/bgzf.c:706:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:35,608 706 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-11T19:38:35,608 | ^ 2021-07-11T19:38:35,609 htslib/bgzf.c:706:78: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:38:35,609 706 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-11T19:38:35,609 | ^~~~~~~~~ 2021-07-11T19:38:35,629 htslib/bgzf.c: In function ‘bgzf_useek’: 2021-07-11T19:38:35,630 htslib/bgzf.c:1301:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-11T19:38:35,630 1301 | if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1; 2021-07-11T19:38:35,630 | ^ 2021-07-11T19:38:35,631 htslib/bgzf.c:1302:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-11T19:38:35,631 1302 | else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1; 2021-07-11T19:38:35,631 | ^~ 2021-07-11T19:38:37,311 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_codecs.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_codecs.o 2021-07-11T19:38:37,519 In file included from htslib/cram/cram.h:52, 2021-07-11T19:38:37,519 from htslib/cram/cram_codecs.c:43: 2021-07-11T19:38:37,520 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:38:37,520 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:37,520 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:38:37,520 | ^~ 2021-07-11T19:38:37,520 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:37,520 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:38:37,521 | ^ 2021-07-11T19:38:37,523 htslib/cram/cram_codecs.c: In function ‘get_one_bits_MSB’: 2021-07-11T19:38:37,523 htslib/cram/cram_codecs.c:77:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:37,523 77 | if (block->byte >= block->uncomp_size) 2021-07-11T19:38:37,524 | ^~ 2021-07-11T19:38:37,524 htslib/cram/cram_codecs.c:84:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:37,524 84 | if (block->byte == block->uncomp_size && (b&1)) 2021-07-11T19:38:37,524 | ^~ 2021-07-11T19:38:37,524 htslib/cram/cram_codecs.c: In function ‘get_zero_bits_MSB’: 2021-07-11T19:38:37,524 htslib/cram/cram_codecs.c:95:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:37,525 95 | if (block->byte >= block->uncomp_size) 2021-07-11T19:38:37,525 | ^~ 2021-07-11T19:38:37,525 htslib/cram/cram_codecs.c:102:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:37,525 102 | if (block->byte == block->uncomp_size && !(b&1)) 2021-07-11T19:38:37,525 | ^~ 2021-07-11T19:38:37,535 htslib/cram/cram_codecs.c: In function ‘cram_beta_decode_init’: 2021-07-11T19:38:37,536 htslib/cram/cram_codecs.c:544:47: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:38:37,536 544 | || c->beta.nbits < 0 || c->beta.nbits > 8 * sizeof(int)) { 2021-07-11T19:38:37,536 | ^ 2021-07-11T19:38:37,567 htslib/cram/cram_codecs.c: In function ‘cram_byte_array_stop_decode_block’: 2021-07-11T19:38:37,568 htslib/cram/cram_codecs.c:1587:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:37,568 1587 | if (cp_end - cp < out->alloc - out->byte) { 2021-07-11T19:38:37,568 | ^ 2021-07-11T19:38:39,938 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_decode.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_decode.o 2021-07-11T19:38:40,206 In file included from htslib/cram/cram.h:52, 2021-07-11T19:38:40,206 from htslib/cram/cram_decode.c:48: 2021-07-11T19:38:40,206 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:38:40,207 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:40,207 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:38:40,207 | ^~ 2021-07-11T19:38:40,207 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:40,207 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:38:40,207 | ^ 2021-07-11T19:38:40,212 htslib/cram/cram_decode.c: In function ‘cram_decode_TD’: 2021-07-11T19:38:40,212 htslib/cram/cram_decode.c:101:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:40,212 101 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-11T19:38:40,212 | ^ 2021-07-11T19:38:40,212 htslib/cram/cram_decode.c:113:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:40,212 113 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-11T19:38:40,213 | ^ 2021-07-11T19:38:40,235 htslib/cram/cram_decode.c: In function ‘cram_dependent_data_series’: 2021-07-11T19:38:40,235 htslib/cram/cram_decode.c:794:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:38:40,235 794 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-11T19:38:40,235 | ^ 2021-07-11T19:38:40,238 htslib/cram/cram_decode.c:886:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:38:40,238 886 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-11T19:38:40,238 | ^ 2021-07-11T19:38:40,243 htslib/cram/cram_decode.c: In function ‘cram_decode_slice_header’: 2021-07-11T19:38:40,243 htslib/cram/cram_decode.c:1102:23: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:38:40,243 1102 | hdr->num_content_ids >= SIZE_MAX / sizeof(int32_t)) { 2021-07-11T19:38:40,244 | ^~ 2021-07-11T19:38:40,249 htslib/cram/cram_decode.c: In function ‘cram_decode_seq’: 2021-07-11T19:38:40,249 htslib/cram/cram_decode.c:1275:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:40,250 1275 | if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) { 2021-07-11T19:38:40,250 | ^ 2021-07-11T19:38:40,254 htslib/cram/cram_decode.c:1425:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:40,255 1425 | if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-11T19:38:40,255 | ^~ 2021-07-11T19:38:40,258 