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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/) 2021-07-14T07:14:15,315 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 2021-07-14T07:14:15,315 Skipping link: not a file: https://pypi.org/simple/cyvcf2/ 2021-07-14T07:14:15,330 Given no hashes to check 1 links for project 'cyvcf2': discarding no candidates 2021-07-14T07:14:15,349 Collecting cyvcf2==0.10.8 2021-07-14T07:14:15,351 Created temporary directory: /tmp/pip-unpack-lif1ov37 2021-07-14T07:14:15,564 Downloading cyvcf2-0.10.8.tar.gz (1.1 MB) 2021-07-14T07:14:16,259 Added cyvcf2==0.10.8 from https://files.pythonhosted.org/packages/63/21/2f7546d7121c001f73b73bc7941c511a4848771afdb4de300f50301ce458/cyvcf2-0.10.8.tar.gz#sha256=62d950c940977243ab5d2d6e6eabad5fb0deb12012e8e0d2611da03384f118d9 to build tracker '/tmp/pip-req-tracker-qybnd105' 2021-07-14T07:14:16,260 Running setup.py (path:/tmp/pip-wheel-ab_f2mwz/cyvcf2_b461307d375f4f729174d1e0452e74a7/setup.py) egg_info for package cyvcf2 2021-07-14T07:14:16,261 Created temporary directory: /tmp/pip-pip-egg-info-lm57ec_l 2021-07-14T07:14:16,261 Running command python setup.py egg_info 2021-07-14T07:14:19,158 Collecting coloredlogs 2021-07-14T07:14:19,199 Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) 2021-07-14T07:14:19,445 Collecting humanfriendly>=9.1 2021-07-14T07:14:19,453 Downloading humanfriendly-9.2-py2.py3-none-any.whl (86 kB) 2021-07-14T07:14:21,960 Installing collected packages: humanfriendly, coloredlogs 2021-07-14T07:14:22,308 Successfully installed coloredlogs-15.0.1 humanfriendly-9.2 2021-07-14T07:14:23,076 running egg_info 2021-07-14T07:14:23,078 creating /tmp/pip-pip-egg-info-lm57ec_l/cyvcf2.egg-info 2021-07-14T07:14:23,080 writing /tmp/pip-pip-egg-info-lm57ec_l/cyvcf2.egg-info/PKG-INFO 2021-07-14T07:14:23,083 writing dependency_links to /tmp/pip-pip-egg-info-lm57ec_l/cyvcf2.egg-info/dependency_links.txt 2021-07-14T07:14:23,085 writing entry points to /tmp/pip-pip-egg-info-lm57ec_l/cyvcf2.egg-info/entry_points.txt 2021-07-14T07:14:23,086 writing requirements to /tmp/pip-pip-egg-info-lm57ec_l/cyvcf2.egg-info/requires.txt 2021-07-14T07:14:23,087 writing top-level names to /tmp/pip-pip-egg-info-lm57ec_l/cyvcf2.egg-info/top_level.txt 2021-07-14T07:14:23,089 writing manifest file '/tmp/pip-pip-egg-info-lm57ec_l/cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:14:23,245 reading manifest file '/tmp/pip-pip-egg-info-lm57ec_l/cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:14:23,247 reading manifest template 'MANIFEST.in' 2021-07-14T07:14:23,259 adding license file 'LICENSE' 2021-07-14T07:14:23,266 writing manifest file '/tmp/pip-pip-egg-info-lm57ec_l/cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:14:23,364 Source in /tmp/pip-wheel-ab_f2mwz/cyvcf2_b461307d375f4f729174d1e0452e74a7 has version 0.10.8, which satisfies requirement cyvcf2==0.10.8 from https://files.pythonhosted.org/packages/63/21/2f7546d7121c001f73b73bc7941c511a4848771afdb4de300f50301ce458/cyvcf2-0.10.8.tar.gz#sha256=62d950c940977243ab5d2d6e6eabad5fb0deb12012e8e0d2611da03384f118d9 2021-07-14T07:14:23,365 Removed cyvcf2==0.10.8 from https://files.pythonhosted.org/packages/63/21/2f7546d7121c001f73b73bc7941c511a4848771afdb4de300f50301ce458/cyvcf2-0.10.8.tar.gz#sha256=62d950c940977243ab5d2d6e6eabad5fb0deb12012e8e0d2611da03384f118d9 from build tracker '/tmp/pip-req-tracker-qybnd105' 2021-07-14T07:14:23,369 Created temporary directory: /tmp/pip-unpack-l3ub_7k7 2021-07-14T07:14:23,370 Building wheels for collected packages: cyvcf2 2021-07-14T07:14:23,374 Created temporary directory: /tmp/pip-wheel-tuxqt7ss 2021-07-14T07:14:23,375 Building wheel for cyvcf2 (setup.py): started 2021-07-14T07:14:23,375 Destination directory: /tmp/pip-wheel-tuxqt7ss 2021-07-14T07:14:23,375 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-ab_f2mwz/cyvcf2_b461307d375f4f729174d1e0452e74a7/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-ab_f2mwz/cyvcf2_b461307d375f4f729174d1e0452e74a7/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-tuxqt7ss 2021-07-14T07:14:24,850 running bdist_wheel 2021-07-14T07:14:24,855 running build 2021-07-14T07:14:24,855 running build_py 2021-07-14T07:14:24,991 creating build 2021-07-14T07:14:24,991 creating build/lib.linux-armv7l-3.9 2021-07-14T07:14:24,992 creating build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:24,993 copying cyvcf2/__main__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:24,995 copying cyvcf2/cli.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:24,997 copying cyvcf2/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:24,999 creating build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,000 copying cyvcf2/tests/test_hemi.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,002 copying cyvcf2/tests/test_reader.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,005 copying cyvcf2/tests/test_cli.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,006 copying cyvcf2/tests/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,008 running egg_info 2021-07-14T07:14:25,023 writing cyvcf2.egg-info/PKG-INFO 2021-07-14T07:14:25,025 writing dependency_links to cyvcf2.egg-info/dependency_links.txt 2021-07-14T07:14:25,027 writing entry points to cyvcf2.egg-info/entry_points.txt 2021-07-14T07:14:25,028 writing requirements to cyvcf2.egg-info/requires.txt 2021-07-14T07:14:25,029 writing top-level names to cyvcf2.egg-info/top_level.txt 2021-07-14T07:14:25,037 reading manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:14:25,042 reading manifest template 'MANIFEST.in' 2021-07-14T07:14:25,054 adding license file 'LICENSE' 2021-07-14T07:14:25,063 writing manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:14:25,069 copying cyvcf2/cyvcf2.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:25,123 copying cyvcf2/cyvcf2.pxd -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:25,125 copying cyvcf2/cyvcf2.pyx -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:25,129 copying cyvcf2/helpers.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:25,131 copying cyvcf2/helpers.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:25,134 copying cyvcf2/relatedness.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:25,136 copying cyvcf2/tests/__init__.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,139 copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,142 copying cyvcf2/tests/decomposed.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,144 copying cyvcf2/tests/empty.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,146 copying cyvcf2/tests/issue_44.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,148 copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,152 copying cyvcf2/tests/seg.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,154 copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,157 copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,159 copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,176 copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,179 copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,181 copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,183 copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,185 copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,188 copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,190 copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,193 copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,195 copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,199 copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,206 copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,208 copying cyvcf2/tests/test_cli.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,211 copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,214 copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,217 copying cyvcf2/tests/test_hemi.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,219 copying cyvcf2/tests/test_reader.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:14:25,223 running build_ext 2021-07-14T07:14:25,293 cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c 2021-07-14T07:14:25,911 /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-ab_f2mwz/cyvcf2_b461307d375f4f729174d1e0452e74a7/cyvcf2/cyvcf2.pxd 2021-07-14T07:14:25,912 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-14T07:14:27,337 warning: cyvcf2/cyvcf2.pxd:26:16: Declarations should not be declared inline. 2021-07-14T07:14:27,347 warning: cyvcf2/cyvcf2.pxd:188:14: 'BCF_HT_FLAG' redeclared 2021-07-14T07:14:27,370 warning: cyvcf2/cyvcf2.pxd:279:30: Declarations should not be declared inline. 2021-07-14T07:14:38,223 building 'cyvcf2.cyvcf2' extension 2021-07-14T07:14:38,224 creating build/temp.linux-armv7l-3.9 2021-07-14T07:14:38,224 creating build/temp.linux-armv7l-3.9/cyvcf2 2021-07-14T07:14:38,225 creating build/temp.linux-armv7l-3.9/htslib 2021-07-14T07:14:38,226 creating build/temp.linux-armv7l-3.9/htslib/cram 2021-07-14T07:14:38,228 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c cyvcf2/cyvcf2.c -o build/temp.linux-armv7l-3.9/cyvcf2/cyvcf2.o 2021-07-14T07:14:38,635 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T07:14:38,635 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T07:14:38,635 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T07:14:38,636 from cyvcf2/cyvcf2.c:613: 2021-07-14T07:14:38,636 /home/piwheels/.local/lib/python3.9/site-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] 2021-07-14T07:14:38,636 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T07:14:38,636 | ^~~~~~~ 2021-07-14T07:14:38,700 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:14:38,701 from cyvcf2/helpers.h:1, 2021-07-14T07:14:38,701 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:38,701 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:14:38,701 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:14:38,701 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:14:38,702 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:14:38,702 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:14:38,702 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:14:38,702 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:14:38,702 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:14:38,716 In file included from cyvcf2/cyvcf2.c:624: 2021-07-14T07:14:38,716 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:14:38,716 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:14:38,717 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:14:38,717 | ^ 2021-07-14T07:14:38,880 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: 2021-07-14T07:14:38,885 cyvcf2/cyvcf2.c:7952:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:38,886 7952 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); 2021-07-14T07:14:38,886 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:14:38,886 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:38,886 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:38,886 htslib/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:38,886 443 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-14T07:14:38,887 | ~~~~~~~~~~~^ 2021-07-14T07:14:38,891 cyvcf2/cyvcf2.c:7994:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:38,892 7994 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-14T07:14:38,892 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:14:38,892 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:38,892 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:38,892 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:38,892 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:14:38,893 | ~~~~~~~~~~~^ 2021-07-14T07:14:38,901 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: 2021-07-14T07:14:38,906 cyvcf2/cyvcf2.c:8522:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:38,906 8522 | __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); 2021-07-14T07:14:38,907 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:14:38,907 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:38,907 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:38,907 htslib/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:38,907 315 | int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); 2021-07-14T07:14:38,907 | ~~~~~~~~~~~^~~ 2021-07-14T07:14:38,916 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: 2021-07-14T07:14:38,922 cyvcf2/cyvcf2.c:8826:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:38,922 8826 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); 2021-07-14T07:14:38,922 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:14:38,922 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:38,922 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:38,923 htslib/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:38,923 443 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-14T07:14:38,923 | ~~~~~~~~~~~^ 2021-07-14T07:14:38,929 cyvcf2/cyvcf2.c:8879:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:38,929 8879 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-14T07:14:38,929 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:14:38,929 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:38,929 