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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/) 2021-07-11T20:04:28,340 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 2021-07-11T20:04:28,340 Skipping link: not a file: https://pypi.org/simple/cyvcf2/ 2021-07-11T20:04:28,355 Given no hashes to check 1 links for project 'cyvcf2': discarding no candidates 2021-07-11T20:04:28,374 Collecting cyvcf2==0.6.1 2021-07-11T20:04:28,376 Created temporary directory: /tmp/pip-unpack-0cqfaxrq 2021-07-11T20:04:29,091 Downloading cyvcf2-0.6.1.tar.gz (963 kB) 2021-07-11T20:04:29,652 Added cyvcf2==0.6.1 from https://files.pythonhosted.org/packages/fd/cb/9c261f27fe3231f02d58afd43bed010e6c211afe9b37328076fa3134eade/cyvcf2-0.6.1.tar.gz#sha256=047b0695aeb1f4f52dc4697154990e66fdad7632c9c696b937c414925a847567 to build tracker '/tmp/pip-req-tracker-o9i39i9l' 2021-07-11T20:04:29,653 Running setup.py (path:/tmp/pip-wheel-fiq1m7b1/cyvcf2_52bd03e9d1a046d5b5f57133ada1bdaf/setup.py) egg_info for package cyvcf2 2021-07-11T20:04:29,653 Created temporary directory: /tmp/pip-pip-egg-info-rae3mld_ 2021-07-11T20:04:29,654 Running command python setup.py egg_info 2021-07-11T20:04:31,034 running egg_info 2021-07-11T20:04:31,036 creating /tmp/pip-pip-egg-info-rae3mld_/cyvcf2.egg-info 2021-07-11T20:04:31,037 writing /tmp/pip-pip-egg-info-rae3mld_/cyvcf2.egg-info/PKG-INFO 2021-07-11T20:04:31,040 writing dependency_links to /tmp/pip-pip-egg-info-rae3mld_/cyvcf2.egg-info/dependency_links.txt 2021-07-11T20:04:31,042 writing requirements to /tmp/pip-pip-egg-info-rae3mld_/cyvcf2.egg-info/requires.txt 2021-07-11T20:04:31,043 writing top-level names to /tmp/pip-pip-egg-info-rae3mld_/cyvcf2.egg-info/top_level.txt 2021-07-11T20:04:31,045 writing manifest file '/tmp/pip-pip-egg-info-rae3mld_/cyvcf2.egg-info/SOURCES.txt' 2021-07-11T20:04:31,190 reading manifest file '/tmp/pip-pip-egg-info-rae3mld_/cyvcf2.egg-info/SOURCES.txt' 2021-07-11T20:04:31,192 reading manifest template 'MANIFEST.in' 2021-07-11T20:04:31,203 adding license file 'LICENSE' 2021-07-11T20:04:31,209 writing manifest file '/tmp/pip-pip-egg-info-rae3mld_/cyvcf2.egg-info/SOURCES.txt' 2021-07-11T20:04:31,304 Source in /tmp/pip-wheel-fiq1m7b1/cyvcf2_52bd03e9d1a046d5b5f57133ada1bdaf has version 0.6.1, which satisfies requirement cyvcf2==0.6.1 from https://files.pythonhosted.org/packages/fd/cb/9c261f27fe3231f02d58afd43bed010e6c211afe9b37328076fa3134eade/cyvcf2-0.6.1.tar.gz#sha256=047b0695aeb1f4f52dc4697154990e66fdad7632c9c696b937c414925a847567 2021-07-11T20:04:31,305 Removed cyvcf2==0.6.1 from https://files.pythonhosted.org/packages/fd/cb/9c261f27fe3231f02d58afd43bed010e6c211afe9b37328076fa3134eade/cyvcf2-0.6.1.tar.gz#sha256=047b0695aeb1f4f52dc4697154990e66fdad7632c9c696b937c414925a847567 from build tracker '/tmp/pip-req-tracker-o9i39i9l' 2021-07-11T20:04:31,309 Created temporary directory: /tmp/pip-unpack-yagk1n00 2021-07-11T20:04:31,309 Building wheels for collected packages: cyvcf2 2021-07-11T20:04:31,313 Created temporary directory: /tmp/pip-wheel-mxdotxxv 2021-07-11T20:04:31,314 Building wheel for cyvcf2 (setup.py): started 2021-07-11T20:04:31,314 Destination directory: /tmp/pip-wheel-mxdotxxv 2021-07-11T20:04:31,314 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-fiq1m7b1/cyvcf2_52bd03e9d1a046d5b5f57133ada1bdaf/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-fiq1m7b1/cyvcf2_52bd03e9d1a046d5b5f57133ada1bdaf/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-mxdotxxv 2021-07-11T20:04:32,753 running bdist_wheel 2021-07-11T20:04:32,756 The [wheel] section is deprecated. Use [bdist_wheel] instead. 2021-07-11T20:04:32,758 running build 2021-07-11T20:04:32,758 running build_py 2021-07-11T20:04:32,894 creating build 2021-07-11T20:04:32,895 creating build/lib.linux-armv7l-3.9 2021-07-11T20:04:32,895 creating build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T20:04:32,896 copying cyvcf2/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T20:04:32,899 creating build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:32,899 copying cyvcf2/tests/test_reader.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:32,902 copying cyvcf2/tests/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:32,903 copying cyvcf2/tests/test_hemi.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:32,905 running egg_info 2021-07-11T20:04:32,918 writing cyvcf2.egg-info/PKG-INFO 2021-07-11T20:04:32,920 writing dependency_links to cyvcf2.egg-info/dependency_links.txt 2021-07-11T20:04:32,922 writing requirements to cyvcf2.egg-info/requires.txt 2021-07-11T20:04:32,923 writing top-level names to cyvcf2.egg-info/top_level.txt 2021-07-11T20:04:32,931 reading manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-11T20:04:32,936 reading manifest template 'MANIFEST.in' 2021-07-11T20:04:32,946 adding license file 'LICENSE' 2021-07-11T20:04:32,955 writing manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-11T20:04:32,961 copying cyvcf2/cyvcf2.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T20:04:33,024 copying cyvcf2/cyvcf2.pxd -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T20:04:33,027 copying cyvcf2/cyvcf2.pyx -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T20:04:33,031 copying cyvcf2/helpers.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T20:04:33,033 copying cyvcf2/helpers.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T20:04:33,035 copying cyvcf2/relatedness.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-11T20:04:33,038 copying cyvcf2/tests/__init__.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,041 copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,044 copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,049 copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,052 copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,070 copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,073 copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,077 copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,080 copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,083 copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,086 copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,094 copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,096 copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,100 copying cyvcf2/tests/test_hemi.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,102 copying cyvcf2/tests/test_reader.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-11T20:04:33,107 running build_ext 2021-07-11T20:04:33,176 cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c 2021-07-11T20:04:33,803 /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-fiq1m7b1/cyvcf2_52bd03e9d1a046d5b5f57133ada1bdaf/cyvcf2/cyvcf2.pxd 2021-07-11T20:04:33,804 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-11T20:04:35,192 warning: cyvcf2/cyvcf2.pxd:24:16: Declarations should not be declared inline. 