htslib/cram/cram_decode.c:1469:25: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:40,258 1469 | if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) { 2021-07-11T19:38:40,259 | ^~ 2021-07-11T19:38:40,260 htslib/cram/cram_decode.c:1480:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:40,260 1480 | if (bfd->ref[cr->ref_id].len >= ref_pos) { 2021-07-11T19:38:40,260 | ^~ 2021-07-11T19:38:40,266 htslib/cram/cram_decode.c:1573:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:40,266 1573 | if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-11T19:38:40,266 | ^~ 2021-07-11T19:38:40,269 htslib/cram/cram_decode.c:1644:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:40,269 1644 | if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-11T19:38:40,270 | ^~ 2021-07-11T19:38:40,276 htslib/cram/cram_decode.c:1748:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:40,276 1748 | if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) { 2021-07-11T19:38:40,276 | ^ 2021-07-11T19:38:40,304 htslib/cram/cram_decode.c: In function ‘cram_decode_slice’: 2021-07-11T19:38:40,306 htslib/cram/cram_decode.c:2367:6: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:38:40,306 2367 | bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap)) 2021-07-11T19:38:40,306 | ^~ 2021-07-11T19:38:45,844 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_encode.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_encode.o 2021-07-11T19:38:46,107 In file included from htslib/cram/cram.h:52, 2021-07-11T19:38:46,107 from htslib/cram/cram_encode.c:43: 2021-07-11T19:38:46,107 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:38:46,108 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:46,108 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:38:46,108 | ^~ 2021-07-11T19:38:46,108 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:46,108 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:38:46,109 | ^ 2021-07-11T19:38:46,161 htslib/cram/cram_encode.c: In function ‘lossy_read_names’: 2021-07-11T19:38:46,162 htslib/cram/cram_encode.c:1297:14: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-11T19:38:46,162 1297 | if (u.e != e) { 2021-07-11T19:38:46,162 | ^~ 2021-07-11T19:38:46,163 htslib/cram/cram_encode.c:1327:23: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:46,164 1327 | if (kh_val(names, k) == -1) 2021-07-11T19:38:46,164 | ^~ 2021-07-11T19:38:46,205 htslib/cram/cram_encode.c: In function ‘process_one_read’: 2021-07-11T19:38:46,207 htslib/cram/cram_encode.c:2650:10: warning: unused variable ‘brg’ [-Wunused-variable] 2021-07-11T19:38:46,207 2650 | SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); 2021-07-11T19:38:46,207 | ^~~ 2021-07-11T19:38:46,211 htslib/cram/cram_encode.c:2758:32: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:46,211 2758 | while (cr->cigar + cr->ncigar >= s->cigar_alloc) { 2021-07-11T19:38:46,212 | ^~ 2021-07-11T19:38:46,213 htslib/cram/cram_encode.c:2788:30: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:46,213 2788 | int end = cig_len+apos < c->ref_end 2021-07-11T19:38:46,213 | ^ 2021-07-11T19:38:46,214 htslib/cram/cram_encode.c:2789:16: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:38:46,215 2789 | ? cig_len : c->ref_end - apos; 2021-07-11T19:38:46,215 | ^~~~~~~~~~~~~~~~~ 2021-07-11T19:38:46,218 htslib/cram/cram_encode.c:2831:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:46,218 2831 | if (l < cig_len && cr->len) { 2021-07-11T19:38:46,218 | ^ 2021-07-11T19:38:46,220 htslib/cram/cram_encode.c:2839:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:46,220 2839 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-11T19:38:46,220 | ^ 2021-07-11T19:38:46,221 htslib/cram/cram_encode.c:2847:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:46,222 2847 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-11T19:38:46,222 | ^ 2021-07-11T19:38:46,225 htslib/cram/cram_encode.c:2878:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:46,226 2878 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-11T19:38:46,226 | ^ 2021-07-11T19:38:46,228 htslib/cram/cram_encode.c:2894:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:46,228 2894 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-11T19:38:46,228 | ^ 2021-07-11T19:38:46,229 htslib/cram/cram_encode.c:2898:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:46,229 2898 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-11T19:38:46,229 | ^ 2021-07-11T19:38:51,616 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_external.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_external.o 2021-07-11T19:38:51,827 In file included from htslib/cram/cram.h:52, 2021-07-11T19:38:51,827 from htslib/cram/cram_external.c:44: 2021-07-11T19:38:51,827 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:38:51,828 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:51,828 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:38:51,828 | ^~ 2021-07-11T19:38:51,828 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:51,828 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:38:51,828 | ^ 2021-07-11T19:38:52,197 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_index.