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:38,930 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:38,930 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:14:38,930 | ~~~~~~~~~~~^ 2021-07-14T07:14:38,932 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’: 2021-07-14T07:14:38,935 cyvcf2/cyvcf2.c:9094:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:38,935 9094 | __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); 2021-07-14T07:14:38,935 htslib/htslib/vcf.h:796:103: note: in definition of macro ‘bcf_itr_querys’ 2021-07-14T07:14:38,936 796 | #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) 2021-07-14T07:14:38,936 | ^~~ 2021-07-14T07:14:38,936 In file included from htslib/htslib/vcf.h:39, 2021-07-14T07:14:38,936 from cyvcf2/helpers.h:1, 2021-07-14T07:14:38,936 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:38,936 htslib/htslib/hts.h:675:97: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:38,936 675 | 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); 2021-07-14T07:14:38,936 | ~~~~~~^~~ 2021-07-14T07:14:38,956 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’: 2021-07-14T07:14:38,963 cyvcf2/cyvcf2.c:10394:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:38,963 10394 | __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, 408, __pyx_L1_error) 2021-07-14T07:14:38,963 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:14:38,965 cyvcf2/cyvcf2.c:2942:107: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:38,965 2942 | static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ 2021-07-14T07:14:38,965 | ^~~~~~~~~~~ 2021-07-14T07:14:39,042 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_35__dealloc__’: 2021-07-14T07:14:39,051 cyvcf2/cyvcf2.c:12077:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:39,051 12077 | bcf_hdr_destroy(__pyx_v_self->hdr); 2021-07-14T07:14:39,051 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:14:39,051 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:39,051 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:39,052 htslib/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:39,052 261 | void bcf_hdr_destroy(bcf_hdr_t *h); 2021-07-14T07:14:39,052 | ~~~~~~~~~~~^ 2021-07-14T07:14:39,055 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: 2021-07-14T07:14:39,063 cyvcf2/cyvcf2.c:12567:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 2021-07-14T07:14:39,064 12567 | __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); 2021-07-14T07:14:39,064 | ^~~~~~~~~ 2021-07-14T07:14:39,064 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:39,064 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:39,064 htslib/htslib/vcf.h:439:11: note: declared here 2021-07-14T07:14:39,064 439 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) 2021-07-14T07:14:39,064 | ^~~~~~~~~~~~~~~~ 2021-07-14T07:14:39,067 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: 2021-07-14T07:14:39,075 cyvcf2/cyvcf2.c:12826:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-14T07:14:39,075 12826 | __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-14T07:14:39,076 | ^ 2021-07-14T07:14:39,081 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:39,082 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:39,082 cyvcf2/cyvcf2.c:12935:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:39,082 12935 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-14T07:14:39,082 htslib/htslib/vcf.h:799:112: note: in definition of macro ‘bcf_index_seqnames’ 2021-07-14T07:14:39,082 799 | #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) 2021-07-14T07:14:39,082 | ^~~ 2021-07-14T07:14:39,082 In file included from htslib/htslib/vcf.h:39, 2021-07-14T07:14:39,083 from cyvcf2/helpers.h:1, 2021-07-14T07:14:39,083 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:39,083 htslib/htslib/hts.h:677:92: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:39,083 677 | 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 2021-07-14T07:14:39,083 | ~~~~~~^~~ 2021-07-14T07:14:39,092 cyvcf2/cyvcf2.c:12935:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-14T07:14:39,092 12935 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-14T07:14:39,092 | ^ 2021-07-14T07:14:39,102 cyvcf2/cyvcf2.c:13018:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-14T07:14:39,102 13018 | __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); 2021-07-14T07:14:39,102 | ^ 2021-07-14T07:14:39,844 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’: 2021-07-14T07:14:39,861 cyvcf2/cyvcf2.c:23944:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:14:39,861 23944 | for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) { 2021-07-14T07:14:39,861 | ^ 2021-07-14T07:14:39,995 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’: 2021-07-14T07:14:40,013 cyvcf2/cyvcf2.c:25988:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,013 25988 | __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id); 2021-07-14T07:14:40,013 | ^ 2021-07-14T07:14:40,343 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’: 2021-07-14T07:14:40,366 cyvcf2/cyvcf2.c:33627:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:14:40,367 33627 | for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-07-14T07:14:40,367 | ^ 2021-07-14T07:14:40,371 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’: 2021-07-14T07:14:40,394 cyvcf2/cyvcf2.c:33898:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:14:40,394 33898 | for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2021-07-14T07:14:40,394 | ^ 2021-07-14T07:14:40,398 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’: 2021-07-14T07:14:40,422 cyvcf2/cyvcf2.c:34113:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:14:40,422 34113 | for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2021-07-14T07:14:40,422 | ^ 2021-07-14T07:14:40,447 cyvcf2/cyvcf2.c:34171:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:14:40,447 34171 | __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0); 2021-07-14T07:14:40,447 | ^~ 2021-07-14T07:14:40,472 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: 2021-07-14T07:14:40,498 cyvcf2/cyvcf2.c:36325:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,498 36325 | __pyx_v_h = __pyx_t_6; 2021-07-14T07:14:40,498 | ^ 2021-07-14T07:14:40,597 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: 2021-07-14T07:14:40,625 cyvcf2/cyvcf2.c:39428:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,625 39428 | __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); 2021-07-14T07:14:40,625 | ^ 2021-07-14T07:14:40,634 cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: 2021-07-14T07:14:40,661 cyvcf2/cyvcf2.c:40423:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,661 40423 | __pyx_v_i->hdr = __pyx_t_4; 2021-07-14T07:14:40,662 | ^ 2021-07-14T07:14:40,672 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: 2021-07-14T07:14:40,700 cyvcf2/cyvcf2.c:41089:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,700 41089 | (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); 2021-07-14T07:14:40,700 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:14:40,700 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:40,701 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:40,701 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:40,701 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:14:40,701 | ~~~~~~~~~~~^ 2021-07-14T07:14:40,728 cyvcf2/cyvcf2.c:41117:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,729 41117 | (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); 2021-07-14T07:14:40,729 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:14:40,729 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:40,729 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:40,729 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:40,730 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:14:40,730 | ~~~~~~~~~~~^ 2021-07-14T07:14:40,730 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2write_header’: 2021-07-14T07:14:40,757 cyvcf2/cyvcf2.c:41185:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,758 41185 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); 2021-07-14T07:14:40,758 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:14:40,758 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:40,758 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:40,758 htslib/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:40,758 320 | int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); 2021-07-14T07:14:40,758 | ~~~~~~~~~~~^ 2021-07-14T07:14:40,760 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record’: 2021-07-14T07:14:40,789 cyvcf2/cyvcf2.c:41363:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,789 41363 | __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); 2021-07-14T07:14:40,789 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:14:40,789 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:40,790 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:40,790 htslib/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:40,790 482 | int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); 2021-07-14T07:14:40,790 | ~~~~~~~~~~~^~~ 2021-07-14T07:14:40,818 cyvcf2/cyvcf2.c:41401:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,819 41401 | (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); 2021-07-14T07:14:40,819 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:14:40,819 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:40,819 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:40,819 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:40,819 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:14:40,820 | ~~~~~~~~~~~^ 2021-07-14T07:14:40,848 cyvcf2/cyvcf2.c:41460:100: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:14:40,848 41460 | __pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2168, __pyx_L1_error) 2021-07-14T07:14:40,848 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:14:40,848 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:14:40,849 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:14:40,849 htslib/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:14:40,849 370 | int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); 2021-07-14T07:14:40,849 | ~~~~~~~~~~~^ 2021-07-14T07:14:45,470 At top level: 2021-07-14T07:14:45,475 cyvcf2/cyvcf2.c:6609:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] 2021-07-14T07:14:45,475 6609 | static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { 2021-07-14T07:14:45,476 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:39,375 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c cyvcf2/helpers.c -o build/temp.linux-armv7l-3.9/cyvcf2/helpers.o 2021-07-14T07:15:39,545 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:15:39,545 from cyvcf2/helpers.h:1, 2021-07-14T07:15:39,545 from cyvcf2/helpers.c:1: 2021-07-14T07:15:39,546 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:15:39,546 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:39,546 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:15:39,546 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:39,546 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:15:39,546 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:39,547 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:15:39,547 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:39,760 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/bcf_sr_sort.c -o build/temp.linux-armv7l-3.9/htslib/bcf_sr_sort.o 2021-07-14T07:15:39,904 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:15:39,904 from htslib/htslib/synced_bcf_reader.h:60, 2021-07-14T07:15:39,904 from htslib/bcf_sr_sort.h:37, 2021-07-14T07:15:39,904 from htslib/bcf_sr_sort.c:29: 2021-07-14T07:15:39,904 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:15:39,904 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:39,905 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:15:39,905 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:39,905 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:15:39,905 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:39,905 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:15:39,905 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:39,930 htslib/bcf_sr_sort.c: In function ‘kbs_bitwise_or’: 2021-07-14T07:15:39,930 htslib/bcf_sr_sort.c:69:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:39,930 69 | for (i=0; in; i++) dst->b[i] |= src->b[i]; 2021-07-14T07:15:39,930 | ^ 2021-07-14T07:15:39,937 htslib/bcf_sr_sort.c: In function ‘bcf_sr_sort_set’: 2021-07-14T07:15:39,937 htslib/bcf_sr_sort.c:363:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:39,937 363 | for (k=0; k < kh_end(hash); k++) 2021-07-14T07:15:39,937 | ^ 2021-07-14T07:15:39,938 htslib/bcf_sr_sort.c:366:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:39,938 366 | for (k=0; k < kh_end(hash); k++) 2021-07-14T07:15:39,938 | ^ 2021-07-14T07:15:41,645 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/bgzf.c -o build/temp.linux-armv7l-3.9/htslib/bgzf.o 2021-07-14T07:15:41,830 In file included from htslib/bgzf.c:44: 2021-07-14T07:15:41,830 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:15:41,830 