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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/) 2021-07-14T07:11:05,499 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 2021-07-14T07:11:05,500 Skipping link: not a file: https://pypi.org/simple/cyvcf2/ 2021-07-14T07:11:05,512 Given no hashes to check 1 links for project 'cyvcf2': discarding no candidates 2021-07-14T07:11:05,531 Collecting cyvcf2==0.10.7 2021-07-14T07:11:05,533 Created temporary directory: /tmp/pip-unpack-0qmpcuxh 2021-07-14T07:11:06,179 Downloading cyvcf2-0.10.7.tar.gz (1.1 MB) 2021-07-14T07:11:07,088 Added cyvcf2==0.10.7 from https://files.pythonhosted.org/packages/1f/35/8c307cae68e5000f45a0b0c739e416c8d62c700acc28c3e06108f065303a/cyvcf2-0.10.7.tar.gz#sha256=7721b28a3f676164df45a15a2efe08e35c5905dd7cc4fe3b86920409d76682a9 to build tracker '/tmp/pip-req-tracker-z01i9hmt' 2021-07-14T07:11:07,089 Running setup.py (path:/tmp/pip-wheel-dtq9mior/cyvcf2_6f734839794f470d855c47025b46762a/setup.py) egg_info for package cyvcf2 2021-07-14T07:11:07,090 Created temporary directory: /tmp/pip-pip-egg-info-kvg5hjof 2021-07-14T07:11:07,090 Running command python setup.py egg_info 2021-07-14T07:11:10,418 Collecting coloredlogs 2021-07-14T07:11:10,539 Downloading coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) 2021-07-14T07:11:10,782 Collecting humanfriendly>=9.1 2021-07-14T07:11:10,789 Downloading humanfriendly-9.2-py2.py3-none-any.whl (86 kB) 2021-07-14T07:11:14,412 Installing collected packages: humanfriendly, coloredlogs 2021-07-14T07:11:14,762 Successfully installed coloredlogs-15.0.1 humanfriendly-9.2 2021-07-14T07:11:15,578 running egg_info 2021-07-14T07:11:15,581 creating /tmp/pip-pip-egg-info-kvg5hjof/cyvcf2.egg-info 2021-07-14T07:11:15,582 writing /tmp/pip-pip-egg-info-kvg5hjof/cyvcf2.egg-info/PKG-INFO 2021-07-14T07:11:15,585 writing dependency_links to /tmp/pip-pip-egg-info-kvg5hjof/cyvcf2.egg-info/dependency_links.txt 2021-07-14T07:11:15,587 writing entry points to /tmp/pip-pip-egg-info-kvg5hjof/cyvcf2.egg-info/entry_points.txt 2021-07-14T07:11:15,588 writing requirements to /tmp/pip-pip-egg-info-kvg5hjof/cyvcf2.egg-info/requires.txt 2021-07-14T07:11:15,589 writing top-level names to /tmp/pip-pip-egg-info-kvg5hjof/cyvcf2.egg-info/top_level.txt 2021-07-14T07:11:15,590 writing manifest file '/tmp/pip-pip-egg-info-kvg5hjof/cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:11:15,769 reading manifest file '/tmp/pip-pip-egg-info-kvg5hjof/cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:11:15,771 reading manifest template 'MANIFEST.in' 2021-07-14T07:11:15,787 adding license file 'LICENSE' 2021-07-14T07:11:15,796 writing manifest file '/tmp/pip-pip-egg-info-kvg5hjof/cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:11:15,907 Source in /tmp/pip-wheel-dtq9mior/cyvcf2_6f734839794f470d855c47025b46762a has version 0.10.7, which satisfies requirement cyvcf2==0.10.7 from https://files.pythonhosted.org/packages/1f/35/8c307cae68e5000f45a0b0c739e416c8d62c700acc28c3e06108f065303a/cyvcf2-0.10.7.tar.gz#sha256=7721b28a3f676164df45a15a2efe08e35c5905dd7cc4fe3b86920409d76682a9 2021-07-14T07:11:15,908 Removed cyvcf2==0.10.7 from https://files.pythonhosted.org/packages/1f/35/8c307cae68e5000f45a0b0c739e416c8d62c700acc28c3e06108f065303a/cyvcf2-0.10.7.tar.gz#sha256=7721b28a3f676164df45a15a2efe08e35c5905dd7cc4fe3b86920409d76682a9 from build tracker '/tmp/pip-req-tracker-z01i9hmt' 2021-07-14T07:11:15,913 Created temporary directory: /tmp/pip-unpack-_7htsi4f 2021-07-14T07:11:15,913 Building wheels for collected packages: cyvcf2 2021-07-14T07:11:15,917 Created temporary directory: /tmp/pip-wheel-e0zr5ctz 2021-07-14T07:11:15,918 Building wheel for cyvcf2 (setup.py): started 2021-07-14T07:11:15,918 Destination directory: /tmp/pip-wheel-e0zr5ctz 2021-07-14T07:11:15,918 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-dtq9mior/cyvcf2_6f734839794f470d855c47025b46762a/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-dtq9mior/cyvcf2_6f734839794f470d855c47025b46762a/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-e0zr5ctz 2021-07-14T07:11:17,583 running bdist_wheel 2021-07-14T07:11:17,588 running build 2021-07-14T07:11:17,588 running build_py 2021-07-14T07:11:17,725 creating build 2021-07-14T07:11:17,725 creating build/lib.linux-armv7l-3.9 2021-07-14T07:11:17,726 creating build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,727 copying cyvcf2/cli.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,730 copying cyvcf2/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,731 copying cyvcf2/__main__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,734 creating build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,734 copying cyvcf2/tests/test_hemi.