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_index.o 2021-07-11T19:38:52,464 In file included from htslib/cram/cram.h:52, 2021-07-11T19:38:52,465 from htslib/cram/cram_index.c:65: 2021-07-11T19:38:52,465 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:38:52,465 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:52,465 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:38:52,465 | ^~ 2021-07-11T19:38:52,466 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:52,466 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:38:52,466 | ^ 2021-07-11T19:38:52,476 htslib/cram/cram_index.c: In function ‘cram_index_build’: 2021-07-11T19:38:52,477 htslib/cram/cram_index.c:502:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] 2021-07-11T19:38:52,477 502 | off_t cpos, spos, hpos; 2021-07-11T19:38:52,478 | ^~~~ 2021-07-11T19:38:53,155 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_io.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_io.o 2021-07-11T19:38:53,410 In file included from htslib/cram/cram.h:52, 2021-07-11T19:38:53,410 from htslib/cram/cram_io.c:67: 2021-07-11T19:38:53,410 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:38:53,410 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:53,410 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:38:53,411 | ^~ 2021-07-11T19:38:53,411 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:53,411 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:38:53,411 | ^ 2021-07-11T19:38:53,481 In file included from htslib/cram/cram_io.h:48, 2021-07-11T19:38:53,482 from htslib/cram/cram.h:48, 2021-07-11T19:38:53,482 from htslib/cram/cram_io.c:67: 2021-07-11T19:38:53,482 htslib/cram/cram_io.c: In function ‘expand_cache_path’: 2021-07-11T19:38:53,482 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:38:53,483 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T19:38:53,483 | ^ 2021-07-11T19:38:53,483 htslib/cram/cram_io.c:2081:10: note: in expansion of macro ‘MIN’ 2021-07-11T19:38:53,483 2081 | l = MIN(l, strlen(fn)); 2021-07-11T19:38:53,483 | ^~~ 2021-07-11T19:38:53,484 htslib/cram/misc.h:103:36: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:38:53,484 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T19:38:53,484 | ^~~ 2021-07-11T19:38:53,484 htslib/cram/cram_io.c:2081:10: note: in expansion of macro ‘MIN’ 2021-07-11T19:38:53,484 2081 | l = MIN(l, strlen(fn)); 2021-07-11T19:38:53,484 | ^~~ 2021-07-11T19:38:53,607 In file included from htslib/cram/cram.h:48, 2021-07-11T19:38:53,607 from htslib/cram/cram_io.c:67: 2021-07-11T19:38:53,607 htslib/cram/cram_io.c: In function ‘cram_write_SAM_hdr’: 2021-07-11T19:38:53,608 htslib/cram/cram_io.h:269:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:53,609 269 | while((b)->alloc <= (l)) { \ 2021-07-11T19:38:53,609 | ^~ 2021-07-11T19:38:53,609 htslib/cram/cram_io.c:3983:6: note: in expansion of macro ‘BLOCK_RESIZE’ 2021-07-11T19:38:53,609 3983 | BLOCK_RESIZE(b, padded_length); 2021-07-11T19:38:53,609 | ^~~~~~~~~~~~ 2021-07-11T19:38:56,145 In file included from /usr/include/string.h:495, 2021-07-11T19:38:56,145 from htslib/cram/cram_io.c:53: 2021-07-11T19:38:56,145 In function ‘strncpy’, 2021-07-11T19:38:56,145 inlined from ‘cram_populate_ref’ at htslib/cram/cram_io.c:2229:2: 2021-07-11T19:38:56,145 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-11T19:38:56,145 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T19:38:56,146 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T19:38:56,146 htslib/cram/cram_io.c: In function ‘cram_populate_ref’: 2021-07-11T19:38:56,147 htslib/cram/cram_io.c:2337:27: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 2021-07-11T19:38:56,147 2337 | sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); 2021-07-11T19:38:56,147 | ^~~~~ 2021-07-11T19:38:56,147 In file included from /usr/include/stdio.h:867, 2021-07-11T19:38:56,147 from htslib/cram/cram_io.c:49: 2021-07-11T19:38:56,147 /usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 11 and 4134 bytes into a destination of size 4096 2021-07-11T19:38:56,148 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-11T19:38:56,148 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T19:38:56,148 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-11T19:38:56,148 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T19:38:57,506 In file included from /usr/include/string.h:495, 2021-07-11T19:38:57,506 from htslib/cram/cram_io.c:53: 2021-07-11T19:38:57,506 In function ‘strncpy’, 2021-07-11T19:38:57,506 inlined from ‘full_path’ at htslib/cram/cram_io.c:3807:6, 2021-07-11T19:38:57,506 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3882:3: 2021-07-11T19:38:57,506 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-11T19:38:57,507 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T19:38:57,507 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T19:38:57,507 In function ‘strncpy’, 2021-07-11T19:38:57,507 inlined from ‘full_path’ at htslib/cram/cram_io.c:3799:2, 2021-07-11T19:38:57,507 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3882:3: 2021-07-11T19:38:57,507 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-11T19:38:57,507 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T19:38:57,507 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T19:38:57,754 In function ‘strncpy’, 2021-07-11T19:38:57,755 inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4182:2: 2021-07-11T19:38:57,755 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 2021-07-11T19:38:57,755 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T19:38:57,755 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T19:38:58,424 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_samtools.