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:41,830 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:15:41,830 | ^ 2021-07-14T07:15:41,834 In file included from htslib/bgzf.c:46: 2021-07-14T07:15:41,834 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:15:41,835 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:41,835 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:15:41,835 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:41,836 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:15:41,836 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:41,836 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:15:41,837 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:41,865 htslib/bgzf.c: In function ‘bgzf_read’: 2021-07-14T07:15:41,865 htslib/bgzf.c:983:23: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:41,866 983 | while (bytes_read < length) { 2021-07-14T07:15:41,866 | ^ 2021-07-14T07:15:41,867 htslib/bgzf.c:996:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:41,867 996 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-14T07:15:41,867 | ^ 2021-07-14T07:15:41,868 htslib/bgzf.c:996:78: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:41,868 996 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-14T07:15:41,868 | ^~~~~~~~~ 2021-07-14T07:15:41,871 htslib/bgzf.c: In function ‘bgzf_mt_writer’: 2021-07-14T07:15:41,871 htslib/bgzf.c:1107:55: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:41,871 1107 | if (hwrite(fp->fp, j->comp_data, j->comp_len) != j->comp_len) { 2021-07-14T07:15:41,872 | ^~ 2021-07-14T07:15:41,883 htslib/bgzf.c: In function ‘bgzf_block_write’: 2021-07-14T07:15:41,884 htslib/bgzf.c:1594:41: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:41,884 1594 | ublock_size = current_block + 1 < fp->idx->moffs ? fp->idx->offs[current_block+1].uaddr-fp->idx->offs[current_block].uaddr : BGZF_MAX_BLOCK_SIZE; 2021-07-14T07:15:41,884 | ^ 2021-07-14T07:15:41,886 htslib/bgzf.c:1602:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-14T07:15:41,886 1602 | if (fp->block_offset == ublock_size) { 2021-07-14T07:15:41,886 | ^~ 2021-07-14T07:15:41,905 htslib/bgzf.c: In function ‘bgzf_useek’: 2021-07-14T07:15:41,907 htslib/bgzf.c:2049:22: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-14T07:15:41,907 2049 | if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1; 2021-07-14T07:15:41,907 | ^ 2021-07-14T07:15:41,908 htslib/bgzf.c:2050:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-14T07:15:41,908 2050 | else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1; 2021-07-14T07:15:41,909 | ^~ 2021-07-14T07:15:44,093 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:15:44,308 In file included from htslib/cram/os.h:80, 2021-07-14T07:15:44,308 from htslib/cram/misc.h:66, 2021-07-14T07:15:44,308 from htslib/cram/cram_io.h:46, 2021-07-14T07:15:44,308 from htslib/cram/cram.h:48, 2021-07-14T07:15:44,308 from htslib/cram/cram_codecs.c:45: 2021-07-14T07:15:44,309 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:15:44,309 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:44,309 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:15:44,309 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:44,309 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:15:44,309 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:44,310 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:15:44,310 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:44,314 In file included from htslib/cram/cram.h:48, 2021-07-14T07:15:44,315 from htslib/cram/cram_codecs.c:45: 2021-07-14T07:15:44,315 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:15:44,315 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:44,315 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:15:44,315 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:44,323 In file included from htslib/cram/cram.h:52, 2021-07-14T07:15:44,324 from htslib/cram/cram_codecs.c:45: 2021-07-14T07:15:44,324 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:15:44,324 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:44,324 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:15:44,325 | ^~ 2021-07-14T07:15:44,325 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:44,325 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:15:44,325 | ^ 2021-07-14T07:15:44,327 htslib/cram/cram_codecs.c: In function ‘get_one_bits_MSB’: 2021-07-14T07:15:44,327 htslib/cram/cram_codecs.c:79:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:44,328 79 | if (block->byte >= block->uncomp_size) 2021-07-14T07:15:44,328 | ^~ 2021-07-14T07:15:44,328 htslib/cram/cram_codecs.c:86:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:44,328 86 | if (block->byte == block->uncomp_size && (b&1)) 2021-07-14T07:15:44,328 | ^~ 2021-07-14T07:15:44,328 htslib/cram/cram_codecs.c: In function ‘get_zero_bits_MSB’: 2021-07-14T07:15:44,329 htslib/cram/cram_codecs.c:97:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:44,329 97 | if (block->byte >= block->uncomp_size) 2021-07-14T07:15:44,329 | ^~ 2021-07-14T07:15:44,329 htslib/cram/cram_codecs.c:104:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:44,329 104 | if (block->byte == block->uncomp_size && !(b&1)) 2021-07-14T07:15:44,329 | ^~ 2021-07-14T07:15:44,338 htslib/cram/cram_codecs.c: In function ‘cram_beta_decode_init’: 2021-07-14T07:15:44,338 htslib/cram/cram_codecs.c:555:47: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:15:44,338 555 | || c->beta.nbits < 0 || c->beta.nbits > 8 * sizeof(int)) { 2021-07-14T07:15:44,338 | ^ 2021-07-14T07:15:44,348 htslib/cram/cram_codecs.c: In function ‘cram_huffman_decode_init’: 2021-07-14T07:15:44,348 htslib/cram/cram_codecs.c:976:16: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:15:44,349 976 | if (ncodes >= SIZE_MAX / sizeof(*codes)) { 2021-07-14T07:15:44,349 | ^~ 2021-07-14T07:15:44,351 htslib/cram/cram_codecs.c:1044:17: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:44,351 1044 | if (val > max_val) 2021-07-14T07:15:44,351 | ^ 2021-07-14T07:15:44,370 htslib/cram/cram_codecs.c: In function ‘cram_byte_array_stop_decode_block’: 2021-07-14T07:15:44,370 htslib/cram/cram_codecs.c:1643:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:44,371 1643 | if (cp_end - cp < out->alloc - out->byte) { 2021-07-14T07:15:44,371 | ^ 2021-07-14T07:15:46,894 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:15:47,158 In file included from htslib/cram/os.h:80, 2021-07-14T07:15:47,158 from htslib/cram/misc.h:66, 2021-07-14T07:15:47,159 from htslib/cram/cram_io.h:46, 2021-07-14T07:15:47,159 from htslib/cram/cram.h:48, 2021-07-14T07:15:47,159 from htslib/cram/cram_decode.c:49: 2021-07-14T07:15:47,159 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:15:47,159 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:47,159 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:15:47,160 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:47,160 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:15:47,160 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:47,160 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:15:47,160 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:47,165 In file included from htslib/cram/cram.h:48, 2021-07-14T07:15:47,165 from htslib/cram/cram_decode.c:49: 2021-07-14T07:15:47,166 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:15:47,166 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:47,166 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:15:47,166 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:47,173 In file included from htslib/cram/cram.h:52, 2021-07-14T07:15:47,174 from htslib/cram/cram_decode.c:49: 2021-07-14T07:15:47,174 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:15:47,174 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:47,174 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:15:47,174 | ^~ 2021-07-14T07:15:47,175 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:47,175 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:15:47,175 | ^ 2021-07-14T07:15:47,180 htslib/cram/cram_decode.c: In function ‘cram_decode_TD’: 2021-07-14T07:15:47,180 htslib/cram/cram_decode.c:102:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:47,180 102 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-14T07:15:47,180 | ^ 2021-07-14T07:15:47,180 htslib/cram/cram_decode.c:114:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:47,180 114 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-14T07:15:47,181 | ^ 2021-07-14T07:15:47,181 htslib/cram/cram_decode.c: In function ‘cram_decode_compression_header’: 2021-07-14T07:15:47,181 htslib/cram/cram_decode.c:156:33: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:15:47,181 156 | hdr->num_landmarks >= SIZE_MAX / sizeof(int32_t))) { 2021-07-14T07:15:47,181 | ^~ 2021-07-14T07:15:47,199 htslib/cram/cram_decode.c: In function ‘cram_dependent_data_series’: 2021-07-14T07:15:47,199 htslib/cram/cram_decode.c:800:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:15:47,199 800 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-14T07:15:47,200 | ^ 2021-07-14T07:15:47,201 htslib/cram/cram_decode.c:894:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:15:47,202 894 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-14T07:15:47,202 | ^ 2021-07-14T07:15:47,206 htslib/cram/cram_decode.c: In function ‘cram_decode_slice_header’: 2021-07-14T07:15:47,207 htslib/cram/cram_decode.c:1114:30: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:15:47,207 1114 | hdr->num_content_ids >= SIZE_MAX / sizeof(int32_t)) { 2021-07-14T07:15:47,207 | ^~ 2021-07-14T07:15:47,212 htslib/cram/cram_decode.c: In function ‘cram_decode_seq’: 2021-07-14T07:15:47,213 htslib/cram/cram_decode.c:1286:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:47,213 1286 | if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) { 2021-07-14T07:15:47,213 | ^ 2021-07-14T07:15:47,217 htslib/cram/cram_decode.c:1437:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:47,217 1437 | if (cr->ref_id < 0 || ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-14T07:15:47,218 | ^~ 2021-07-14T07:15:47,221 htslib/cram/cram_decode.c:1483:39: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:47,221 1483 | if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) { 2021-07-14T07:15:47,221 | ^~ 2021-07-14T07:15:47,223 htslib/cram/cram_decode.c:1494:54: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:47,223 1494 | if (bfd->ref[cr->ref_id].len >= ref_pos) { 2021-07-14T07:15:47,223 | ^~ 2021-07-14T07:15:47,228 htslib/cram/cram_decode.c:1587:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:47,228 1587 | if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-14T07:15:47,228 | ^~ 2021-07-14T07:15:47,232 htslib/cram/cram_decode.c:1660:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:47,233 1660 | if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-14T07:15:47,233 | ^~ 2021-07-14T07:15:47,238 htslib/cram/cram_decode.c:1767:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:47,238 1767 | if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) { 2021-07-14T07:15:47,239 | ^ 2021-07-14T07:15:47,265 htslib/cram/cram_decode.c: In function ‘cram_decode_slice’: 2021-07-14T07:15:47,266 htslib/cram/cram_decode.c:2403:20: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:15:47,266 2403 | bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap)) 2021-07-14T07:15:47,266 | ^~ 2021-07-14T07:15:53,044 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:15:53,314 In file included from htslib/cram/os.h:80, 2021-07-14T07:15:53,315 from htslib/cram/misc.h:66, 2021-07-14T07:15:53,315 from htslib/cram/cram_io.h:46, 2021-07-14T07:15:53,315 from htslib/cram/cram.h:48, 2021-07-14T07:15:53,315 from htslib/cram/cram_encode.c:43: 2021-07-14T07:15:53,315 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:15:53,316 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:53,316 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:15:53,316 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:53,316 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:15:53,316 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:53,316 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:15:53,316 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:53,322 In file included from htslib/cram/cram.h:48, 2021-07-14T07:15:53,322 from htslib/cram/cram_encode.c:43: 2021-07-14T07:15:53,322 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:15:53,322 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:53,322 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:15:53,322 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:53,330 In file included from htslib/cram/cram.h:52, 2021-07-14T07:15:53,330 from htslib/cram/cram_encode.c:43: 2021-07-14T07:15:53,330 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:15:53,330 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:53,330 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:15:53,331 | ^~ 2021-07-14T07:15:53,331 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:53,331 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:15:53,331 | ^ 2021-07-14T07:15:53,367 htslib/cram/cram_encode.c: In function ‘cram_encode_slice’: 2021-07-14T07:15:53,368 