2021-07-11T20:04:44,967 building 'cyvcf2.cyvcf2' extension 2021-07-11T20:04:44,969 creating build/temp.linux-armv7l-3.9 2021-07-11T20:04:44,969 creating build/temp.linux-armv7l-3.9/cyvcf2 2021-07-11T20:04:44,970 creating build/temp.linux-armv7l-3.9/htslib 2021-07-11T20:04:44,971 creating build/temp.linux-armv7l-3.9/htslib/cram 2021-07-11T20:04:44,973 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 2021-07-11T20:04:45,379 In file included from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-11T20:04:45,379 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-11T20:04:45,379 from /usr/local/lib/python3.9/dist-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-11T20:04:45,380 from cyvcf2/cyvcf2.c:613: 2021-07-11T20:04:45,380 /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] 2021-07-11T20:04:45,380 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-11T20:04:45,380 | ^~~~~~~ 2021-07-11T20:04:45,596 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_2add_to_header’: 2021-07-11T20:04:45,600 cyvcf2/cyvcf2.c:7484:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:45,600 7484 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); 2021-07-11T20:04:45,600 | ~~~~~~~~~~~~^~~~~ 2021-07-11T20:04:45,601 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T20:04:45,601 htslib/htslib/vcf.h:441:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T20:04:45,601 441 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-11T20:04:45,601 | ~~~~~~~~~~~^ 2021-07-11T20:04:45,604 cyvcf2/cyvcf2.c:7526:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:45,605 7526 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-11T20:04:45,605 | ~~~~~~~~~~~~^~~~~ 2021-07-11T20:04:45,605 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T20:04:45,605 htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T20:04:45,605 477 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-11T20:04:45,605 | ~~~~~~~~~~~^ 2021-07-11T20:04:45,613 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10set_samples’: 2021-07-11T20:04:45,617 cyvcf2/cyvcf2.c:8050:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:45,617 8050 | __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); 2021-07-11T20:04:45,617 | ~~~~~~~~~~~~^~~~~ 2021-07-11T20:04:45,618 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T20:04:45,618 htslib/htslib/vcf.h:313:40: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T20:04:45,618 313 | int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); 2021-07-11T20:04:45,618 | ~~~~~~~~~~~^~~ 2021-07-11T20:04:45,626 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12update’: 2021-07-11T20:04:45,630 cyvcf2/cyvcf2.c:8341:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:45,630 8341 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); 2021-07-11T20:04:45,630 | ~~~~~~~~~~~~^~~~~ 2021-07-11T20:04:45,630 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T20:04:45,630 htslib/htslib/vcf.h:441:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T20:04:45,631 441 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-11T20:04:45,631 | ~~~~~~~~~~~^ 2021-07-11T20:04:45,635 cyvcf2/cyvcf2.c:8394:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:45,635 8394 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-11T20:04:45,635 | ~~~~~~~~~~~~^~~~~ 2021-07-11T20:04:45,636 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T20:04:45,636 htslib/htslib/vcf.h:477:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T20:04:45,636 477 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-11T20:04:45,636 | ~~~~~~~~~~~^ 2021-07-11T20:04:45,638 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_16generator’: 2021-07-11T20:04:45,640 cyvcf2/cyvcf2.c:8608:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:45,640 8608 | __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); 2021-07-11T20:04:45,641 htslib/htslib/vcf.h:762:103: note: in definition of macro ‘bcf_itr_querys’ 2021-07-11T20:04:45,641 762 | #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) 2021-07-11T20:04:45,641 | ^~~ 2021-07-11T20:04:45,641 In file included from cyvcf2/cyvcf2.c:624: 2021-07-11T20:04:45,641 htslib/htslib/hts.h:534:97: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T20:04:45,641 534 | 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); 2021-07-11T20:04:45,642 | ~~~~~~^~~ 2021-07-11T20:04:45,662 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_22generator2’: 2021-07-11T20:04:45,667 cyvcf2/cyvcf2.c:9795:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:45,667 9795 | __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, 287, __pyx_L1_error) 2021-07-11T20:04:45,667 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-11T20:04:45,668 cyvcf2/cyvcf2.c:2913:107: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T20:04:45,669 2913 | static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ 2021-07-11T20:04:45,669 | ^~~~~~~~~~~ 2021-07-11T20:04:45,721 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_29__dealloc__’: 2021-07-11T20:04:45,727 cyvcf2/cyvcf2.c:11052:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:45,727 11052 | bcf_hdr_destroy(__pyx_v_self->hdr); 2021-07-11T20:04:45,727 | ~~~~~~~~~~~~^~~~~ 2021-07-11T20:04:45,727 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T20:04:45,727 htslib/htslib/vcf.h:259:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T20:04:45,728 259 | void bcf_hdr_destroy(bcf_hdr_t *h); 2021-07-11T20:04:45,728 | ~~~~~~~~~~~^ 2021-07-11T20:04:45,730 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: 2021-07-11T20:04:45,736 cyvcf2/cyvcf2.c:11514:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 2021-07-11T20:04:45,736 11514 | __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); 2021-07-11T20:04:45,736 | ^~~~~~~~~ 2021-07-11T20:04:45,736 In file included from cyvcf2/cyvcf2.c:626: 2021-07-11T20:04:45,736 htslib/htslib/vcf.h:437:11: note: declared here 2021-07-11T20:04:45,736 437 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) 2021-07-11T20:04:45,737 | ^~~~~~~~~~~~~~~~ 2021-07-11T20:04:45,740 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: 2021-07-11T20:04:45,742 cyvcf2/cyvcf2.c:11729:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:45,742 11729 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-11T20:04:45,742 htslib/htslib/vcf.h:765:112: note: in definition of macro ‘bcf_index_seqnames’ 2021-07-11T20:04:45,743 765 | #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) 2021-07-11T20:04:45,743 | ^~~ 2021-07-11T20:04:45,743 In file included from cyvcf2/cyvcf2.c:624: 2021-07-11T20:04:45,743 htslib/htslib/hts.h:536:92: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-11T20:04:45,743 536 | 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 2021-07-11T20:04:45,743 | ~~~~~~^~~ 2021-07-11T20:04:45,749 cyvcf2/cyvcf2.c:11729:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-11T20:04:45,749 11729 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-11T20:04:45,749 | ^ 2021-07-11T20:04:45,759 cyvcf2/cyvcf2.c:11893:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-11T20:04:45,759 11893 | __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); 2021-07-11T20:04:45,759 | ^ 2021-07-11T20:04:45,765 cyvcf2/cyvcf2.c:11923:20: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-11T20:04:45,765 