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_samtools.o 2021-07-11T19:38:58,632 In file included from htslib/cram/cram.h:52, 2021-07-11T19:38:58,632 from htslib/cram/cram_samtools.c:37: 2021-07-11T19:38:58,632 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:38:58,632 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:58,632 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:38:58,633 | ^~ 2021-07-11T19:38:58,633 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:58,633 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:38:58,633 | ^ 2021-07-11T19:38:58,798 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/cram_stats.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_stats.o 2021-07-11T19:38:59,058 In file included from htslib/cram/cram.h:52, 2021-07-11T19:38:59,058 from htslib/cram/cram_stats.c:43: 2021-07-11T19:38:59,058 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:38:59,059 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:38:59,059 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:38:59,059 | ^~ 2021-07-11T19:38:59,059 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:38:59,059 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:38:59,059 | ^ 2021-07-11T19:38:59,428 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/files.c -o build/temp.linux-armv7l-3.9/htslib/cram/files.o 2021-07-11T19:38:59,615 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/mFILE.c -o build/temp.linux-armv7l-3.9/htslib/cram/mFILE.o 2021-07-11T19:38:59,772 htslib/cram/mFILE.c: In function ‘mfload’: 2021-07-11T19:38:59,773 htslib/cram/mFILE.c:103:47: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘__off_t’ {aka ‘long int’} [-Wsign-compare] 2021-07-11T19:38:59,773 103 | } while (!feof(fp) && (fn == NULL || used < sb.st_size)); 2021-07-11T19:38:59,773 | ^ 2021-07-11T19:38:59,777 htslib/cram/mFILE.c: In function ‘mftruncate’: 2021-07-11T19:38:59,777 htslib/cram/mFILE.c:476:31: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:38:59,778 476 | mf->size = offset != -1 ? offset : mf->offset; 2021-07-11T19:38:59,778 | ^~~~~~ 2021-07-11T19:39:00,213 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/open_trace_file.c -o build/temp.linux-armv7l-3.9/htslib/cram/open_trace_file.o 2021-07-11T19:39:00,368 In file included from htslib/cram/open_trace_file.c:79: 2021-07-11T19:39:00,368 htslib/cram/open_trace_file.c: In function ‘expand_path’: 2021-07-11T19:39:00,368 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-11T19:39:00,368 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T19:39:00,369 | ^ 2021-07-11T19:39:00,369 htslib/cram/open_trace_file.c:243:15: note: in expansion of macro ‘MIN’ 2021-07-11T19:39:00,369 243 | path_end += MIN(strlen(file), l); 2021-07-11T19:39:00,369 | ^~~ 2021-07-11T19:39:00,369 htslib/cram/misc.h:103:42: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:39:00,369 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T19:39:00,370 | ^~~ 2021-07-11T19:39:00,370 htslib/cram/open_trace_file.c:243:15: note: in expansion of macro ‘MIN’ 2021-07-11T19:39:00,370 243 | path_end += MIN(strlen(file), l); 2021-07-11T19:39:00,370 | ^~~ 2021-07-11T19:39:00,370 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-11T19:39:00,370 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T19:39:00,370 | ^ 2021-07-11T19:39:00,371 htslib/cram/open_trace_file.c:244:15: note: in expansion of macro ‘MIN’ 2021-07-11T19:39:00,371 244 | file += MIN(strlen(file), l); 2021-07-11T19:39:00,371 | ^~~ 2021-07-11T19:39:00,371 htslib/cram/misc.h:103:42: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:39:00,371 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T19:39:00,372 | ^~~ 2021-07-11T19:39:00,372 htslib/cram/open_trace_file.c:244:15: note: in expansion of macro ‘MIN’ 2021-07-11T19:39:00,372 244 | file += MIN(strlen(file), l); 2021-07-11T19:39:00,373 | ^~~ 2021-07-11T19:39:00,719 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/pooled_alloc.c -o build/temp.linux-armv7l-3.9/htslib/cram/pooled_alloc.o 2021-07-11T19:39:00,936 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/rANS_static.c -o build/temp.linux-armv7l-3.9/htslib/cram/rANS_static.o 2021-07-11T19:39:01,089 htslib/cram/rANS_static.c: In function ‘rans_compress_O0’: 2021-07-11T19:39:01,090 htslib/cram/rANS_static.c:86:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:39:01,090 86 | for (i = 0; i < in_size; i++) { 2021-07-11T19:39:01,090 | ^ 2021-07-11T19:39:01,094 htslib/cram/rANS_static.c: In function ‘rans_uncompress_O0’: 2021-07-11T19:39:01,094 htslib/cram/rANS_static.c:222:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:39:01,094 222 | if (in_sz != in_size-9) 2021-07-11T19:39:01,095 | ^~ 2021-07-11T19:39:01,099 htslib/cram/rANS_static.c: In function ‘rans_compress_O1’: 2021-07-11T19:39:01,099 htslib/cram/rANS_static.c:390:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:39:01,100 390 | for (last_i=i=0; ih, type, &new))) 2021-07-11T19:39:02,657 | ^~ 2021-07-11T19:39:02,659 htslib/cram/sam_header.c: In function ‘sam_hdr_vadd’: 2021-07-11T19:39:02,660 htslib/cram/sam_header.c:450:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:02,660 450 | if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new))) 2021-07-11T19:39:02,660 | ^~ 2021-07-11T19:39:02,668 htslib/cram/sam_header.c: In function ‘sam_hdr_rebuild’: 2021-07-11T19:39:02,668 htslib/cram/sam_header.c:821:24: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:39:02,668 821 | if (kh_key(hdr->h, k) == K("HD")) 2021-07-11T19:39:02,668 | ^~ 2021-07-11T19:39:04,690 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/string_alloc.c -o build/temp.linux-armv7l-3.9/htslib/cram/string_alloc.o 2021-07-11T19:39:04,917 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/thread_pool.c -o build/temp.linux-armv7l-3.9/htslib/cram/thread_pool.o 2021-07-11T19:39:05,416 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/vlen.c -o build/temp.linux-armv7l-3.9/htslib/cram/vlen.o 2021-07-11T19:39:05,552 htslib/cram/vlen.c: In function ‘vflen’: 2021-07-11T19:39:05,553 htslib/cram/vlen.c:77:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:05,553 77 | #define MAX(a,b) ((a)>(b)?