htslib/cram/cram_encode.c:1044:21: warning: comparison of integer expressions of different signedness: ‘enum cram_DS_ID’ and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:53,368 1044 | for (id = 1; id < s->hdr->num_blocks; id++) { 2021-07-14T07:15:53,368 | ^ 2021-07-14T07:15:53,371 htslib/cram/cram_encode.c: In function ‘lossy_read_names’: 2021-07-14T07:15:53,372 htslib/cram/cram_encode.c:1168:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-14T07:15:53,372 1168 | if (u.counts.e != e) { 2021-07-14T07:15:53,372 | ^~ 2021-07-14T07:15:53,374 htslib/cram/cram_encode.c:1198:30: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:53,374 1198 | if (kh_val(names, k) == -1) 2021-07-14T07:15:53,374 | ^~ 2021-07-14T07:15:53,418 htslib/cram/cram_encode.c: In function ‘process_one_read’: 2021-07-14T07:15:53,420 htslib/cram/cram_encode.c:2636:39: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:53,420 2636 | while (cr->cigar + cr->ncigar >= s->cigar_alloc) { 2021-07-14T07:15:53,420 | ^~ 2021-07-14T07:15:53,422 htslib/cram/cram_encode.c:2666:44: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:53,422 2666 | int end = cig_len+apos < c->ref_end 2021-07-14T07:15:53,423 | ^ 2021-07-14T07:15:53,424 htslib/cram/cram_encode.c:2667:37: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:53,424 2667 | ? cig_len : c->ref_end - apos; 2021-07-14T07:15:53,424 | ^~~~~~~~~~~~~~~~~ 2021-07-14T07:15:53,429 htslib/cram/cram_encode.c:2710:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:53,430 2710 | if (l < cig_len && cr->len) { 2021-07-14T07:15:53,430 | ^ 2021-07-14T07:15:53,432 htslib/cram/cram_encode.c:2718:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:53,432 2718 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-14T07:15:53,432 | ^ 2021-07-14T07:15:53,434 htslib/cram/cram_encode.c:2727:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:53,434 2727 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-14T07:15:53,434 | ^ 2021-07-14T07:15:53,439 htslib/cram/cram_encode.c:2759:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:53,439 2759 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-14T07:15:53,440 | ^ 2021-07-14T07:15:53,442 htslib/cram/cram_encode.c:2776:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:53,442 2776 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-14T07:15:53,442 | ^ 2021-07-14T07:15:53,444 htslib/cram/cram_encode.c:2780:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:53,444 2780 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-14T07:15:53,444 | ^ 2021-07-14T07:15:53,450 htslib/cram/cram_encode.c:2834:17: warning: unused variable ‘brg’ [-Wunused-variable] 2021-07-14T07:15:53,450 2834 | SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); 2021-07-14T07:15:53,450 | ^~~ 2021-07-14T07:15:53,470 htslib/cram/cram_encode.c: In function ‘cram_put_bam_seq’: 2021-07-14T07:15:53,472 htslib/cram/cram_encode.c:3077:25: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:53,472 3077 | (c->s_num_bases >= fd->bases_per_slice)) { 2021-07-14T07:15:53,472 | ^~ 2021-07-14T07:15:53,474 htslib/cram/cram_encode.c:3100:28: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:53,475 3100 | c->s_num_bases >= fd->bases_per_slice) { 2021-07-14T07:15:53,475 | ^~ 2021-07-14T07:15:58,627 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:15:58,720 In file included from htslib/cram/cram_external.c:43: 2021-07-14T07:15:58,721 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:15:58,721 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:58,721 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:15:58,721 | ^ 2021-07-14T07:15:58,840 In file included from htslib/cram/os.h:80, 2021-07-14T07:15:58,840 from htslib/cram/misc.h:66, 2021-07-14T07:15:58,840 from htslib/cram/cram_io.h:46, 2021-07-14T07:15:58,840 from htslib/cram/cram.h:48, 2021-07-14T07:15:58,840 from htslib/cram/cram_external.c:44: 2021-07-14T07:15:58,840 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:15:58,841 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:58,841 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:15:58,841 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:58,842 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:15:58,842 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:58,842 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:15:58,843 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:58,848 In file included from htslib/cram/cram.h:48, 2021-07-14T07:15:58,848 from htslib/cram/cram_external.c:44: 2021-07-14T07:15:58,848 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:15:58,849 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:58,849 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:15:58,850 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:58,857 In file included from htslib/cram/cram.h:52, 2021-07-14T07:15:58,857 from htslib/cram/cram_external.c:44: 2021-07-14T07:15:58,858 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:15:58,858 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:58,858 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:15:58,859 | ^~ 2021-07-14T07:15:58,859 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:58,859 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:15:58,860 | ^ 2021-07-14T07:15:59,227 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:15:59,415 In file included from htslib/cram/cram_index.c:64: 2021-07-14T07:15:59,416 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:15:59,416 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:15:59,416 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:15:59,416 | ^ 2021-07-14T07:15:59,506 In file included from htslib/cram/os.h:80, 2021-07-14T07:15:59,506 from htslib/cram/misc.h:66, 2021-07-14T07:15:59,506 from htslib/cram/cram_io.h:46, 2021-07-14T07:15:59,506 from htslib/cram/cram.h:48, 2021-07-14T07:15:59,506 from htslib/cram/cram_index.c:66: 2021-07-14T07:15:59,506 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:15:59,507 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:59,507 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:15:59,507 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:59,507 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:15:59,507 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:59,507 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:15:59,507 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:59,512 In file included from htslib/cram/cram.h:48, 2021-07-14T07:15:59,512 from htslib/cram/cram_index.c:66: 2021-07-14T07:15:59,512 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:15:59,513 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:15:59,513 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:15:59,513 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:15:59,521 In file included from htslib/cram/cram.h:52, 2021-07-14T07:15:59,522 from htslib/cram/cram_index.c:66: 2021-07-14T07:15:59,522 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:15:59,522 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:15:59,522 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:15:59,523 | ^~ 2021-07-14T07:15:59,523 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:15:59,523 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:15:59,523 | ^ 2021-07-14T07:15:59,534 htslib/cram/cram_index.c: In function ‘cram_index_build’: 2021-07-14T07:15:59,534 htslib/cram/cram_index.c:587:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] 2021-07-14T07:15:59,535 587 | off_t cpos, spos, hpos; 2021-07-14T07:15:59,535 | ^~~~ 2021-07-14T07:16:00,275 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:00,539 In file included from htslib/cram/os.h:80, 2021-07-14T07:16:00,540 from htslib/cram/misc.h:66, 2021-07-14T07:16:00,540 from htslib/cram/cram_io.h:46, 2021-07-14T07:16:00,540 from htslib/cram/cram.h:48, 2021-07-14T07:16:00,540 from htslib/cram/cram_io.c:77: 2021-07-14T07:16:00,540 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:00,540 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:00,541 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:00,541 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:00,541 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:00,541 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:00,541 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:00,541 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:00,546 In file included from htslib/cram/cram.h:48, 2021-07-14T07:16:00,546 from htslib/cram/cram_io.c:77: 2021-07-14T07:16:00,547 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:16:00,547 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:00,547 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:16:00,547 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:00,554 In file included from htslib/cram/cram.h:52, 2021-07-14T07:16:00,555 from htslib/cram/cram_io.c:77: 2021-07-14T07:16:00,555 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:16:00,555 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:16:00,555 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:16:00,555 | ^~ 2021-07-14T07:16:00,555 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:00,556 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:16:00,556 | ^ 2021-07-14T07:16:00,562 In file included from htslib/cram/cram_io.c:94: 2021-07-14T07:16:00,562 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:00,562 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:00,562 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:00,563 | ^ 2021-07-14T07:16:00,576 htslib/cram/cram_io.c: In function ‘itf8_decode_crc’: 2021-07-14T07:16:00,577 htslib/cram/cram_io.c:241:47: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:00,577 241 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:16:00,577 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:00,621 htslib/cram/cram_io.c: In function ‘expand_cache_path’: 2021-07-14T07:16:00,621 htslib/cram/cram_io.c:1920:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:00,621 1920 | if (cp-dir >= sz) return -1; 2021-07-14T07:16:00,622 | ^~ 2021-07-14T07:16:00,624 In file included from htslib/cram/cram_io.h:46, 2021-07-14T07:16:00,624 from htslib/cram/cram.h:48, 2021-07-14T07:16:00,624 from htslib/cram/cram_io.c:77: 2021-07-14T07:16:00,624 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:00,624 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:16:00,624 | ^ 2021-07-14T07:16:00,625 htslib/cram/cram_io.c:1938:17: note: in expansion of macro ‘MIN’ 2021-07-14T07:16:00,625 1938 | l = MIN(l, strlen(fn)); 2021-07-14T07:16:00,625 | ^~~ 2021-07-14T07:16:00,625 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] 2021-07-14T07:16:00,625 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:16:00,625 | ^~~ 2021-07-14T07:16:00,625 htslib/cram/cram_io.c:1938:17: note: in expansion of macro ‘MIN’ 2021-07-14T07:16:00,625 1938 | l = MIN(l, strlen(fn)); 2021-07-14T07:16:00,625 | ^~~ 2021-07-14T07:16:00,626 htslib/cram/cram_io.c:1940:23: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:00,626 1940 | if (l >= sz) return -1; 2021-07-14T07:16:00,626 | ^~ 2021-07-14T07:16:00,667 htslib/cram/cram_io.c: In function ‘cram_read_container’: 2021-07-14T07:16:00,668 htslib/cram/cram_io.c:2882:50: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:16:00,669 2882 | if (c2.num_landmarks < 0 || c2.num_landmarks >= SIZE_MAX / sizeof(int32_t)) 2021-07-14T07:16:00,669 | ^~ 2021-07-14T07:16:00,742 In file included from htslib/cram/cram.h:48, 2021-07-14T07:16:00,742 from htslib/cram/cram_io.c:77: 2021-07-14T07:16:00,742 htslib/cram/cram_io.c: In function ‘cram_write_SAM_hdr’: 2021-07-14T07:16:00,744 htslib/cram/cram_io.h:511:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:00,744 511 | while((b)->alloc <= (l)) { \ 2021-07-14T07:16:00,744 | ^~ 2021-07-14T07:16:00,744 htslib/cram/cram_io.c:3925:13: note: in expansion of macro ‘BLOCK_RESIZE’ 2021-07-14T07:16:00,744 3925 | BLOCK_RESIZE(b, padded_length); 2021-07-14T07:16:00,744 | ^~~~~~~~~~~~ 2021-07-14T07:16:04,763 In file included from /usr/include/string.h:495, 2021-07-14T07:16:04,763 from htslib/cram/cram_io.c:53: 2021-07-14T07:16:04,764 In function ‘strncpy’, 2021-07-14T07:16:04,764 inlined from ‘full_path’ at htslib/cram/cram_io.c:3748:13, 2021-07-14T07:16:04,764 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-14T07:16:04,764 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-14T07:16:04,764 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-14T07:16:04,764 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:04,765 In function ‘strncpy’, 2021-07-14T07:16:04,765 inlined from ‘full_path’ at htslib/cram/cram_io.c:3740:9, 2021-07-14T07:16:04,765 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-14T07:16:04,765 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-14T07:16:04,765 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-14T07:16:04,765 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:05,038 In function ‘strncpy’, 2021-07-14T07:16:05,038 inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4126:9: 2021-07-14T07:16:05,038 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 2021-07-14T07:16:05,039 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-14T07:16:05,039 