11923 | __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-11T20:04:45,765 | ^ 2021-07-11T20:04:46,288 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’: 2021-07-11T20:04:46,299 cyvcf2/cyvcf2.c:21286:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:04:46,299 21286 | for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) { 2021-07-11T20:04:46,299 | ^ 2021-07-11T20:04:46,544 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’: 2021-07-11T20:04:46,558 cyvcf2/cyvcf2.c:28262:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:04:46,559 28262 | for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-07-11T20:04:46,559 | ^ 2021-07-11T20:04:46,560 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’: 2021-07-11T20:04:46,574 cyvcf2/cyvcf2.c:28357:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:04:46,574 28357 | for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2021-07-11T20:04:46,575 | ^ 2021-07-11T20:04:46,582 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’: 2021-07-11T20:04:46,596 cyvcf2/cyvcf2.c:28572:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:04:46,597 28572 | for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2021-07-11T20:04:46,597 | ^ 2021-07-11T20:04:46,612 cyvcf2/cyvcf2.c:28630:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-11T20:04:46,612 28630 | __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0); 2021-07-11T20:04:46,613 | ^~ 2021-07-11T20:04:46,635 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: 2021-07-11T20:04:46,651 cyvcf2/cyvcf2.c:30607:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:46,651 30607 | __pyx_v_h = __pyx_t_6; 2021-07-11T20:04:46,651 | ^ 2021-07-11T20:04:46,721 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_10__next__’: 2021-07-11T20:04:46,738 cyvcf2/cyvcf2.c:33242:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:46,738 33242 | __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); 2021-07-11T20:04:46,738 | ^ 2021-07-11T20:04:46,746 cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: 2021-07-11T20:04:46,764 cyvcf2/cyvcf2.c:34235:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:46,764 34235 | __pyx_v_i->hdr = __pyx_t_4; 2021-07-11T20:04:46,764 | ^ 2021-07-11T20:04:46,777 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: 2021-07-11T20:04:46,795 cyvcf2/cyvcf2.c:34631:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-11T20:04:46,795 34631 | __pyx_v_h = __pyx_t_3; 2021-07-11T20:04:46,795 | ^ 2021-07-11T20:04:50,155 At top level: 2021-07-11T20:04:50,159 cyvcf2/cyvcf2.c:6455:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] 2021-07-11T20:04:50,159 6455 | static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { 2021-07-11T20:04:50,159 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:05:14,545 cyvcf2/cyvcf2.c: In function ‘__pyx_getprop_6cyvcf2_6cyvcf2_3VCF_seqnames’: 2021-07-11T20:05:14,551 cyvcf2/cyvcf2.c:11575:10: warning: ‘__pyx_v_cnames’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2021-07-11T20:05:14,551 11575 | char **__pyx_v_cnames; 2021-07-11T20:05:14,551 | ^~~~~~~~~~~~~~ 2021-07-11T20:05:39,832 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 2021-07-11T20:05:40,125 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 2021-07-11T20:05:40,328 htslib/bgzf.c: In function ‘bgzf_read’: 2021-07-11T20:05:40,329 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] 2021-07-11T20:05:40,329 691 | while (bytes_read < length) { 2021-07-11T20:05:40,329 | ^ 2021-07-11T20:05:40,329 htslib/bgzf.c:706:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:40,329 706 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-11T20:05:40,329 | ^ 2021-07-11T20:05:40,330 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] 2021-07-11T20:05:40,330 706 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-11T20:05:40,330 | ^~~~~~~~~ 2021-07-11T20:05:40,352 htslib/bgzf.c: In function ‘bgzf_useek’: 2021-07-11T20:05:40,352 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] 2021-07-11T20:05:40,352 1301 | if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1; 2021-07-11T20:05:40,352 | ^ 2021-07-11T20:05:40,353 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] 2021-07-11T20:05:40,353 1302 | else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1; 2021-07-11T20:05:40,353 | ^~ 2021-07-11T20:05:42,050 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 2021-07-11T20:05:42,258 In file included from htslib/cram/cram.h:52, 2021-07-11T20:05:42,258 from htslib/cram/cram_codecs.c:43: 2021-07-11T20:05:42,258 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:05:42,258 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] 2021-07-11T20:05:42,258 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:05:42,259 | ^~ 2021-07-11T20:05:42,259 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:42,259 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:05:42,259 | ^ 2021-07-11T20:05:42,261 htslib/cram/cram_codecs.c: In function ‘get_one_bits_MSB’: 2021-07-11T20:05:42,261 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] 2021-07-11T20:05:42,261 77 | if (block->byte >= block->uncomp_size) 2021-07-11T20:05:42,262 | ^~ 2021-07-11T20:05:42,262 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] 2021-07-11T20:05:42,262 84 | if (block->byte == block->uncomp_size && (b&1)) 2021-07-11T20:05:42,262 | ^~ 2021-07-11T20:05:42,262 htslib/cram/cram_codecs.c: In function ‘get_zero_bits_MSB’: 2021-07-11T20:05:42,262 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] 2021-07-11T20:05:42,263 95 | if (block->byte >= block->uncomp_size) 2021-07-11T20:05:42,263 | ^~ 2021-07-11T20:05:42,263 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] 2021-07-11T20:05:42,263 102 | if (block->byte == block->uncomp_size && !(b&1)) 2021-07-11T20:05:42,263 | ^~ 2021-07-11T20:05:42,274 htslib/cram/cram_codecs.c: In function ‘cram_beta_decode_init’: 2021-07-11T20:05:42,274 htslib/cram/cram_codecs.c:544:47: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:05:42,274 544 | || c->beta.nbits < 0 || c->beta.nbits > 8 * sizeof(int)) { 2021-07-11T20:05:42,274 | ^ 2021-07-11T20:05:42,306 htslib/cram/cram_codecs.c: In function ‘cram_byte_array_stop_decode_block’: 2021-07-11T20:05:42,306 htslib/cram/cram_codecs.c:1587:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:42,306 1587 | if (cp_end - cp < out->alloc - out->byte) { 2021-07-11T20:05:42,307 | ^ 2021-07-11T20:05:44,671 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 2021-07-11T20:05:44,936 In file included from htslib/cram/cram.h:52, 2021-07-11T20:05:44,937 from htslib/cram/cram_decode.c:48: 2021-07-11T20:05:44,937 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:05:44,937 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] 2021-07-11T20:05:44,938 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:05:44,938 | ^~ 2021-07-11T20:05:44,938 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:44,938 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:05:44,939 | ^ 2021-07-11T20:05:44,944 htslib/cram/cram_decode.c: In function ‘cram_decode_TD’: 2021-07-11T20:05:44,944 