(a):(b)) 2021-07-11T19:39:05,553 | ^ 2021-07-11T19:39:05,553 htslib/cram/vlen.c:239:10: note: in expansion of macro ‘MAX’ 2021-07-11T19:39:05,553 239 | len += MAX(conv_len1, i>=0x80 ?MB_CUR_MAX :1); 2021-07-11T19:39:05,553 | ^~~ 2021-07-11T19:39:05,554 htslib/cram/vlen.c:77:27: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:39:05,554 77 | #define MAX(a,b) ((a)>(b)?(a):(b)) 2021-07-11T19:39:05,554 | ^~~ 2021-07-11T19:39:05,554 htslib/cram/vlen.c:239:10: note: in expansion of macro ‘MAX’ 2021-07-11T19:39:05,554 239 | len += MAX(conv_len1, i>=0x80 ?MB_CUR_MAX :1); 2021-07-11T19:39:05,554 | ^~~ 2021-07-11T19:39:05,707 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/cram/zfio.c -o build/temp.linux-armv7l-3.9/htslib/cram/zfio.o 2021-07-11T19:39:06,002 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/errmod.c -o build/temp.linux-armv7l-3.9/htslib/errmod.o 2021-07-11T19:39:06,757 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/faidx.c -o build/temp.linux-armv7l-3.9/htslib/faidx.o 2021-07-11T19:39:08,076 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hfile.c -o build/temp.linux-armv7l-3.9/htslib/hfile.o 2021-07-11T19:39:08,292 htslib/hfile.c: In function ‘find_scheme_handler’: 2021-07-11T19:39:08,292 htslib/hfile.c:717:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:39:08,292 717 | for (i = 0; i < sizeof scheme; i++) 2021-07-11T19:39:08,292 | ^ 2021-07-11T19:39:08,293 htslib/hfile.c:723:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T19:39:08,293 723 | if (i == 0 || i >= sizeof scheme) return NULL; 2021-07-11T19:39:08,293 | ^~ 2021-07-11T19:39:09,061 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hfile_net.c -o build/temp.linux-armv7l-3.9/htslib/hfile_net.o 2021-07-11T19:39:09,255 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hts.c -o build/temp.linux-armv7l-3.9/htslib/hts.o 2021-07-11T19:39:09,491 In file included from htslib/cram/cram.h:52, 2021-07-11T19:39:09,491 from htslib/hts.c:39: 2021-07-11T19:39:09,491 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:39:09,491 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:39:09,492 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:39:09,492 | ^~ 2021-07-11T19:39:09,492 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:39:09,492 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:39:09,492 | ^ 2021-07-11T19:39:09,547 htslib/hts.c: In function ‘hts_idx_init’: 2021-07-11T19:39:09,547 htslib/hts.c:1222:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 2021-07-11T19:39:09,547 1222 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; 2021-07-11T19:39:09,548 | ^~~ 2021-07-11T19:39:09,549 htslib/hts.c: In function ‘update_loff’: 2021-07-11T19:39:09,550 htslib/hts.c:1256:34: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:39:09,550 1256 | if ( kh_key(bidx, k) < idx->n_bins ) 2021-07-11T19:39:09,550 | ^ 2021-07-11T19:39:09,551 htslib/hts.c: In function ‘compress_binning’: 2021-07-11T19:39:09,552 htslib/hts.c:1283:55: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:39:09,552 1283 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue; 2021-07-11T19:39:09,552 | ^~ 2021-07-11T19:39:09,554 htslib/hts.c:1308:51: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:39:09,554 1308 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue; 2021-07-11T19:39:09,554 | ^~ 2021-07-11T19:39:09,575 htslib/hts.c: In function ‘hts_idx_load_local’: 2021-07-11T19:39:09,575 htslib/hts.c:1618:43: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:09,576 1618 | if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail; 2021-07-11T19:39:09,576 | ^~ 2021-07-11T19:39:09,579 htslib/hts.c:1636:49: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:09,579 1636 | if (bgzf_read(fp, idx->meta + 28, x[7]) != x[7]) goto fail; 2021-07-11T19:39:09,580 | ^~ 2021-07-11T19:39:13,565 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/kfunc.c -o build/temp.linux-armv7l-3.9/htslib/kfunc.o 2021-07-11T19:39:14,000 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/knetfile.c -o build/temp.linux-armv7l-3.9/htslib/knetfile.o 2021-07-11T19:39:14,779 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/kstring.c -o build/temp.linux-armv7l-3.9/htslib/kstring.o 2021-07-11T19:39:14,906 htslib/kstring.c: In function ‘kvsprintf’: 2021-07-11T19:39:14,907 htslib/kstring.c:42:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:14,907 42 | if (l + 1 > s->m - s->l) { 2021-07-11T19:39:14,908 | ^ 2021-07-11T19:39:15,292 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/md5.c -o build/temp.linux-armv7l-3.9/htslib/md5.o 2021-07-11T19:39:15,858 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/probaln.c -o build/temp.linux-armv7l-3.9/htslib/probaln.o 2021-07-11T19:39:16,566 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/realn.c -o build/temp.linux-armv7l-3.9/htslib/realn.o 2021-07-11T19:39:17,254 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/regidx.c -o build/temp.linux-armv7l-3.9/htslib/regidx.o 2021-07-11T19:39:17,408 htslib/regidx.c: In function ‘regidx_insert’: 2021-07-11T19:39:17,408 htslib/regidx.c:155:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:17,409 155 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-11T19:39:17,409 | ^ 2021-07-11T19:39:17,409 htslib/regidx.c:155:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:17,409 155 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-11T19:39:17,409 | ^~ 2021-07-11T19:39:17,409 htslib/regidx.c:155:89: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:17,410 155 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-11T19:39:17,410 | ^ 2021-07-11T19:39:18,172 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/sam.c -o build/temp.linux-armv7l-3.9/htslib/sam.o 2021-07-11T19:39:18,398 In file included from htslib/cram/cram.h:52, 2021-07-11T19:39:18,398 from htslib/sam.c:35: 2021-07-11T19:39:18,399 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T19:39:18,399 htslib/cram/cram_codecs.h:162:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T19:39:18,399 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T19:39:18,399 | ^~ 2021-07-11T19:39:18,399 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:39:18,399 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T19:39:18,400 | ^ 2021-07-11T19:39:18,413 htslib/sam.c: In function ‘bam_hdr_read’: 2021-07-11T19:39:18,413 htslib/sam.c:147:15: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:18,413 147 | if (bytes != h->l_text) goto read_err; 2021-07-11T19:39:18,413 | ^~ 2021-07-11T19:39:18,421 htslib/sam.c: In function ‘bam_write1’: 2021-07-11T19:39:18,421 htslib/sam.c:467:32: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:39:18,422 467 | return ok? 4 + block_len : -1; 2021-07-11T19:39:18,422 | ^~ 2021-07-11T19:39:18,432 htslib/sam.c: In function ‘sam_hdr_write’: 2021-07-11T19:39:18,432 htslib/sam.c:818:67: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:18,432 818 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-11T19:39:18,433 | ^~ 2021-07-11T19:39:18,448 htslib/sam.c: In function ‘sam_format1’: 2021-07-11T19:39:18,448 htslib/sam.c:1181:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:18,448 1181 | if ((b->data + b->l_data - s) / sub_type_size < n) 2021-07-11T19:39:18,448 | ^ 2021-07-11T19:39:18,449 htslib/sam.c:1184:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:18,449 1184 | for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if" 2021-07-11T19:39:18,449 | ^ 2021-07-11T19:39:18,450 htslib/sam.c: In function ‘sam_write1’: 2021-07-11T19:39:18,451 htslib/sam.c:1220:59: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:18,451 1220 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-11T19:39:18,451 | ^~ 2021-07-11T19:39:18,659 In file included from /usr/include/string.h:495, 2021-07-11T19:39:18,659 from htslib/sam.c:30: 2021-07-11T19:39:18,659 In function ‘strncpy’, 2021-07-11T19:39:18,659 inlined from ‘bam_hdr_write’ at htslib/sam.c:229:5: 2021-07-11T19:39:18,659 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] 2021-07-11T19:39:18,660 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T19:39:18,660 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T19:39:23,994 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/synced_bcf_reader.c -o build/temp.linux-armv7l-3.9/htslib/synced_bcf_reader.o 2021-07-11T19:39:24,203 htslib/synced_bcf_reader.c: In function ‘_regions_add’: 2021-07-11T19:39:24,203 htslib/synced_bcf_reader.c:860:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:24,203 860 | if ( start < creg->regs[i].start ) max = i - 1; 2021-07-11T19:39:24,203 | ^ 2021-07-11T19:39:24,203 htslib/synced_bcf_reader.c:861:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:24,203 861 | else if ( start > creg->regs[i].start ) min = i + 1; 2021-07-11T19:39:24,204 | ^ 2021-07-11T19:39:24,204 htslib/synced_bcf_reader.c:864:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:39:24,204 864 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-11T19:39:24,204 | ^~ 2021-07-11T19:39:24,204 htslib/synced_bcf_reader.c:864:68: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:39:24,204 864 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-11T19:39:24,205 | ^~ 2021-07-11T19:39:26,194 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/tbx.c -o build/temp.linux-armv7l-3.9/htslib/tbx.o 2021-07-11T19:39:26,843 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/vcf.c -o build/temp.linux-armv7l-3.9/htslib/vcf.o 2021-07-11T19:39:27,047 htslib/vcf.c: In function ‘bcf_hdr_sync’: 2021-07-11T19:39:27,047 htslib/vcf.c:151:22: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,048 151 | if ( h->n[i] < kh_size(d) ) 2021-07-11T19:39:27,048 | ^ 2021-07-11T19:39:27,068 htslib/vcf.c: In function ‘bcf_hdr_read’: 2021-07-11T19:39:27,069 htslib/vcf.c:861:35: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,069 861 | if (bgzf_read(fp, htxt, hlen) != hlen) goto fail; 2021-07-11T19:39:27,069 | ^~ 2021-07-11T19:39:27,070 htslib/vcf.c: In function ‘bcf_hdr_write’: 2021-07-11T19:39:27,070 htslib/vcf.c:888:41: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,071 