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:05,813 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:06,022 In file included from htslib/cram/os.h:80, 2021-07-14T07:16:06,023 from htslib/cram/misc.h:66, 2021-07-14T07:16:06,023 from htslib/cram/cram_io.h:46, 2021-07-14T07:16:06,023 from htslib/cram/cram.h:48, 2021-07-14T07:16:06,023 from htslib/cram/cram_samtools.c:37: 2021-07-14T07:16:06,023 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:06,023 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:06,023 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:06,024 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:06,024 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:06,024 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:06,024 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:06,024 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:06,029 In file included from htslib/cram/cram.h:48, 2021-07-14T07:16:06,029 from htslib/cram/cram_samtools.c:37: 2021-07-14T07:16:06,029 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:16:06,029 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:06,029 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:16:06,030 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:06,037 In file included from htslib/cram/cram.h:52, 2021-07-14T07:16:06,037 from htslib/cram/cram_samtools.c:37: 2021-07-14T07:16:06,037 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:16:06,037 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:16:06,037 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:16:06,038 | ^~ 2021-07-14T07:16:06,038 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:06,038 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:16:06,038 | ^ 2021-07-14T07:16:06,041 htslib/cram/cram_samtools.c: In function ‘bam_construct_seq’: 2021-07-14T07:16:06,042 htslib/cram/cram_samtools.c:85:19: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:06,042 85 | if (b->m_data < bam_len) { 2021-07-14T07:16:06,042 | ^ 2021-07-14T07:16:06,214 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:06,479 In file included from htslib/cram/os.h:80, 2021-07-14T07:16:06,479 from htslib/cram/misc.h:66, 2021-07-14T07:16:06,479 from htslib/cram/cram_io.h:46, 2021-07-14T07:16:06,479 from htslib/cram/cram.h:48, 2021-07-14T07:16:06,480 from htslib/cram/cram_stats.c:43: 2021-07-14T07:16:06,480 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:06,480 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:06,480 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:06,480 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:06,480 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:06,481 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:06,481 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:06,481 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:06,486 In file included from htslib/cram/cram.h:48, 2021-07-14T07:16:06,486 from htslib/cram/cram_stats.c:43: 2021-07-14T07:16:06,486 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:16:06,486 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:06,487 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:16:06,487 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:06,494 In file included from htslib/cram/cram.h:52, 2021-07-14T07:16:06,494 from htslib/cram/cram_stats.c:43: 2021-07-14T07:16:06,494 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:16:06,494 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:16:06,495 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:16:06,495 | ^~ 2021-07-14T07:16:06,495 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:06,495 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:16:06,495 | ^ 2021-07-14T07:16:06,826 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:06,901 In file included from htslib/cram/os.h:80, 2021-07-14T07:16:06,901 from htslib/cram/misc.h:66, 2021-07-14T07:16:06,901 from htslib/cram/files.c:34: 2021-07-14T07:16:06,902 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:06,902 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:06,902 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:06,902 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:06,902 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:06,902 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:06,902 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:06,903 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:07,017 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:07,178 In file included from htslib/cram/os.h:80, 2021-07-14T07:16:07,178 from htslib/cram/mFILE.c:44: 2021-07-14T07:16:07,179 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:07,179 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:07,179 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:07,179 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:07,179 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:07,180 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:07,180 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:07,180 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:07,186 htslib/cram/mFILE.c: In function ‘mfload’: 2021-07-14T07:16:07,186 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] 2021-07-14T07:16:07,186 103 | } while (!feof(fp) && (fn == NULL || used < sb.st_size)); 2021-07-14T07:16:07,186 | ^ 2021-07-14T07:16:07,191 htslib/cram/mFILE.c: In function ‘mftruncate’: 2021-07-14T07:16:07,191 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] 2021-07-14T07:16:07,191 476 | mf->size = offset != -1 ? offset : mf->offset; 2021-07-14T07:16:07,192 | ^~~~~~ 2021-07-14T07:16:07,627 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:07,783 In file included from htslib/cram/os.h:80, 2021-07-14T07:16:07,783 from htslib/cram/open_trace_file.c:74: 2021-07-14T07:16:07,783 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:07,783 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:07,783 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:07,784 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:07,784 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:07,784 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:07,784 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:07,784 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:07,789 In file included from htslib/cram/open_trace_file.c:81: 2021-07-14T07:16:07,789 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:07,790 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:07,790 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:07,790 | ^ 2021-07-14T07:16:07,794 In file included from htslib/cram/open_trace_file.c:80: 2021-07-14T07:16:07,794 htslib/cram/open_trace_file.c: In function ‘expand_path’: 2021-07-14T07:16:07,794 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-14T07:16:07,795 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:16:07,795 | ^ 2021-07-14T07:16:07,795 htslib/cram/open_trace_file.c:251:29: note: in expansion of macro ‘MIN’ 2021-07-14T07:16:07,795 251 | path_end += MIN(strlen(file), l); 2021-07-14T07:16:07,795 | ^~~ 2021-07-14T07:16:07,795 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] 2021-07-14T07:16:07,796 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:16:07,796 | ^~~ 2021-07-14T07:16:07,796 htslib/cram/open_trace_file.c:251:29: note: in expansion of macro ‘MIN’ 2021-07-14T07:16:07,796 251 | path_end += MIN(strlen(file), l); 2021-07-14T07:16:07,796 | ^~~ 2021-07-14T07:16:07,796 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-14T07:16:07,796 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:16:07,797 | ^ 2021-07-14T07:16:07,797 htslib/cram/open_trace_file.c:252:29: note: in expansion of macro ‘MIN’ 2021-07-14T07:16:07,797 252 | file += MIN(strlen(file), l); 2021-07-14T07:16:07,797 | ^~~ 2021-07-14T07:16:07,797 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] 2021-07-14T07:16:07,797 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:16:07,797 | ^~~ 2021-07-14T07:16:07,797 htslib/cram/open_trace_file.c:252:29: note: in expansion of macro ‘MIN’ 2021-07-14T07:16:07,798 252 | file += MIN(strlen(file), l); 2021-07-14T07:16:07,798 | ^~~ 2021-07-14T07:16:08,161 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:08,283 In file included from htslib/cram/os.h:80, 2021-07-14T07:16:08,283 from htslib/cram/misc.h:66, 2021-07-14T07:16:08,283 from htslib/cram/pooled_alloc.c:38: 2021-07-14T07:16:08,284 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:08,284 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:08,284 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:08,284 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:08,284 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:08,284 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:08,285 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:08,285 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:08,389 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:08,530 htslib/cram/rANS_static.c: In function ‘rans_compress_O0’: 2021-07-14T07:16:08,531 htslib/cram/rANS_static.c:86:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:16:08,531 86 | for (i = 0; i < in_size; i++) { 2021-07-14T07:16:08,531 | ^ 2021-07-14T07:16:08,537 htslib/cram/rANS_static.c: In function ‘rans_compress_O1’: 2021-07-14T07:16:08,538 htslib/cram/rANS_static.c:388:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:16:08,538 388 | for (last_i=i=0; ih, type, &new))) 2021-07-14T07:16:10,015 | ^~ 2021-07-14T07:16:10,018 htslib/cram/sam_header.c: In function ‘sam_hdr_vadd’: 2021-07-14T07:16:10,018 htslib/cram/sam_header.c:451:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:10,018 451 | if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new))) 2021-07-14T07:16:10,019 | ^~ 2021-07-14T07:16:10,027 htslib/cram/sam_header.c: In function ‘sam_hdr_rebuild’: 2021-07-14T07:16:10,028 htslib/cram/sam_header.c:821:31: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:10,028 821 | if (kh_key(hdr->h, k) == K("HD")) 2021-07-14T07:16:10,028 | ^~ 2021-07-14T07:16:12,057 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:12,277 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/errmod.c -o build/temp.linux-armv7l-3.9/htslib/errmod.o 2021-07-14T07:16:13,019 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/faidx.c -o build/temp.linux-armv7l-3.9/htslib/faidx.o 2021-07-14T07:16:13,175 In file included from htslib/faidx.c:40: 2021-07-14T07:16:13,175 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:13,175 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:13,175 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:13,176 | ^ 2021-07-14T07:16:13,209 htslib/faidx.c: In function ‘fai_retrieve’: 2021-07-14T07:16:13,209 htslib/faidx.c:711:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-14T07:16:13,209 711 | while ( l < end - beg && (c=bgzf_getc(fai->bgzf))>=0 ) 2021-07-14T07:16:13,209 | ^ 2021-07-14T07:16:13,212 htslib/faidx.c: In function ‘fai_get_val’: 2021-07-14T07:16:13,212 htslib/faidx.c:789:22: warning: operand of ‘?:’ changes signedness from ‘long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:13,213 789 | end = i < k? strtol(s + i, &ep, 10) : val->len; 2021-07-14T07:16:13,213 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:13,213 htslib/faidx.c:801:13: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-14T07:16:13,214 801 | if (beg >= val->len) beg = val->len; 2021-07-14T07:16:13,214 | ^~ 2021-07-14T07:16:13,214 htslib/faidx.c:802:13: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-14T07:16:13,214 802 | if (end >= val->len) end = val->len; 2021-07-14T07:16:13,214 | ^~ 2021-07-14T07:16:13,215 htslib/faidx.c: In function ‘faidx_adjust_position’: 2021-07-14T07:16:13,216 htslib/faidx.c:882:22: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:13,216 882 | else if(val->len <= *p_beg_i) 2021-07-14T07:16:13,216 | ^~ 2021-07-14T07:16:13,216 htslib/faidx.c:887:22: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:13,217 887 | else if(val->len <= *p_end_i) 2021-07-14T07:16:13,217 | ^~ 2021-07-14T07:16:14,679 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hfile.c -o build/temp.linux-armv7l-3.9/htslib/hfile.o 2021-07-14T07:16:14,828 In file included from htslib/hfile.c:36: 2021-07-14T07:16:14,828 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:14,829 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:14,829 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:14,829 | ^ 2021-07-14T07:16:14,845 htslib/hfile.c: In function ‘hfile_set_blksize’: 2021-07-14T07:16:14,846 htslib/hfile.c:200:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘ptrdiff_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:16:14,846 200 | if (bufsiz < curr_used) 2021-07-14T07:16:14,846 | ^ 2021-07-14T07:16:14,849 htslib/hfile.c: In function ‘hseek’: 2021-07-14T07:16:14,850 htslib/hfile.c:436:35: warning: comparison of integer expressions of different signedness: ‘off_t’ {aka ‘long int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:14,850 436 | if (offset > 0 || -offset > length) { 2021-07-14T07:16:14,850 | ^ 2021-07-14T07:16:14,920 htslib/hfile.c: In function ‘find_scheme_handler’: 2021-07-14T07:16:14,920 