htslib/cram/cram_decode.c:101:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:44,944 101 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-11T20:05:44,944 | ^ 2021-07-11T20:05:44,945 htslib/cram/cram_decode.c:113:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:44,945 113 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-11T20:05:44,945 | ^ 2021-07-11T20:05:44,964 htslib/cram/cram_decode.c: In function ‘cram_dependent_data_series’: 2021-07-11T20:05:44,965 htslib/cram/cram_decode.c:794:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:05:44,965 794 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-11T20:05:44,965 | ^ 2021-07-11T20:05:44,967 htslib/cram/cram_decode.c:886:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:05:44,968 886 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-11T20:05:44,968 | ^ 2021-07-11T20:05:44,972 htslib/cram/cram_decode.c: In function ‘cram_decode_slice_header’: 2021-07-11T20:05:44,973 htslib/cram/cram_decode.c:1102:23: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:05:44,973 1102 | hdr->num_content_ids >= SIZE_MAX / sizeof(int32_t)) { 2021-07-11T20:05:44,973 | ^~ 2021-07-11T20:05:44,978 htslib/cram/cram_decode.c: In function ‘cram_decode_seq’: 2021-07-11T20:05:44,979 htslib/cram/cram_decode.c:1275:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:44,979 1275 | if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) { 2021-07-11T20:05:44,979 | ^ 2021-07-11T20:05:44,984 htslib/cram/cram_decode.c:1425:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:44,984 1425 | if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-11T20:05:44,984 | ^~ 2021-07-11T20:05:44,988 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] 2021-07-11T20:05:44,988 1469 | if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) { 2021-07-11T20:05:44,988 | ^~ 2021-07-11T20:05:44,990 htslib/cram/cram_decode.c:1480:33: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:44,990 1480 | if (bfd->ref[cr->ref_id].len >= ref_pos) { 2021-07-11T20:05:44,990 | ^~ 2021-07-11T20:05:44,996 htslib/cram/cram_decode.c:1573:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:44,996 1573 | if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-11T20:05:44,996 | ^~ 2021-07-11T20:05:44,999 htslib/cram/cram_decode.c:1644:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:45,000 1644 | if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-11T20:05:45,000 | ^~ 2021-07-11T20:05:45,005 htslib/cram/cram_decode.c:1748:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:45,006 1748 | if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) { 2021-07-11T20:05:45,006 | ^ 2021-07-11T20:05:45,030 htslib/cram/cram_decode.c: In function ‘cram_decode_slice’: 2021-07-11T20:05:45,031 htslib/cram/cram_decode.c:2367:6: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:05:45,031 2367 | bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap)) 2021-07-11T20:05:45,031 | ^~ 2021-07-11T20:05:50,530 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 2021-07-11T20:05:50,789 In file included from htslib/cram/cram.h:52, 2021-07-11T20:05:50,790 from htslib/cram/cram_encode.c:43: 2021-07-11T20:05:50,790 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:05:50,790 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] 2021-07-11T20:05:50,790 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:05:50,790 | ^~ 2021-07-11T20:05:50,791 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:50,791 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:05:50,791 | ^ 2021-07-11T20:05:50,839 htslib/cram/cram_encode.c: In function ‘lossy_read_names’: 2021-07-11T20:05:50,840 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] 2021-07-11T20:05:50,840 1297 | if (u.e != e) { 2021-07-11T20:05:50,840 | ^~ 2021-07-11T20:05:50,841 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] 2021-07-11T20:05:50,841 1327 | if (kh_val(names, k) == -1) 2021-07-11T20:05:50,841 | ^~ 2021-07-11T20:05:50,883 htslib/cram/cram_encode.c: In function ‘process_one_read’: 2021-07-11T20:05:50,885 htslib/cram/cram_encode.c:2650:10: warning: unused variable ‘brg’ [-Wunused-variable] 2021-07-11T20:05:50,885 2650 | SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); 2021-07-11T20:05:50,885 | ^~~ 2021-07-11T20:05:50,889 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] 2021-07-11T20:05:50,889 2758 | while (cr->cigar + cr->ncigar >= s->cigar_alloc) { 2021-07-11T20:05:50,890 | ^~ 2021-07-11T20:05:50,891 htslib/cram/cram_encode.c:2788:30: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:50,891 2788 | int end = cig_len+apos < c->ref_end 2021-07-11T20:05:50,891 | ^ 2021-07-11T20:05:50,892 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] 2021-07-11T20:05:50,892 2789 | ? cig_len : c->ref_end - apos; 2021-07-11T20:05:50,893 | ^~~~~~~~~~~~~~~~~ 2021-07-11T20:05:50,896 htslib/cram/cram_encode.c:2831:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:50,896 2831 | if (l < cig_len && cr->len) { 2021-07-11T20:05:50,896 | ^ 2021-07-11T20:05:50,898 htslib/cram/cram_encode.c:2839:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:50,898 2839 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-11T20:05:50,898 | ^ 2021-07-11T20:05:50,899 htslib/cram/cram_encode.c:2847:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:50,900 2847 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-11T20:05:50,900 | ^ 2021-07-11T20:05:50,903 htslib/cram/cram_encode.c:2878:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:50,904 2878 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-11T20:05:50,904 | ^ 2021-07-11T20:05:50,906 htslib/cram/cram_encode.c:2894:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:50,906 2894 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-11T20:05:50,906 | ^ 2021-07-11T20:05:50,907 htslib/cram/cram_encode.c:2898:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:50,907 2898 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-11T20:05:50,907 | ^ 2021-07-11T20:05:56,293 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 2021-07-11T20:05:56,498 In file included from htslib/cram/cram.h:52, 2021-07-11T20:05:56,498 from htslib/cram/cram_external.c:44: 2021-07-11T20:05:56,499 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:05:56,499 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] 2021-07-11T20:05:56,499 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:05:56,499 | ^~ 2021-07-11T20:05:56,499 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:56,500 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:05:56,500 | ^ 2021-07-11T20:05:56,875 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 2021-07-11T20:05:57,139 In file included from htslib/cram/cram.h:52, 2021-07-11T20:05:57,139 from htslib/cram/cram_index.c:65: 2021-07-11T20:05:57,139 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:05:57,139 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] 2021-07-11T20:05:57,139 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:05:57,140 | ^~ 2021-07-11T20:05:57,140 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:57,140 