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,736 copying cyvcf2/tests/test_cli.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,738 copying cyvcf2/tests/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,740 copying cyvcf2/tests/test_reader.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,742 running egg_info 2021-07-14T07:11:17,757 writing cyvcf2.egg-info/PKG-INFO 2021-07-14T07:11:17,760 writing dependency_links to cyvcf2.egg-info/dependency_links.txt 2021-07-14T07:11:17,762 writing entry points to cyvcf2.egg-info/entry_points.txt 2021-07-14T07:11:17,763 writing requirements to cyvcf2.egg-info/requires.txt 2021-07-14T07:11:17,764 writing top-level names to cyvcf2.egg-info/top_level.txt 2021-07-14T07:11:17,806 reading manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:11:17,812 reading manifest template 'MANIFEST.in' 2021-07-14T07:11:17,825 adding license file 'LICENSE' 2021-07-14T07:11:17,835 writing manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-14T07:11:17,842 copying cyvcf2/cyvcf2.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,906 copying cyvcf2/cyvcf2.pxd -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,909 copying cyvcf2/cyvcf2.pyx -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,913 copying cyvcf2/helpers.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,915 copying cyvcf2/helpers.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,918 copying cyvcf2/relatedness.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:17,920 copying cyvcf2/tests/__init__.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,923 copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,926 copying cyvcf2/tests/decomposed.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,928 copying cyvcf2/tests/empty.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,930 copying cyvcf2/tests/issue_44.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,932 copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,937 copying cyvcf2/tests/seg.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,940 copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,942 copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,945 copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,964 copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,967 copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,970 copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,972 copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,974 copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,976 copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,979 copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,982 copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,985 copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,988 copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,996 copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:17,998 copying cyvcf2/tests/test_cli.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:18,000 copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:18,004 copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:18,007 copying cyvcf2/tests/test_hemi.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:18,009 copying cyvcf2/tests/test_reader.pyc -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-14T07:11:18,015 running build_ext 2021-07-14T07:11:18,112 cythoning cyvcf2/cyvcf2.pyx to cyvcf2/cyvcf2.c 2021-07-14T07:11:18,716 /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-dtq9mior/cyvcf2_6f734839794f470d855c47025b46762a/cyvcf2/cyvcf2.pxd 2021-07-14T07:11:18,716 tree = Parsing.p_module(s, pxd, full_module_name) 2021-07-14T07:11:20,143 warning: cyvcf2/cyvcf2.pxd:26:16: Declarations should not be declared inline. 2021-07-14T07:11:20,152 warning: cyvcf2/cyvcf2.pxd:188:14: 'BCF_HT_FLAG' redeclared 2021-07-14T07:11:20,164 warning: cyvcf2/cyvcf2.pxd:279:30: Declarations should not be declared inline. 