htslib/hfile.c:1004:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:16:14,921 1004 | for (i = 0; i < sizeof scheme; i++) 2021-07-14T07:16:14,921 | ^ 2021-07-14T07:16:14,922 htslib/hfile.c:1011:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:16:14,922 1011 | if (i <= 1 || i >= sizeof scheme) return NULL; 2021-07-14T07:16:14,922 | ^~ 2021-07-14T07:16:15,919 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hfile_gcs.c -o build/temp.linux-armv7l-3.9/htslib/hfile_gcs.o 2021-07-14T07:16:16,060 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:16:16,060 from htslib/hfile_gcs.c:35: 2021-07-14T07:16:16,060 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:16,061 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:16,061 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:16,061 | ^ 2021-07-14T07:16:16,389 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hfile_libcurl.c -o build/temp.linux-armv7l-3.9/htslib/hfile_libcurl.o 2021-07-14T07:16:16,512 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:16:16,512 from htslib/hfile_libcurl.c:37: 2021-07-14T07:16:16,512 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:16,513 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:16,513 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:16,513 | ^ 2021-07-14T07:16:18,389 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:18,498 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:16:18,498 from htslib/hfile_net.c:30: 2021-07-14T07:16:18,498 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:18,499 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:18,499 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:18,499 | ^ 2021-07-14T07:16:18,612 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hfile_s3.c -o build/temp.linux-armv7l-3.9/htslib/hfile_s3.o 2021-07-14T07:16:18,740 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:16:18,740 from htslib/hfile_s3.c:33: 2021-07-14T07:16:18,741 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:18,741 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:18,741 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:18,741 | ^ 2021-07-14T07:16:19,845 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hts.c -o build/temp.linux-armv7l-3.9/htslib/hts.o 2021-07-14T07:16:20,095 In file included from htslib/cram/os.h:80, 2021-07-14T07:16:20,095 from htslib/cram/misc.h:66, 2021-07-14T07:16:20,095 from htslib/cram/cram_io.h:46, 2021-07-14T07:16:20,096 from htslib/cram/cram.h:48, 2021-07-14T07:16:20,096 from htslib/hts.c:41: 2021-07-14T07:16:20,096 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:20,096 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:20,096 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:20,096 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:20,096 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:20,097 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:20,097 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:20,097 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:20,101 In file included from htslib/cram/cram.h:48, 2021-07-14T07:16:20,102 from htslib/hts.c:41: 2021-07-14T07:16:20,102 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:16:20,102 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:20,102 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:16:20,102 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:20,110 In file included from htslib/cram/cram.h:52, 2021-07-14T07:16:20,110 from htslib/hts.c:41: 2021-07-14T07:16:20,110 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:16:20,111 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:16:20,111 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:16:20,111 | ^~ 2021-07-14T07:16:20,111 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:20,111 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:16:20,111 | ^ 2021-07-14T07:16:20,116 In file included from htslib/hts.c:42: 2021-07-14T07:16:20,116 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:20,116 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:20,116 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:20,116 | ^ 2021-07-14T07:16:20,180 htslib/hts.c: In function ‘hts_idx_init’: 2021-07-14T07:16:20,181 htslib/hts.c:1386:59: warning: overflow in conversion from ‘uint32_t’ {aka ‘unsigned int’} to ‘int’ changes value from ‘idx->z.last_bin = 4294967295’ to ‘-1’ [-Woverflow] 2021-07-14T07:16:20,181 1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; 2021-07-14T07:16:20,181 | ^~~ 2021-07-14T07:16:20,183 htslib/hts.c: In function ‘update_loff’: 2021-07-14T07:16:20,184 htslib/hts.c:1420:34: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:20,184 1420 | if ( kh_key(bidx, k) < idx->n_bins ) 2021-07-14T07:16:20,184 | ^ 2021-07-14T07:16:20,185 htslib/hts.c: In function ‘compress_binning’: 2021-07-14T07:16:20,186 htslib/hts.c:1447:55: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:20,186 1447 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue; 2021-07-14T07:16:20,186 | ^~ 2021-07-14T07:16:20,188 htslib/hts.c:1472:51: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:20,188 1472 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue; 2021-07-14T07:16:20,188 | ^~ 2021-07-14T07:16:20,212 htslib/hts.c: In function ‘hts_idx_load_local’: 2021-07-14T07:16:20,213 htslib/hts.c:1832:43: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:20,213 1832 | if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail; 2021-07-14T07:16:20,213 | ^~ 2021-07-14T07:16:20,217 htslib/hts.c:1859:46: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:20,217 1859 | if (bgzf_read(fp, idx->meta + 28, n) != n) goto fail; 2021-07-14T07:16:20,217 | ^~ 2021-07-14T07:16:20,235 htslib/hts.c: In function ‘hts_itr_multi_bam’: 2021-07-14T07:16:20,236 htslib/hts.c:2230:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:20,236 2230 | for(j=0; jcount; j++) { 2021-07-14T07:16:20,236 | ^ 2021-07-14T07:16:20,242 htslib/hts.c: In function ‘hts_itr_multi_cram’: 2021-07-14T07:16:20,243 htslib/hts.c:2341:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:20,243 2341 | for (j=0; j < curr_reg->count; j++) { 2021-07-14T07:16:20,243 | ^ 2021-07-14T07:16:20,265 htslib/hts.c: In function ‘hts_itr_multi_next’: 2021-07-14T07:16:20,266 htslib/hts.c:2737:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-14T07:16:20,266 2737 | if (beg > iter->off[iter->i].max) { 2021-07-14T07:16:20,266 | ^ 2021-07-14T07:16:20,267 htslib/hts.c:2741:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:20,268 2741 | if (beg > iter->reg_list[cr].max_end) 2021-07-14T07:16:20,268 | ^ 2021-07-14T07:16:20,269 htslib/hts.c:2744:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:20,270 2744 | for (i = ci; i < iter->reg_list[cr].count; i++) { 2021-07-14T07:16:20,270 | ^ 2021-07-14T07:16:20,271 htslib/hts.c:2745:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:20,271 2745 | if (end > iter->reg_list[cr].intervals[i].beg && iter->reg_list[cr].intervals[i].end > beg) { 2021-07-14T07:16:20,271 | ^ 2021-07-14T07:16:20,272 htslib/hts.c:2745:98: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:20,273 2745 | if (end > iter->reg_list[cr].intervals[i].beg && iter->reg_list[cr].intervals[i].end > beg) { 2021-07-14T07:16:20,273 | ^ 2021-07-14T07:16:20,275 htslib/hts.c: In function ‘test_and_fetch’: 2021-07-14T07:16:20,276 htslib/hts.c:2798:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:20,276 2798 | if (fwrite(buf, 1, l, local_fp) != l) { 2021-07-14T07:16:20,277 | ^~ 2021-07-14T07:16:20,283 htslib/hts.c: In function ‘hts_log’: 2021-07-14T07:16:20,284 htslib/hts.c:2967:18: warning: comparison of integer expressions of different signedness: ‘enum htsLogLevel’ and ‘int’ [-Wsign-compare] 2021-07-14T07:16:20,285 2967 | if (severity <= hts_verbose) { 2021-07-14T07:16:20,285 | ^~ 2021-07-14T07:16:25,667 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hts_os.c -o build/temp.linux-armv7l-3.9/htslib/hts_os.o 2021-07-14T07:16:25,807 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/kfunc.c -o build/temp.linux-armv7l-3.9/htslib/kfunc.o 2021-07-14T07:16:26,244 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/knetfile.c -o build/temp.linux-armv7l-3.9/htslib/knetfile.o 2021-07-14T07:16:27,010 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/kstring.c -o build/temp.linux-armv7l-3.9/htslib/kstring.o 2021-07-14T07:16:27,169 htslib/kstring.c: In function ‘kvsprintf’: 2021-07-14T07:16:27,170 htslib/kstring.c:156:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:27,170 156 | if (l + 1 > s->m - s->l) { 2021-07-14T07:16:27,170 | ^ 2021-07-14T07:16:27,738 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/md5.c -o build/temp.linux-armv7l-3.9/htslib/md5.o 2021-07-14T07:16:27,848 In file included from htslib/md5.c:53: 2021-07-14T07:16:27,849 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:27,849 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:27,849 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:27,849 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:27,849 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:27,850 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:27,850 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:27,850 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:28,319 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/multipart.c -o build/temp.linux-armv7l-3.9/htslib/multipart.o 2021-07-14T07:16:28,462 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:16:28,462 from htslib/multipart.c:34: 2021-07-14T07:16:28,462 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:28,462 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:28,462 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:28,463 | ^ 2021-07-14T07:16:28,839 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/probaln.c -o build/temp.linux-armv7l-3.9/htslib/probaln.o 2021-07-14T07:16:29,004 htslib/probaln.c: In function ‘probaln_glocal’: 2021-07-14T07:16:29,004 htslib/probaln.c:177:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:29,004 177 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-14T07:16:29,004 | ^~ 2021-07-14T07:16:29,005 htslib/probaln.c:201:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:29,006 201 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-14T07:16:29,006 | ^~ 2021-07-14T07:16:29,008 htslib/probaln.c:239:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:29,008 239 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-14T07:16:29,009 | ^~ 2021-07-14T07:16:29,534 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/realn.c -o build/temp.linux-armv7l-3.9/htslib/realn.o 2021-07-14T07:16:29,686 htslib/realn.c: In function ‘sam_cap_mapq’: 2021-07-14T07:16:29,686 htslib/realn.c:47:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:29,686 47 | for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { 2021-07-14T07:16:29,686 | ^ 2021-07-14T07:16:29,688 htslib/realn.c: In function ‘realn_check_tag’: 2021-07-14T07:16:29,688 htslib/realn.c:96:24: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘const int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:29,688 96 | if (b->core.l_qseq != strlen((const char *) tg + 1)) { 2021-07-14T07:16:29,688 | ^~ 2021-07-14T07:16:29,690 htslib/realn.c: In function ‘sam_prob_realn’: 2021-07-14T07:16:29,691 htslib/realn.c:158:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:29,691 158 | for (k = 0; k < c->n_cigar; ++k) { 2021-07-14T07:16:29,691 | ^ 2021-07-14T07:16:29,692 htslib/realn.c:188:32: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:16:29,692 188 | if (extend_baq && lref < c->l_qseq) 2021-07-14T07:16:29,692 | ^ 2021-07-14T07:16:29,693 htslib/realn.c:221:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:29,693 221 | for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { 2021-07-14T07:16:29,693 | ^ 2021-07-14T07:16:29,694 htslib/realn.c:247:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:29,694 247 | for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { 2021-07-14T07:16:29,694 | ^ 2021-07-14T07:16:30,295 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/regidx.c -o build/temp.linux-armv7l-3.9/htslib/regidx.o 2021-07-14T07:16:30,454 htslib/regidx.c: In function ‘regidx_insert’: 2021-07-14T07:16:30,454 htslib/regidx.c:156:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:30,454 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-14T07:16:30,455 | ^ 2021-07-14T07:16:30,455 htslib/regidx.c:156:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:30,455 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-14T07:16:30,455 | ^~ 2021-07-14T07:16:30,455 htslib/regidx.c:156:89: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:30,455 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-14T07:16:30,455 | ^ 2021-07-14T07:16:31,205 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/sam.c -o build/temp.linux-armv7l-3.9/htslib/sam.o 2021-07-14T07:16:31,440 In file included from htslib/cram/os.h:80, 2021-07-14T07:16:31,440 from htslib/cram/misc.h:66, 2021-07-14T07:16:31,440 from htslib/cram/cram_io.h:46, 2021-07-14T07:16:31,440 from htslib/cram/cram.h:48, 2021-07-14T07:16:31,441 from htslib/sam.c:37: 2021-07-14T07:16:31,441 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:31,441 