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:05:57,140 | ^ 2021-07-11T20:05:57,150 htslib/cram/cram_index.c: In function ‘cram_index_build’: 2021-07-11T20:05:57,151 htslib/cram/cram_index.c:502:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] 2021-07-11T20:05:57,151 502 | off_t cpos, spos, hpos; 2021-07-11T20:05:57,152 | ^~~~ 2021-07-11T20:05:57,823 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 2021-07-11T20:05:58,081 In file included from htslib/cram/cram.h:52, 2021-07-11T20:05:58,081 from htslib/cram/cram_io.c:67: 2021-07-11T20:05:58,081 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:05:58,082 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] 2021-07-11T20:05:58,082 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:05:58,082 | ^~ 2021-07-11T20:05:58,083 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:58,083 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:05:58,083 | ^ 2021-07-11T20:05:58,154 In file included from htslib/cram/cram_io.h:48, 2021-07-11T20:05:58,154 from htslib/cram/cram.h:48, 2021-07-11T20:05:58,154 from htslib/cram/cram_io.c:67: 2021-07-11T20:05:58,154 htslib/cram/cram_io.c: In function ‘expand_cache_path’: 2021-07-11T20:05:58,155 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:05:58,155 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T20:05:58,155 | ^ 2021-07-11T20:05:58,156 htslib/cram/cram_io.c:2081:10: note: in expansion of macro ‘MIN’ 2021-07-11T20:05:58,156 2081 | l = MIN(l, strlen(fn)); 2021-07-11T20:05:58,156 | ^~~ 2021-07-11T20:05:58,156 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] 2021-07-11T20:05:58,156 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T20:05:58,157 | ^~~ 2021-07-11T20:05:58,157 htslib/cram/cram_io.c:2081:10: note: in expansion of macro ‘MIN’ 2021-07-11T20:05:58,157 2081 | l = MIN(l, strlen(fn)); 2021-07-11T20:05:58,157 | ^~~ 2021-07-11T20:05:58,279 In file included from htslib/cram/cram.h:48, 2021-07-11T20:05:58,280 from htslib/cram/cram_io.c:67: 2021-07-11T20:05:58,280 htslib/cram/cram_io.c: In function ‘cram_write_SAM_hdr’: 2021-07-11T20:05:58,281 htslib/cram/cram_io.h:269:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:05:58,281 269 | while((b)->alloc <= (l)) { \ 2021-07-11T20:05:58,281 | ^~ 2021-07-11T20:05:58,282 htslib/cram/cram_io.c:3983:6: note: in expansion of macro ‘BLOCK_RESIZE’ 2021-07-11T20:05:58,282 3983 | BLOCK_RESIZE(b, padded_length); 2021-07-11T20:05:58,282 | ^~~~~~~~~~~~ 2021-07-11T20:06:00,819 In file included from /usr/include/string.h:495, 2021-07-11T20:06:00,820 from htslib/cram/cram_io.c:53: 2021-07-11T20:06:00,820 In function ‘strncpy’, 2021-07-11T20:06:00,820 inlined from ‘cram_populate_ref’ at htslib/cram/cram_io.c:2229:2: 2021-07-11T20:06:00,820 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-11T20:06:00,820 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T20:06:00,820 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:06:00,820 htslib/cram/cram_io.c: In function ‘cram_populate_ref’: 2021-07-11T20:06:00,821 htslib/cram/cram_io.c:2337:27: warning: ‘.tmp_’ directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 2021-07-11T20:06:00,822 2337 | sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t); 2021-07-11T20:06:00,822 | ^~~~~ 2021-07-11T20:06:00,822 In file included from /usr/include/stdio.h:867, 2021-07-11T20:06:00,822 from htslib/cram/cram_io.c:49: 2021-07-11T20:06:00,822 /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 2021-07-11T20:06:00,822 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, 2021-07-11T20:06:00,822 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:06:00,823 37 | __bos (__s), __fmt, __va_arg_pack ()); 2021-07-11T20:06:00,823 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:06:02,217 In file included from /usr/include/string.h:495, 2021-07-11T20:06:02,217 from htslib/cram/cram_io.c:53: 2021-07-11T20:06:02,217 In function ‘strncpy’, 2021-07-11T20:06:02,217 inlined from ‘full_path’ at htslib/cram/cram_io.c:3807:6, 2021-07-11T20:06:02,217 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3882:3: 2021-07-11T20:06:02,217 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-11T20:06:02,218 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T20:06:02,218 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:06:02,218 In function ‘strncpy’, 2021-07-11T20:06:02,218 inlined from ‘full_path’ at htslib/cram/cram_io.c:3799:2, 2021-07-11T20:06:02,218 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3882:3: 2021-07-11T20:06:02,218 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-11T20:06:02,218 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T20:06:02,218 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:06:02,464 In function ‘strncpy’, 2021-07-11T20:06:02,465 inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4182:2: 2021-07-11T20:06:02,465 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 2021-07-11T20:06:02,465 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T20:06:02,465 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:06:03,132 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 2021-07-11T20:06:03,335 In file included from htslib/cram/cram.h:52, 2021-07-11T20:06:03,335 from htslib/cram/cram_samtools.c:37: 2021-07-11T20:06:03,335 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:06:03,336 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] 2021-07-11T20:06:03,336 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:06:03,336 | ^~ 2021-07-11T20:06:03,336 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:03,336 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:06:03,337 | ^ 2021-07-11T20:06:03,503 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 2021-07-11T20:06:03,766 In file included from htslib/cram/cram.h:52, 2021-07-11T20:06:03,766 from htslib/cram/cram_stats.c:43: 2021-07-11T20:06:03,766 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:06:03,767 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] 2021-07-11T20:06:03,767 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:06:03,767 | ^~ 2021-07-11T20:06:03,767 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:03,767 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:06:03,767 | ^ 2021-07-11T20:06:04,136 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 2021-07-11T20:06:04,325 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 2021-07-11T20:06:04,482 htslib/cram/mFILE.c: In function ‘mfload’: 2021-07-11T20:06:04,482 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] 2021-07-11T20:06:04,482 103 | } while (!feof(fp) && (fn == NULL || used < sb.st_size)); 2021-07-11T20:06:04,483 | ^ 2021-07-11T20:06:04,487 htslib/cram/mFILE.c: In function ‘mftruncate’: 2021-07-11T20:06:04,487 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] 2021-07-11T20:06:04,487 476 | mf->size = offset != -1 ? offset : mf->offset; 2021-07-11T20:06:04,487 | ^~~~~~ 2021-07-11T20:06:04,931 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 2021-07-11T20:06:05,086 In file included from htslib/cram/open_trace_file.c:79: 2021-07-11T20:06:05,086 htslib/cram/open_trace_file.c: In function ‘expand_path’: 2021-07-11T20:06:05,087 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-11T20:06:05,087 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T20:06:05,087 | ^ 2021-07-11T20:06:05,087 htslib/cram/open_trace_file.c:243:15: note: in expansion of macro ‘MIN’ 2021-07-11T20:06:05,087 243 | path_end += MIN(strlen(file), l); 2021-07-11T20:06:05,087 | ^~~ 2021-07-11T20:06:05,088 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] 2021-07-11T20:06:05,088 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T20:06:05,088 | ^~~ 2021-07-11T20:06:05,088 htslib/cram/open_trace_file.c:243:15: note: in expansion of macro ‘MIN’ 2021-07-11T20:06:05,088 243 | path_end += MIN(strlen(file), l); 2021-07-11T20:06:05,088 | ^~~ 2021-07-11T20:06:05,089 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-11T20:06:05,089 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T20:06:05,089 | ^ 2021-07-11T20:06:05,089 htslib/cram/open_trace_file.c:244:15: note: in expansion of macro ‘MIN’ 2021-07-11T20:06:05,089 244 | file += MIN(strlen(file), l); 2021-07-11T20:06:05,089 | ^~~ 2021-07-11T20:06:05,089 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] 2021-07-11T20:06:05,090 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-11T20:06:05,090 | ^~~ 2021-07-11T20:06:05,090 htslib/cram/open_trace_file.c:244:15: note: in expansion of macro ‘MIN’ 2021-07-11T20:06:05,091 244 | file += MIN(strlen(file), l); 2021-07-11T20:06:05,091 | ^~~ 2021-07-11T20:06:05,443 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 2021-07-11T20:06:05,658 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 2021-07-11T20:06:05,802 htslib/cram/rANS_static.c: In function ‘rans_compress_O0’: 2021-07-11T20:06:05,803 htslib/cram/rANS_static.c:86:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:06:05,803 86 | for (i = 0; i < in_size; i++) { 2021-07-11T20:06:05,803 | ^ 2021-07-11T20:06:05,805 htslib/cram/rANS_static.c: In function ‘rans_uncompress_O0’: 2021-07-11T20:06:05,806 htslib/cram/rANS_static.c:222:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:06:05,806 222 | if (in_sz != in_size-9) 2021-07-11T20:06:05,806 | ^~ 2021-07-11T20:06:05,809 htslib/cram/rANS_static.c: In function ‘rans_compress_O1’: 2021-07-11T20:06:05,809 htslib/cram/rANS_static.c:390:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:06:05,809 390 | for (last_i=i=0; ih, type, &new))) 2021-07-11T20:06:07,329 | ^~ 2021-07-11T20:06:07,332 htslib/cram/sam_header.c: In function ‘sam_hdr_vadd’: 2021-07-11T20:06:07,332 htslib/cram/sam_header.c:450:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:07,332 450 | if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new))) 2021-07-11T20:06:07,332 | ^~ 2021-07-11T20:06:07,340 htslib/cram/sam_header.c: In function ‘sam_hdr_rebuild’: 2021-07-11T20:06:07,340 htslib/cram/sam_header.c:821:24: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:07,341 821 | if (kh_key(hdr->h, k) == K("HD")) 2021-07-11T20:06:07,341 | ^~ 2021-07-11T20:06:09,363 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 2021-07-11T20:06:09,582 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 2021-07-11T20:06:10,073 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 2021-07-11T20:06:10,196 htslib/cram/vlen.c: In function ‘vflen’: 2021-07-11T20:06:10,196 htslib/cram/vlen.c:77:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:10,196 77 | #define MAX(a,b) ((a)>(b)?(a):(b)) 2021-07-11T20:06:10,196 | ^ 2021-07-11T20:06:10,196 htslib/cram/vlen.c:239:10: note: in expansion of macro ‘MAX’ 2021-07-11T20:06:10,197 239 | len += MAX(conv_len1, i>=0x80 ?MB_CUR_MAX :1); 2021-07-11T20:06:10,197 | ^~~ 2021-07-11T20:06:10,197 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] 2021-07-11T20:06:10,197 77 | #define MAX(a,b) ((a)>(b)?(a):(b)) 2021-07-11T20:06:10,198 | ^~~ 2021-07-11T20:06:10,198 htslib/cram/vlen.c:239:10: note: in expansion of macro ‘MAX’ 2021-07-11T20:06:10,198 239 | len += MAX(conv_len1, i>=0x80 ?MB_CUR_MAX :1); 2021-07-11T20:06:10,198 | ^~~ 2021-07-11T20:06:10,353 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 2021-07-11T20:06:10,644 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 2021-07-11T20:06:11,384 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 2021-07-11T20:06:12,718 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 2021-07-11T20:06:12,944 htslib/hfile.c: In function ‘find_scheme_handler’: 2021-07-11T20:06:12,944 htslib/hfile.c:717:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:06:12,944 717 | for (i = 0; i < sizeof scheme; i++) 2021-07-11T20:06:12,945 | ^ 2021-07-11T20:06:12,946 htslib/hfile.c:723:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-11T20:06:12,946 723 | if (i == 0 || i >= sizeof scheme) return NULL; 2021-07-11T20:06:12,946 | ^~ 2021-07-11T20:06:13,714 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 2021-07-11T20:06:13,913 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 2021-07-11T20:06:14,147 In file included from htslib/cram/cram.h:52, 2021-07-11T20:06:14,148 from htslib/hts.c:39: 2021-07-11T20:06:14,148 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:06:14,149 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] 2021-07-11T20:06:14,149 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:06:14,149 | ^~ 2021-07-11T20:06:14,149 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:14,149 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:06:14,150 | ^ 2021-07-11T20:06:14,205 htslib/hts.c: In function ‘hts_idx_init’: 2021-07-11T20:06:14,205 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] 2021-07-11T20:06:14,206 1222 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; 2021-07-11T20:06:14,206 | ^~~ 2021-07-11T20:06:14,208 htslib/hts.c: In function ‘update_loff’: 2021-07-11T20:06:14,209 htslib/hts.c:1256:34: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:14,209 1256 | if ( kh_key(bidx, k) < idx->n_bins ) 2021-07-11T20:06:14,209 | ^ 2021-07-11T20:06:14,211 htslib/hts.c: In function ‘compress_binning’: 2021-07-11T20:06:14,211 htslib/hts.c:1283:55: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:14,212 1283 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue; 2021-07-11T20:06:14,212 | ^~ 2021-07-11T20:06:14,214 htslib/hts.c:1308:51: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:14,215 1308 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue; 2021-07-11T20:06:14,215 | ^~ 2021-07-11T20:06:14,236 htslib/hts.c: In function ‘hts_idx_load_local’: 2021-07-11T20:06:14,237 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] 2021-07-11T20:06:14,237 1618 | if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail; 2021-07-11T20:06:14,237 | ^~ 2021-07-11T20:06:14,241 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] 2021-07-11T20:06:14,241 1636 | if (bgzf_read(fp, idx->meta + 28, x[7]) != x[7]) goto fail; 2021-07-11T20:06:14,241 | ^~ 2021-07-11T20:06:18,228 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 2021-07-11T20:06:18,659 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 2021-07-11T20:06:19,427 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 