888 | if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1; 2021-07-11T19:39:27,071 | ^~ 2021-07-11T19:39:27,073 htslib/vcf.c: In function ‘bcf_read1_core’: 2021-07-11T19:39:27,073 htslib/vcf.c:972:49: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,074 972 | if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -1; 2021-07-11T19:39:27,074 | ^~ 2021-07-11T19:39:27,074 htslib/vcf.c:973:47: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,074 973 | if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -1; 2021-07-11T19:39:27,074 | ^~ 2021-07-11T19:39:27,086 htslib/vcf.c: In function ‘bcf_write’: 2021-07-11T19:39:27,086 htslib/vcf.c:1287:51: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,086 1287 | if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1; 2021-07-11T19:39:27,086 | ^~ 2021-07-11T19:39:27,087 htslib/vcf.c:1288:49: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,087 1288 | if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1; 2021-07-11T19:39:27,087 | ^~ 2021-07-11T19:39:27,102 htslib/vcf.c: In function ‘vcf_parse_format’: 2021-07-11T19:39:27,102 htslib/vcf.c:1680:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-11T19:39:27,102 1680 | if (fmt[j].max_l < l) fmt[j].max_l = l; 2021-07-11T19:39:27,103 | ^ 2021-07-11T19:39:27,106 htslib/vcf.c:1709:33: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:39:27,107 1709 | f->size = f->is_gt? f->max_g << 2 : f->max_l; 2021-07-11T19:39:27,107 | ^~~~~~~~~~~~~ 2021-07-11T19:39:27,144 htslib/vcf.c: In function ‘vcf_write_line’: 2021-07-11T19:39:27,145 htslib/vcf.c:2274:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,145 2274 | return ret==line->l ? 0 : -1; 2021-07-11T19:39:27,145 | ^~ 2021-07-11T19:39:27,146 htslib/vcf.c: In function ‘vcf_write’: 2021-07-11T19:39:27,147 htslib/vcf.c:2286:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,147 2286 | return ret==fp->line.l ? 0 : -1; 2021-07-11T19:39:27,147 | ^~ 2021-07-11T19:39:27,172 htslib/vcf.c: In function ‘bcf_hdr_set_samples’: 2021-07-11T19:39:27,173 htslib/vcf.c:2755:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T19:39:27,173 2755 | for (k = kh_begin(d); k != kh_end(d); ++k) 2021-07-11T19:39:27,174 | ^~ 2021-07-11T19:39:27,217 htslib/vcf.c: In function ‘_bcf1_sync_alleles’: 2021-07-11T19:39:27,218 htslib/vcf.c:3204:29: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-11T19:39:27,219 3204 | line->rlen = end_info ? end_info->v1.i : strlen(line->d.allele[0]); 2021-07-11T19:39:27,219 | ^~~~~~~~~~~~~~ 2021-07-11T19:39:27,229 htslib/vcf.c: In function ‘bcf_get_info_values’: 2021-07-11T19:39:27,230 htslib/vcf.c:3334:49: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-11T19:39:27,230 3334 | if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2; // expected different type 2021-07-11T19:39:27,231 | ^~ 2021-07-11T19:39:27,245 htslib/vcf.c: In function ‘bcf_get_format_values’: 2021-07-11T19:39:27,247 htslib/vcf.c:3456:53: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-11T19:39:27,247 3456 | else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2; // expected different type 2021-07-11T19:39:27,247 | ^~ 2021-07-11T19:39:35,570 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/vcf_sweep.c -o build/temp.linux-armv7l-3.9/htslib/vcf_sweep.o 2021-07-11T19:39:35,757 htslib/vcf_sweep.c: In function ‘bcf_sweep_fwd’: 2021-07-11T19:39:35,757 htslib/vcf_sweep.c:164:53: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T19:39:35,757 164 | if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size ) 2021-07-11T19:39:35,757 | ^ 2021-07-11T19:39:35,955 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/usr/local/lib/python3.9/dist-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/vcfutils.c -o build/temp.linux-armv7l-3.9/htslib/vcfutils.o 2021-07-11T19:39:38,042 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-3.9/cyvcf2/cyvcf2.o build/temp.linux-armv7l-3.9/cyvcf2/helpers.o build/temp.linux-armv7l-3.9/htslib/bgzf.o build/temp.linux-armv7l-3.9/htslib/cram/cram_codecs.o build/temp.linux-armv7l-3.9/htslib/cram/cram_decode.o build/temp.linux-armv7l-3.9/htslib/cram/cram_encode.o build/temp.linux-armv7l-3.9/htslib/cram/cram_external.o build/temp.linux-armv7l-3.9/htslib/cram/cram_index.o build/temp.linux-armv7l-3.9/htslib/cram/cram_io.o build/temp.linux-armv7l-3.9/htslib/cram/cram_samtools.o build/temp.linux-armv7l-3.9/htslib/cram/cram_stats.o build/temp.linux-armv7l-3.9/htslib/cram/files.o build/temp.linux-armv7l-3.9/htslib/cram/mFILE.o build/temp.linux-armv7l-3.9/htslib/cram/open_trace_file.o build/temp.linux-armv7l-3.9/htslib/cram/pooled_alloc.o build/temp.linux-armv7l-3.9/htslib/cram/rANS_static.o build/temp.linux-armv7l-3.9/htslib/cram/sam_header.o build/temp.linux-armv7l-3.9/htslib/cram/string_alloc.o build/temp.linux-armv7l-3.9/htslib/cram/thread_pool.o build/temp.linux-armv7l-3.9/htslib/cram/vlen.o build/temp.linux-armv7l-3.9/htslib/cram/zfio.o build/temp.linux-armv7l-3.9/htslib/errmod.o build/temp.linux-armv7l-3.9/htslib/faidx.o build/temp.linux-armv7l-3.9/htslib/hfile.o build/temp.linux-armv7l-3.9/htslib/hfile_net.o build/temp.linux-armv7l-3.9/htslib/hts.o build/temp.linux-armv7l-3.9/htslib/kfunc.o build/temp.linux-armv7l-3.9/htslib/knetfile.o build/temp.linux-armv7l-3.9/htslib/kstring.o build/temp.linux-armv7l-3.9/htslib/md5.o build/temp.linux-armv7l-3.9/htslib/probaln.o build/temp.linux-armv7l-3.9/htslib/realn.o build/temp.linux-armv7l-3.9/htslib/regidx.o