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:31,441 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:31,441 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:31,441 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:31,441 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:31,442 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:31,442 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:31,446 In file included from htslib/cram/cram.h:48, 2021-07-14T07:16:31,446 from htslib/sam.c:37: 2021-07-14T07:16:31,447 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:16:31,447 htslib/cram/cram_io.h:296:43: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:31,447 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:16:31,447 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:31,455 In file included from htslib/cram/cram.h:52, 2021-07-14T07:16:31,455 from htslib/sam.c:37: 2021-07-14T07:16:31,455 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:16:31,455 htslib/cram/cram_codecs.h:169:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:16:31,456 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:16:31,456 | ^~ 2021-07-14T07:16:31,456 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:31,456 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:16:31,456 | ^ 2021-07-14T07:16:31,467 In file included from htslib/sam.c:39: 2021-07-14T07:16:31,467 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:31,467 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,467 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:31,468 | ^ 2021-07-14T07:16:31,473 htslib/sam.c: In function ‘bam_hdr_read’: 2021-07-14T07:16:31,473 htslib/sam.c:155:15: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,473 155 | if (bytes != h->l_text) goto read_err; 2021-07-14T07:16:31,473 | ^~ 2021-07-14T07:16:31,476 htslib/sam.c: In function ‘possibly_expand_bam_data’: 2021-07-14T07:16:31,477 htslib/sam.c:323:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:31,477 323 | if (new_len > INT32_MAX || new_len < b->l_data) { 2021-07-14T07:16:31,477 | ^ 2021-07-14T07:16:31,479 htslib/sam.c: In function ‘bam_tag2cigar’: 2021-07-14T07:16:31,479 htslib/sam.c:408:81: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:16:31,479 408 | if (bam_cigar_op(cigar0[0]) != BAM_CSOFT_CLIP || bam_cigar_oplen(cigar0[0]) != c->l_qseq) return 0; 2021-07-14T07:16:31,480 | ^~ 2021-07-14T07:16:31,486 htslib/sam.c: In function ‘bam_write1’: 2021-07-14T07:16:31,486 htslib/sam.c:564:32: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:31,487 564 | return ok? 4 + block_len : -1; 2021-07-14T07:16:31,487 | ^~ 2021-07-14T07:16:31,502 htslib/sam.c: In function ‘sam_hdr_write’: 2021-07-14T07:16:31,502 htslib/sam.c:1108:67: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,503 1108 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-14T07:16:31,503 | ^~ 2021-07-14T07:16:31,504 htslib/sam.c: In function ‘sam_hdr_change_HD’: 2021-07-14T07:16:31,504 htslib/sam.c:1143:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:31,505 1143 | && strlen(val) == end - beg - 4) 2021-07-14T07:16:31,505 | ^~ 2021-07-14T07:16:31,511 htslib/sam.c: In function ‘sam_parse1’: 2021-07-14T07:16:31,512 htslib/sam.c:1262:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,512 1262 | for (i = 0; i < c->n_cigar; ++i, ++q) { 2021-07-14T07:16:31,512 | ^ 2021-07-14T07:16:31,519 htslib/sam.c:1392:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int32_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:16:31,519 1392 | _parse_err(bytes / size != n 2021-07-14T07:16:31,520 | ^~ 2021-07-14T07:16:31,520 htslib/sam.c:1202:40: note: in definition of macro ‘_parse_err’ 2021-07-14T07:16:31,520 1202 | #define _parse_err(cond, msg) do { if (cond) { hts_log_error(msg); goto err_ret; } } while (0) 2021-07-14T07:16:31,520 | ^~~~ 2021-07-14T07:16:31,523 htslib/sam.c: In function ‘sam_format1’: 2021-07-14T07:16:31,524 htslib/sam.c:1495:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,524 1495 | for (i = 0; i < c->n_cigar; ++i) { 2021-07-14T07:16:31,524 | ^ 2021-07-14T07:16:31,529 htslib/sam.c:1586:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,530 1586 | if ((end - s) / sub_type_size < n) 2021-07-14T07:16:31,530 | ^ 2021-07-14T07:16:31,530 htslib/sam.c:1589:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,531 1589 | for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if" 2021-07-14T07:16:31,531 | ^ 2021-07-14T07:16:31,532 htslib/sam.c: In function ‘sam_write1’: 2021-07-14T07:16:31,533 htslib/sam.c:1633:59: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,533 1633 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-14T07:16:31,533 | ^~ 2021-07-14T07:16:31,533 htslib/sam.c: In function ‘bam_aux_append’: 2021-07-14T07:16:31,534 htslib/sam.c:1695:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:31,534 1695 | if (new_len > INT32_MAX || new_len < b->l_data) goto nomem; 2021-07-14T07:16:31,535 | ^ 2021-07-14T07:16:31,537 htslib/sam.c: In function ‘skip_aux’: 2021-07-14T07:16:31,538 htslib/sam.c:1737:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,538 1737 | if (size == 0 || end - s < size * n) return NULL; 2021-07-14T07:16:31,538 | ^ 2021-07-14T07:16:31,571 htslib/sam.c: In function ‘resolve_cigar2’: 2021-07-14T07:16:31,572 htslib/sam.c:2287:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,573 2287 | for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) { 2021-07-14T07:16:31,573 | ^ 2021-07-14T07:16:31,575 htslib/sam.c:2309:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,576 2309 | for (k = s->k + 1; k < c->n_cigar; ++k) { 2021-07-14T07:16:31,576 | ^ 2021-07-14T07:16:31,577 htslib/sam.c:2323:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,577 2323 | if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation 2021-07-14T07:16:31,577 | ^ 2021-07-14T07:16:31,578 htslib/sam.c:2328:50: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,579 2328 | else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding 2021-07-14T07:16:31,579 | ^ 2021-07-14T07:16:31,580 htslib/sam.c:2330:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:31,580 2330 | for (k = s->k + 2; k < c->n_cigar; ++k) { 2021-07-14T07:16:31,580 | ^ 2021-07-14T07:16:37,989 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:38,159 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:16:38,159 from htslib/htslib/synced_bcf_reader.h:60, 2021-07-14T07:16:38,159 from htslib/synced_bcf_reader.c:34: 2021-07-14T07:16:38,159 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:38,159 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:38,160 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:38,160 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:38,160 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:38,160 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:38,160 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:38,160 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:38,210 htslib/synced_bcf_reader.c: In function ‘_regions_add’: 2021-07-14T07:16:38,210 htslib/synced_bcf_reader.c:801:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:38,211 801 | if ( start < creg->regs[i].start ) max = i - 1; 2021-07-14T07:16:38,211 | ^ 2021-07-14T07:16:38,211 htslib/synced_bcf_reader.c:802:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:38,211 802 | else if ( start > creg->regs[i].start ) min = i + 1; 2021-07-14T07:16:38,211 | ^ 2021-07-14T07:16:38,211 htslib/synced_bcf_reader.c:805:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:38,211 805 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-14T07:16:38,212 | ^~ 2021-07-14T07:16:38,212 htslib/synced_bcf_reader.c:805:68: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:38,212 805 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-14T07:16:38,212 | ^~ 2021-07-14T07:16:40,021 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/tbx.c -o build/temp.linux-armv7l-3.9/htslib/tbx.o 2021-07-14T07:16:40,192 In file included from htslib/tbx.c:35: 2021-07-14T07:16:40,192 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:40,193 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:40,193 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:40,193 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:40,193 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:40,193 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:40,193 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:40,194 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:40,214 htslib/tbx.c: In function ‘tbx_index_load2’: 2021-07-14T07:16:40,214 htslib/tbx.c:321:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:40,214 321 | for (; p - nm < l_nm; p += strlen(p) + 1) { 2021-07-14T07:16:40,215 | ^ 2021-07-14T07:16:40,716 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/textutils.c -o build/temp.linux-armv7l-3.9/htslib/textutils.o 2021-07-14T07:16:40,821 In file included from htslib/textutils.c:30: 2021-07-14T07:16:40,822 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:40,822 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:40,822 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:40,822 | ^ 2021-07-14T07:16:41,471 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/thread_pool.c -o build/temp.linux-armv7l-3.9/htslib/thread_pool.o 2021-07-14T07:16:42,216 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/vcf.c -o build/temp.linux-armv7l-3.9/htslib/vcf.o 2021-07-14T07:16:42,361 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:16:42,361 from htslib/vcf.c:38: 2021-07-14T07:16:42,361 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:42,362 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:42,362 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:42,362 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:42,362 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:42,362 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:42,362 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:42,362 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:42,400 In file included from htslib/vcf.c:41: 2021-07-14T07:16:42,400 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:16:42,400 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,401 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:16:42,401 | ^ 2021-07-14T07:16:42,427 htslib/vcf.c: In function ‘bcf_hdr_sync’: 2021-07-14T07:16:42,428 htslib/vcf.c:149:22: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,428 149 | if ( h->n[i] < kh_size(d) ) 2021-07-14T07:16:42,428 | ^ 2021-07-14T07:16:42,438 htslib/vcf.c: In function ‘bcf_hdr_register_hrec’: 2021-07-14T07:16:42,438 htslib/vcf.c:499:18: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:42,439 499 | if (type == -1) { 2021-07-14T07:16:42,439 | ^~ 2021-07-14T07:16:42,439 htslib/vcf.c:504:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:42,439 504 | if (var == -1) { 2021-07-14T07:16:42,439 | ^~ 2021-07-14T07:16:42,452 htslib/vcf.c: In function ‘bcf_hdr_read’: 2021-07-14T07:16:42,452 htslib/vcf.c:917:35: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,452 917 | if (bgzf_read(fp, htxt, hlen) != hlen) goto fail; 2021-07-14T07:16:42,452 | ^~ 2021-07-14T07:16:42,454 htslib/vcf.c: In function ‘bcf_hdr_write’: 2021-07-14T07:16:42,454 htslib/vcf.c:948:41: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,454 948 | if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1; 2021-07-14T07:16:42,455 | ^~ 2021-07-14T07:16:42,457 htslib/vcf.c: In function ‘bcf_read1_core’: 2021-07-14T07:16:42,458 htslib/vcf.c:1033:49: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,458 1033 | if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -2; 2021-07-14T07:16:42,458 | ^~ 2021-07-14T07:16:42,459 htslib/vcf.c:1034:47: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,459 1034 | if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -2; 2021-07-14T07:16:42,459 | ^~ 2021-07-14T07:16:42,460 htslib/vcf.c: In function ‘bcf_dec_typed_int1_safe’: 2021-07-14T07:16:42,461 htslib/vcf.c:1058:33: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:42,461 1058 | *val = v < 0x8000 ? v : -((int32_t) (0xffff - v)) - 1; 2021-07-14T07:16:42,461 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:42,462 htslib/vcf.c:1063:39: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:42,462 1063 | *val = v < 0x80000000UL ? v : -((int32_t) (0xffffffffUL - v)) - 1; 2021-07-14T07:16:42,462 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:42,464 htslib/vcf.c: In function ‘bcf_record_check’: 2021-07-14T07:16:42,464 htslib/vcf.c:1125:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,464 1125 | if (end - ptr < bytes) goto bad_shared; 2021-07-14T07:16:42,464 | ^ 2021-07-14T07:16:42,466 htslib/vcf.c:1138:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,466 1138 | if (end - ptr < bytes) goto bad_shared; 2021-07-14T07:16:42,466 | ^ 2021-07-14T07:16:42,467 htslib/vcf.c:1151:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,467 1151 | if (end - ptr < bytes) goto bad_shared; 2021-07-14T07:16:42,467 | ^ 2021-07-14T07:16:42,468 htslib/vcf.c:1152:23: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:16:42,468 1152 | for (i = 0; i < num; i++) { 2021-07-14T07:16:42,468 | ^ 2021-07-14T07:16:42,470 htslib/vcf.c:1179:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,470 1179 | if (end - ptr < bytes) goto bad_shared; 2021-07-14T07:16:42,470 | ^ 2021-07-14T07:16:42,472 htslib/vcf.c:1202:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,472 1202 | if (end - ptr < bytes) goto bad_indiv; 2021-07-14T07:16:42,472 | ^ 2021-07-14T07:16:42,483 htslib/vcf.c: In function ‘bcf_write’: 2021-07-14T07:16:42,484 htslib/vcf.c:1533:51: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,484 1533 | if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1; 2021-07-14T07:16:42,484 | ^~ 2021-07-14T07:16:42,485 htslib/vcf.c:1534:49: warning: comparison of integer expressions of different signedness: ‘ssize_t’ {aka ‘int’} and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,485 1534 | if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1; 2021-07-14T07:16:42,485 | ^~ 2021-07-14T07:16:42,503 htslib/vcf.c: In function ‘vcf_parse_format’: 2021-07-14T07:16:42,504 htslib/vcf.c:1970:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:16:42,504 1970 | if (fmt[j].max_l < l) fmt[j].max_l = l; 2021-07-14T07:16:42,504 | ^ 2021-07-14T07:16:42,508 htslib/vcf.c:2000:33: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:42,509 2000 | f->size = f->is_gt? f->max_g << 2 : f->max_l; 2021-07-14T07:16:42,509 | ^~~~~~~~~~~~~ 2021-07-14T07:16:42,548 htslib/vcf.c: In function ‘vcf_write_line’: 2021-07-14T07:16:42,550 htslib/vcf.c:2611:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,550 2611 | return ret==line->l ? 