2021-07-11T20:06:19,557 htslib/kstring.c: In function ‘kvsprintf’: 2021-07-11T20:06:19,557 htslib/kstring.c:42:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:19,557 42 | if (l + 1 > s->m - s->l) { 2021-07-11T20:06:19,558 | ^ 2021-07-11T20:06:19,943 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 2021-07-11T20:06:20,512 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 2021-07-11T20:06:21,220 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 2021-07-11T20:06:21,911 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 2021-07-11T20:06:22,068 htslib/regidx.c: In function ‘regidx_insert’: 2021-07-11T20:06:22,068 htslib/regidx.c:155:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:22,069 155 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-11T20:06:22,069 | ^ 2021-07-11T20:06:22,069 htslib/regidx.c:155:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:22,069 155 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-11T20:06:22,069 | ^~ 2021-07-11T20:06:22,069 htslib/regidx.c:155:89: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:22,069 155 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-11T20:06:22,070 | ^ 2021-07-11T20:06:22,830 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 2021-07-11T20:06:23,063 In file included from htslib/cram/cram.h:52, 2021-07-11T20:06:23,063 from htslib/sam.c:35: 2021-07-11T20:06:23,063 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-11T20:06:23,064 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] 2021-07-11T20:06:23,064 162 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-11T20:06:23,064 | ^~ 2021-07-11T20:06:23,064 htslib/cram/cram_codecs.h:164:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:23,064 164 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-11T20:06:23,065 | ^ 2021-07-11T20:06:23,078 htslib/sam.c: In function ‘bam_hdr_read’: 2021-07-11T20:06:23,078 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] 2021-07-11T20:06:23,078 147 | if (bytes != h->l_text) goto read_err; 2021-07-11T20:06:23,078 | ^~ 2021-07-11T20:06:23,086 htslib/sam.c: In function ‘bam_write1’: 2021-07-11T20:06:23,087 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] 2021-07-11T20:06:23,087 467 | return ok? 4 + block_len : -1; 2021-07-11T20:06:23,087 | ^~ 2021-07-11T20:06:23,097 htslib/sam.c: In function ‘sam_hdr_write’: 2021-07-11T20:06:23,098 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] 2021-07-11T20:06:23,098 818 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-11T20:06:23,098 | ^~ 2021-07-11T20:06:23,114 htslib/sam.c: In function ‘sam_format1’: 2021-07-11T20:06:23,115 htslib/sam.c:1181:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:23,115 1181 | if ((b->data + b->l_data - s) / sub_type_size < n) 2021-07-11T20:06:23,115 | ^ 2021-07-11T20:06:23,116 htslib/sam.c:1184:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:23,116 1184 | for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if" 2021-07-11T20:06:23,116 | ^ 2021-07-11T20:06:23,117 htslib/sam.c: In function ‘sam_write1’: 2021-07-11T20:06:23,118 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] 2021-07-11T20:06:23,118 1220 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-11T20:06:23,118 | ^~ 2021-07-11T20:06:23,324 In file included from /usr/include/string.h:495, 2021-07-11T20:06:23,324 from htslib/sam.c:30: 2021-07-11T20:06:23,325 In function ‘strncpy’, 2021-07-11T20:06:23,325 inlined from ‘bam_hdr_write’ at htslib/sam.c:229:5: 2021-07-11T20:06:23,325 /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] 2021-07-11T20:06:23,325 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-11T20:06:23,325 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-11T20:06:28,678 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 2021-07-11T20:06:28,889 htslib/synced_bcf_reader.c: In function ‘_regions_add’: 2021-07-11T20:06:28,890 htslib/synced_bcf_reader.c:860:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:28,890 860 | if ( start < creg->regs[i].start ) max = i - 1; 2021-07-11T20:06:28,890 | ^ 2021-07-11T20:06:28,890 htslib/synced_bcf_reader.c:861:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:28,891 861 | else if ( start > creg->regs[i].start ) min = i + 1; 2021-07-11T20:06:28,891 | ^ 2021-07-11T20:06:28,891 htslib/synced_bcf_reader.c:864:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:28,891 864 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-11T20:06:28,891 | ^~ 2021-07-11T20:06:28,892 htslib/synced_bcf_reader.c:864:68: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-11T20:06:28,892 864 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-11T20:06:28,892 | ^~ 2021-07-11T20:06:30,891 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 2021-07-11T20:06:31,538 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 2021-07-11T20:06:31,742 htslib/vcf.c: In function ‘bcf_hdr_sync’: 2021-07-11T20:06:31,743 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] 2021-07-11T20:06:31,743 151 | if ( h->n[i] < kh_size(d) ) 2021-07-11T20:06:31,743 | ^ 2021-07-11T20:06:31,765 htslib/vcf.c: In function ‘bcf_hdr_read’: 2021-07-11T20:06:31,766 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] 2021-07-11T20:06:31,766 861 | if (bgzf_read(fp, htxt, hlen) != hlen) goto fail; 2021-07-11T20:06:31,766 | ^~ 2021-07-11T20:06:31,768 htslib/vcf.c: In function ‘bcf_hdr_write’: 2021-07-11T20:06:31,769 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] 2021-07-11T20:06:31,769 888 | if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1; 2021-07-11T20:06:31,769 | ^~ 2021-07-11T20:06:31,772 htslib/vcf.c: In function ‘bcf_read1_core’: 2021-07-11T20:06:31,772 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] 2021-07-11T20:06:31,773 972 | if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -1; 2021-07-11T20:06:31,773 | ^~ 2021-07-11T20:06:31,774 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] 2021-07-11T20:06:31,774 973 | if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -1; 2021-07-11T20:06:31,774 | ^~ 2021-07-11T20:06:31,786 htslib/vcf.c: In function ‘bcf_write’: 2021-07-11T20:06:31,787 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] 2021-07-11T20:06:31,787 1287 | if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1; 2021-07-11T20:06:31,787 | ^~ 2021-07-11T20:06:31,788 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] 2021-07-11T20:06:31,788 1288 | if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1; 2021-07-11T20:06:31,788 | ^~ 2021-07-11T20:06:31,803 htslib/vcf.c: In function ‘vcf_parse_format’: 2021-07-11T20:06:31,804 htslib/vcf.c:1680:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-11T20:06:31,804 1680 | if (fmt[j].max_l < l) fmt[j].max_l = l; 2021-07-11T20:06:31,804 | ^ 2021-07-11T20:06:31,809 htslib/vcf.c:1709:33: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2021-07-11T20:06:31,809 1709 | f->size = f->is_gt? f->max_g << 2 : f->max_l; 2021-07-11T20:06:31,809 | ^~~~~~~~~~~~~ 2021-07-11T20:06:31,847 htslib/vcf.c: In function ‘vcf_write_line’: 2021-07-11T20:06:31,848 htslib/vcf.c:2274:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:31,848 2274 | return ret==line->l ? 