build/temp.linux-armv7l-3.9/htslib/sam.o build/temp.linux-armv7l-3.9/htslib/synced_bcf_reader.o build/temp.linux-armv7l-3.9/htslib/tbx.o build/temp.linux-armv7l-3.9/htslib/vcf.o build/temp.linux-armv7l-3.9/htslib/vcf_sweep.o build/temp.linux-armv7l-3.9/htslib/vcfutils.o -lz -o build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so 2021-07-11T19:39:38,628 installing to build/bdist.linux-armv7l/wheel 2021-07-11T19:39:38,628 running install 2021-07-11T19:39:38,629 running install_lib 2021-07-11T19:39:38,633 creating build/bdist.linux-armv7l 2021-07-11T19:39:38,633 creating build/bdist.linux-armv7l/wheel 2021-07-11T19:39:38,636 creating build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T19:39:38,638 creating build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,639 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,642 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,661 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,663 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,666 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,668 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,675 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,678 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,681 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,685 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,687 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,689 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,693 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,696 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,698 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,700 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,703 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,706 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T19:39:38,708 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T19:39:38,832 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T19:39:38,835 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T19:39:38,837 copying build/lib.linux-armv7l-3.9/cyvcf2/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T19:39:38,839 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T19:39:38,841 copying build/lib.linux-armv7l-3.9/cyvcf2/relatedness.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T19:39:38,843 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T19:39:38,896 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T19:39:38,897 running install_egg_info 2021-07-11T19:39:38,908 Copying cyvcf2.egg-info to build/bdist.linux-armv7l/wheel/cyvcf2-0.5.5-py3.9.egg-info 2021-07-11T19:39:38,922 running install_scripts 2021-07-11T19:39:38,961 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-11T19:39:38,965 creating build/bdist.linux-armv7l/wheel/cyvcf2-0.5.5.dist-info/WHEEL 2021-07-11T19:39:38,968 creating '/tmp/pip-wheel-ac4sl253/cyvcf2-0.5.5-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-11T19:39:38,971 adding 'cyvcf2/__init__.py' 2021-07-11T19:39:39,140 adding 'cyvcf2/cyvcf2.c' 2021-07-11T19:39:40,344 adding 'cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so' 2021-07-11T19:39:40,391 adding 'cyvcf2/cyvcf2.pxd' 2021-07-11T19:39:40,398 adding 'cyvcf2/cyvcf2.pyx' 2021-07-11T19:39:40,399 adding 'cyvcf2/helpers.c' 2021-07-11T19:39:40,401 adding 'cyvcf2/helpers.h' 2021-07-11T19:39:40,403 adding 'cyvcf2/relatedness.h' 2021-07-11T19:39:40,405 adding 'cyvcf2/tests/__init__.py' 2021-07-11T19:39:40,407 adding 'cyvcf2/tests/__init__.pyc' 2021-07-11T19:39:40,408 adding 'cyvcf2/tests/bug.vcf.gz' 2021-07-11T19:39:40,414 adding 'cyvcf2/tests/o.vcf.gz' 2021-07-11T19:39:40,415 adding 'cyvcf2/tests/test-format-string.vcf' 2021-07-11T19:39:40,458 adding 'cyvcf2/tests/test-haploidX.vcf' 2021-07-11T19:39:40,465 adding 'cyvcf2/tests/test-hemi.vcf' 2021-07-11T19:39:40,467 adding 'cyvcf2/tests/test.comp_het.3.vcf' 2021-07-11T19:39:40,469 adding 'cyvcf2/tests/test.snpeff.bcf' 2021-07-11T19:39:40,471 adding 'cyvcf2/tests/test.snpeff.bcf.csi' 2021-07-11T19:39:40,473 adding 'cyvcf2/tests/test.snpeff.vcf' 2021-07-11T19:39:40,493 adding 'cyvcf2/tests/test.vcf.gz' 2021-07-11T19:39:40,496 adding 'cyvcf2/tests/test.vcf.gz.tbi' 2021-07-11T19:39:40,499 adding 'cyvcf2/tests/test_gt_bases.vcf.gz' 2021-07-11T19:39:40,500 adding 'cyvcf2/tests/test_hemi.py' 2021-07-11T19:39:40,502 adding 'cyvcf2/tests/test_hemi.pyc' 2021-07-11T19:39:40,505 adding 'cyvcf2/tests/test_reader.py' 2021-07-11T19:39:40,508 adding 'cyvcf2/tests/test_reader.pyc' 2021-07-11T19:39:40,511 adding 'cyvcf2-0.5.5.dist-info/LICENSE' 2021-07-11T19:39:40,512 adding 'cyvcf2-0.5.5.dist-info/METADATA' 2021-07-11T19:39:40,513 adding 'cyvcf2-0.5.5.dist-info/WHEEL' 2021-07-11T19:39:40,514 adding 'cyvcf2-0.5.5.dist-info/top_level.txt' 2021-07-11T19:39:40,515 adding 'cyvcf2-0.5.5.dist-info/RECORD' 2021-07-11T19:39:40,572 removing build/bdist.linux-armv7l/wheel 2021-07-11T19:39:41,079 Building wheel for cyvcf2 (setup.py): finished with status 'done' 2021-07-11T19:39:41,120 Created wheel for cyvcf2: filename=cyvcf2-0.5.5-cp39-cp39-linux_armv7l.whl size=2832864 sha256=55e61ff71fb450ed6f345e003611ade6246af73d0c9b80462dcf34eb07e20f58 2021-07-11T19:39:41,120 Stored in directory: /tmp/pip-ephem-wheel-cache-pj78qmid/wheels/a6/e2/45/78528aa496f442cd64176db346ba4246362b4fd7baf024d640 2021-07-11T19:39:41,132 Successfully built cyvcf2 2021-07-11T19:39:41,231 Removed build tracker: '/tmp/pip-req-tracker-f5x_aykg'