0 : -1; 2021-07-14T07:16:42,550 | ^~ 2021-07-14T07:16:42,551 htslib/vcf.c: In function ‘vcf_write’: 2021-07-14T07:16:42,552 htslib/vcf.c:2624:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,552 2624 | return ret==fp->line.l ? 0 : -1; 2021-07-14T07:16:42,553 | ^~ 2021-07-14T07:16:42,586 htslib/vcf.c: In function ‘bcf_hdr_set_samples’: 2021-07-14T07:16:42,587 htslib/vcf.c:3136:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:16:42,587 3136 | for (k = kh_begin(d); k != kh_end(d); ++k) 2021-07-14T07:16:42,587 | ^~ 2021-07-14T07:16:42,635 htslib/vcf.c: In function ‘_bcf1_sync_alleles’: 2021-07-14T07:16:42,637 htslib/vcf.c:3586:29: warning: operand of ‘?:’ changes signedness from ‘int32_t’ {aka ‘int’} to ‘size_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:42,637 3586 | line->rlen = end_info ? end_info->v1.i - line->pos : strlen(line->d.allele[0]); 2021-07-14T07:16:42,637 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:42,648 htslib/vcf.c: In function ‘bcf_get_info_values’: 2021-07-14T07:16:42,650 htslib/vcf.c:3716:49: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:16:42,650 3716 | if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2; // expected different type 2021-07-14T07:16:42,651 | ^~ 2021-07-14T07:16:42,666 htslib/vcf.c: In function ‘bcf_get_format_values’: 2021-07-14T07:16:42,668 htslib/vcf.c:3819:53: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:16:42,668 3819 | else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2; // expected different type 2021-07-14T07:16:42,668 | ^~ 2021-07-14T07:16:51,493 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/home/piwheels/.local/lib/python3.9/site-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 2021-07-14T07:16:51,638 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:16:51,638 from htslib/htslib/vcf_sweep.h:30, 2021-07-14T07:16:51,638 from htslib/vcf_sweep.c:27: 2021-07-14T07:16:51,639 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:51,639 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:51,639 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:51,639 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:51,639 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:51,640 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:51,640 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:51,640 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:51,677 htslib/vcf_sweep.c: In function ‘bcf_sweep_fwd’: 2021-07-14T07:16:51,678 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] 2021-07-14T07:16:51,678 164 | if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size ) 2021-07-14T07:16:51,678 | ^ 2021-07-14T07:16:51,869 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/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/vcfutils.c -o build/temp.linux-armv7l-3.9/htslib/vcfutils.o 2021-07-14T07:16:52,011 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:16:52,011 from htslib/htslib/vcfutils.h:29, 2021-07-14T07:16:52,012 from htslib/vcfutils.c:27: 2021-07-14T07:16:52,012 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:16:52,012 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:52,012 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:16:52,012 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:52,012 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:16:52,013 htslib/htslib/hts_endian.h:257:19: warning: operand of ‘?:’ changes signedness from ‘long long int’ to ‘uint64_t’ {aka ‘long long unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:16:52,013 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:16:52,013 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:16:54,332 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/bcf_sr_sort.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/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_gcs.o build/temp.linux-armv7l-3.9/htslib/hfile_libcurl.o build/temp.linux-armv7l-3.9/htslib/hfile_net.o build/temp.linux-armv7l-3.9/htslib/hfile_s3.o build/temp.linux-armv7l-3.9/htslib/hts.o build/temp.linux-armv7l-3.9/htslib/hts_os.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/multipart.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/textutils.o build/temp.linux-armv7l-3.9/htslib/thread_pool.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 -lbz2 -llzma -lcurl -lssl -lcrypt -o build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so 2021-07-14T07:16:55,022 installing to build/bdist.linux-armv7l/wheel 2021-07-14T07:16:55,023 running install 2021-07-14T07:16:55,024 running install_lib 2021-07-14T07:16:55,028 creating build/bdist.linux-armv7l 2021-07-14T07:16:55,028 creating build/bdist.linux-armv7l/wheel 2021-07-14T07:16:55,030 creating build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,031 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,034 copying build/lib.linux-armv7l-3.9/cyvcf2/relatedness.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,036 copying build/lib.linux-armv7l-3.9/cyvcf2/__main__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,038 copying build/lib.linux-armv7l-3.9/cyvcf2/cli.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,041 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,044 creating build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,045 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,047 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,049 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,050 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,054 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,056 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/decomposed.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,058 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_cli.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,060 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/empty.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,061 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,068 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,070 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,073 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,076 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-alt-repr.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,078 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,094 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,096 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,098 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,100 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,102 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,105 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,107 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,110 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,111 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,115 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,118 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/issue_44.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,120 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,122 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,124 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,126 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_alt_freqs.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,129 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/seg.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:16:55,131 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,268 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,273 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,275 copying build/lib.linux-armv7l-3.9/cyvcf2/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,276 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:16:55,332 running install_egg_info 2021-07-14T07:16:55,342 Copying cyvcf2.egg-info to build/bdist.linux-armv7l/wheel/cyvcf2-0.10.8-py3.9.egg-info 2021-07-14T07:16:55,358 running install_scripts 2021-07-14T07:16:55,399 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-14T07:16:55,404 creating build/bdist.linux-armv7l/wheel/cyvcf2-0.10.8.dist-info/WHEEL 2021-07-14T07:16:55,407 creating '/tmp/pip-wheel-tuxqt7ss/cyvcf2-0.10.8-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-14T07:16:55,410 adding 'cyvcf2/__init__.py' 2021-07-14T07:16:55,412 adding 'cyvcf2/__main__.py' 2021-07-14T07:16:55,413 adding 'cyvcf2/cli.py' 2021-07-14T07:16:55,622 adding 'cyvcf2/cyvcf2.c' 2021-07-14T07:16:57,005 adding 'cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T07:16:57,059 adding 'cyvcf2/cyvcf2.pxd' 2021-07-14T07:16:57,069 adding 'cyvcf2/cyvcf2.pyx' 2021-07-14T07:16:57,071 adding 'cyvcf2/helpers.c' 2021-07-14T07:16:57,073 adding 'cyvcf2/helpers.h' 2021-07-14T07:16:57,075 adding 'cyvcf2/relatedness.h' 2021-07-14T07:16:57,077 adding 'cyvcf2/tests/__init__.py' 2021-07-14T07:16:57,078 adding 'cyvcf2/tests/__init__.pyc' 2021-07-14T07:16:57,080 adding 'cyvcf2/tests/bug.vcf.gz' 2021-07-14T07:16:57,082 adding 'cyvcf2/tests/decomposed.vcf' 2021-07-14T07:16:57,083 adding 'cyvcf2/tests/empty.vcf' 2021-07-14T07:16:57,084 adding 'cyvcf2/tests/issue_44.vcf' 2021-07-14T07:16:57,089 adding 'cyvcf2/tests/o.vcf.gz' 2021-07-14T07:16:57,092 adding 'cyvcf2/tests/seg.vcf.gz' 2021-07-14T07:16:57,093 adding 'cyvcf2/tests/test-alt-repr.vcf' 2021-07-14T07:16:57,095 adding 'cyvcf2/tests/test-format-string.vcf' 2021-07-14T07:16:57,137 adding 'cyvcf2/tests/test-haploidX.vcf' 2021-07-14T07:16:57,144 adding 'cyvcf2/tests/test-hemi.vcf' 2021-07-14T07:16:57,146 adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz' 2021-07-14T07:16:57,147 adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi' 2021-07-14T07:16:57,149 adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz' 2021-07-14T07:16:57,150 adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi' 2021-07-14T07:16:57,152 adding 'cyvcf2/tests/test.comp_het.3.vcf' 2021-07-14T07:16:57,154 adding 'cyvcf2/tests/test.snpeff.bcf' 2021-07-14T07:16:57,156 adding 'cyvcf2/tests/test.snpeff.bcf.csi' 2021-07-14T07:16:57,158 adding 'cyvcf2/tests/test.snpeff.vcf' 2021-07-14T07:16:57,179 adding 'cyvcf2/tests/test.vcf.gz' 2021-07-14T07:16:57,182 adding 'cyvcf2/tests/test.vcf.gz.tbi' 2021-07-14T07:16:57,184 adding 'cyvcf2/tests/test_cli.py' 2021-07-14T07:16:57,185 adding 'cyvcf2/tests/test_cli.pyc' 2021-07-14T07:16:57,188 adding 'cyvcf2/tests/test_gt_alt_freqs.vcf' 2021-07-14T07:16:57,190 adding 'cyvcf2/tests/test_gt_bases.vcf.gz' 2021-07-14T07:16:57,191 adding 'cyvcf2/tests/test_hemi.py' 2021-07-14T07:16:57,193 adding 'cyvcf2/tests/test_hemi.pyc' 2021-07-14T07:16:57,196 adding 'cyvcf2/tests/test_reader.py' 2021-07-14T07:16:57,204 adding 'cyvcf2/tests/test_reader.pyc' 2021-07-14T07:16:57,207 adding 'cyvcf2-0.10.8.dist-info/LICENSE' 2021-07-14T07:16:57,208 adding 'cyvcf2-0.10.8.dist-info/METADATA' 2021-07-14T07:16:57,210 adding 'cyvcf2-0.10.8.dist-info/WHEEL' 2021-07-14T07:16:57,211 adding 'cyvcf2-0.10.8.dist-info/entry_points.txt' 2021-07-14T07:16:57,212 adding 'cyvcf2-0.10.8.dist-info/top_level.txt' 2021-07-14T07:16:57,214 adding 'cyvcf2-0.10.8.dist-info/RECORD' 2021-07-14T07:16:57,263 removing build/bdist.linux-armv7l/wheel 2021-07-14T07:16:57,829 Building wheel for cyvcf2 (setup.py): finished with status 'done' 2021-07-14T07:16:57,872 Created wheel for cyvcf2: filename=cyvcf2-0.10.8-cp39-cp39-linux_armv7l.whl size=3262862 sha256=ac8a366f1c294646010a461e56a51f1f7b9411aa721f6a5ff0d4fa35d7cbf322 2021-07-14T07:16:57,872 Stored in directory: /tmp/pip-ephem-wheel-cache-3_rs41uo/wheels/34/22/3b/04b05a602a73c49818cfff7a2d1540c17bcf47322204e04e5c 2021-07-14T07:16:57,884 Successfully built cyvcf2 2021-07-14T07:16:58,004 Removed build tracker: '/tmp/pip-req-tracker-qybnd105'