0 : -1; 2021-07-11T20:06:31,848 | ^~ 2021-07-11T20:06:31,849 htslib/vcf.c: In function ‘vcf_write’: 2021-07-11T20:06:31,851 htslib/vcf.c:2286:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:31,851 2286 | return ret==fp->line.l ? 0 : -1; 2021-07-11T20:06:31,851 | ^~ 2021-07-11T20:06:31,876 htslib/vcf.c: In function ‘bcf_hdr_set_samples’: 2021-07-11T20:06:31,878 htslib/vcf.c:2755:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-11T20:06:31,878 2755 | for (k = kh_begin(d); k != kh_end(d); ++k) 2021-07-11T20:06:31,878 | ^~ 2021-07-11T20:06:31,922 htslib/vcf.c: In function ‘_bcf1_sync_alleles’: 2021-07-11T20:06:31,924 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] 2021-07-11T20:06:31,924 3204 | line->rlen = end_info ? end_info->v1.i : strlen(line->d.allele[0]); 2021-07-11T20:06:31,924 | ^~~~~~~~~~~~~~ 2021-07-11T20:06:31,935 htslib/vcf.c: In function ‘bcf_get_info_values’: 2021-07-11T20:06:31,937 htslib/vcf.c:3334:49: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-11T20:06:31,937 3334 | if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2; // expected different type 2021-07-11T20:06:31,937 | ^~ 2021-07-11T20:06:31,952 htslib/vcf.c: In function ‘bcf_get_format_values’: 2021-07-11T20:06:31,954 htslib/vcf.c:3456:53: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-11T20:06:31,954 3456 | else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2; // expected different type 2021-07-11T20:06:31,954 | ^~ 2021-07-11T20:06:40,265 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 2021-07-11T20:06:40,444 htslib/vcf_sweep.c: In function ‘bcf_sweep_fwd’: 2021-07-11T20:06:40,445 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] 2021-07-11T20:06:40,445 164 | if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size ) 2021-07-11T20:06:40,445 | ^ 2021-07-11T20:06:40,637 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 2021-07-11T20:06:42,761 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 2021-07-11T20:06:43,355 installing to build/bdist.linux-armv7l/wheel 2021-07-11T20:06:43,355 running install 2021-07-11T20:06:43,356 running install_lib 2021-07-11T20:06:43,360 creating build/bdist.linux-armv7l 2021-07-11T20:06:43,361 creating build/bdist.linux-armv7l/wheel 2021-07-11T20:06:43,363 creating build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T20:06:43,364 copying build/lib.linux-armv7l-3.9/cyvcf2/relatedness.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T20:06:43,367 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T20:06:43,369 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T20:06:43,490 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T20:06:43,492 creating build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,493 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,497 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,499 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,522 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,525 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,527 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,529 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,531 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,533 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,536 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,538 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,540 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,543 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,545 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,549 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,551 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,553 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,560 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-11T20:06:43,563 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T20:06:43,622 copying build/lib.linux-armv7l-3.9/cyvcf2/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T20:06:43,623 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T20:06:43,625 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-11T20:06:43,628 running install_egg_info 2021-07-11T20:06:43,638 Copying cyvcf2.egg-info to build/bdist.linux-armv7l/wheel/cyvcf2-0.6.1-py3.9.egg-info 2021-07-11T20:06:43,652 running install_scripts 2021-07-11T20:06:43,948 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-11T20:06:43,953 creating build/bdist.linux-armv7l/wheel/cyvcf2-0.6.1.dist-info/WHEEL 2021-07-11T20:06:43,956 creating '/tmp/pip-wheel-mxdotxxv/cyvcf2-0.6.1-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-11T20:06:43,959 adding 'cyvcf2/__init__.py' 2021-07-11T20:06:44,158 adding 'cyvcf2/cyvcf2.c' 2021-07-11T20:06:45,355 adding 'cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so' 2021-07-11T20:06:45,402 adding 'cyvcf2/cyvcf2.pxd' 2021-07-11T20:06:45,408 adding 'cyvcf2/cyvcf2.pyx' 2021-07-11T20:06:45,410 adding 'cyvcf2/helpers.c' 2021-07-11T20:06:45,411 adding 'cyvcf2/helpers.h' 2021-07-11T20:06:45,413 adding 'cyvcf2/relatedness.h' 2021-07-11T20:06:45,415 adding 'cyvcf2/tests/__init__.py' 2021-07-11T20:06:45,416 adding 'cyvcf2/tests/__init__.pyc' 2021-07-11T20:06:45,417 adding 'cyvcf2/tests/bug.vcf.gz' 2021-07-11T20:06:45,422 adding 'cyvcf2/tests/o.vcf.gz' 2021-07-11T20:06:45,424 adding 'cyvcf2/tests/test-format-string.vcf' 2021-07-11T20:06:45,466 adding 'cyvcf2/tests/test-haploidX.vcf' 2021-07-11T20:06:45,473 adding 'cyvcf2/tests/test-hemi.vcf' 2021-07-11T20:06:45,475 adding 'cyvcf2/tests/test.comp_het.3.vcf' 2021-07-11T20:06:45,477 adding 'cyvcf2/tests/test.snpeff.bcf' 2021-07-11T20:06:45,478 adding 'cyvcf2/tests/test.snpeff.bcf.csi' 2021-07-11T20:06:45,480 adding 'cyvcf2/tests/test.snpeff.vcf' 2021-07-11T20:06:45,499 adding 'cyvcf2/tests/test.vcf.gz' 2021-07-11T20:06:45,501 adding 'cyvcf2/tests/test.vcf.gz.tbi' 2021-07-11T20:06:45,503 adding 'cyvcf2/tests/test_gt_bases.vcf.gz' 2021-07-11T20:06:45,504 adding 'cyvcf2/tests/test_hemi.py' 2021-07-11T20:06:45,505 adding 'cyvcf2/tests/test_hemi.pyc' 2021-07-11T20:06:45,507 adding 'cyvcf2/tests/test_reader.py' 2021-07-11T20:06:45,511 adding 'cyvcf2/tests/test_reader.pyc' 2021-07-11T20:06:45,513 adding 'cyvcf2-0.6.1.dist-info/LICENSE' 2021-07-11T20:06:45,514 adding 'cyvcf2-0.6.1.dist-info/METADATA' 2021-07-11T20:06:45,515 adding 'cyvcf2-0.6.1.dist-info/WHEEL' 2021-07-11T20:06:45,516 adding 'cyvcf2-0.6.1.dist-info/top_level.txt' 2021-07-11T20:06:45,517 adding 'cyvcf2-0.6.1.dist-info/RECORD' 2021-07-11T20:06:45,561 removing build/bdist.linux-armv7l/wheel 2021-07-11T20:06:45,902 Building wheel for cyvcf2 (setup.py): finished with status 'done' 2021-07-11T20:06:45,940 Created wheel for cyvcf2: filename=cyvcf2-0.6.1-cp39-cp39-linux_armv7l.whl size=2835446 sha256=e528d5cd686f500d94954cd3a5f0eedeb0f96f84f0c4628dbb5add4072a8c0a7 2021-07-11T20:06:45,941 Stored in directory: /tmp/pip-ephem-wheel-cache-64vljhyi/wheels/7c/39/11/f05f2c91e253b8832ab902abed94cd2def0a2b5c5448ef0a65 2021-07-11T20:06:45,953 Successfully built cyvcf2 2021-07-11T20:06:46,064 Removed build tracker: '/tmp/pip-req-tracker-o9i39i9l'