2021-07-14T07:11:30,703 building 'cyvcf2.cyvcf2' extension 2021-07-14T07:11:30,705 creating build/temp.linux-armv7l-3.9 2021-07-14T07:11:30,705 creating build/temp.linux-armv7l-3.9/cyvcf2 2021-07-14T07:11:30,706 creating build/temp.linux-armv7l-3.9/htslib 2021-07-14T07:11:30,707 creating build/temp.linux-armv7l-3.9/htslib/cram 2021-07-14T07:11:30,708 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 2021-07-14T07:11:31,129 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-14T07:11:31,129 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-14T07:11:31,129 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-14T07:11:31,129 from cyvcf2/cyvcf2.c:613: 2021-07-14T07:11:31,129 /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] 2021-07-14T07:11:31,130 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-14T07:11:31,130 | ^~~~~~~ 2021-07-14T07:11:31,191 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:11:31,191 from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,192 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,192 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:11:31,192 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] 2021-07-14T07:11:31,192 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:11:31,192 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:11:31,192 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:11:31,193 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] 2021-07-14T07:11:31,193 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:11:31,193 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:11:31,206 In file included from cyvcf2/cyvcf2.c:624: 2021-07-14T07:11:31,207 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:11:31,207 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:11:31,207 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:11:31,207 | ^ 2021-07-14T07:11:31,363 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: 2021-07-14T07:11:31,366 cyvcf2/cyvcf2.c:7867:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:31,367 7867 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); 2021-07-14T07:11:31,367 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:11:31,367 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,367 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,367 htslib/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:31,367 443 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-14T07:11:31,368 | ~~~~~~~~~~~^ 2021-07-14T07:11:31,371 cyvcf2/cyvcf2.c:7909:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:31,371 7909 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-14T07:11:31,371 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:11:31,372 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,372 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,372 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:31,372 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:11:31,372 | ~~~~~~~~~~~^ 2021-07-14T07:11:31,380 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: 2021-07-14T07:11:31,384 cyvcf2/cyvcf2.c:8437:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:31,384 8437 | __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); 2021-07-14T07:11:31,385 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:11:31,385 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,385 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,385 htslib/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:31,385 315 | int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); 2021-07-14T07:11:31,385 | ~~~~~~~~~~~^~~ 2021-07-14T07:11:31,393 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: 2021-07-14T07:11:31,397 cyvcf2/cyvcf2.c:8741:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:31,398 8741 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); 2021-07-14T07:11:31,398 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:11:31,398 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,398 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,398 htslib/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:31,398 443 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-14T07:11:31,398 | ~~~~~~~~~~~^ 2021-07-14T07:11:31,403 cyvcf2/cyvcf2.c:8794:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:31,403 8794 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-14T07:11:31,403 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:11:31,403 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,403 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,404 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:31,404 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:11:31,404 | ~~~~~~~~~~~^ 2021-07-14T07:11:31,406 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_18generator’: 2021-07-14T07:11:31,408 cyvcf2/cyvcf2.c:9009:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:31,409 9009 | __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); 2021-07-14T07:11:31,409 htslib/htslib/vcf.h:796:103: note: in definition of macro ‘bcf_itr_querys’ 2021-07-14T07:11:31,409 796 | #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) 2021-07-14T07:11:31,409 | ^~~ 2021-07-14T07:11:31,409 In file included from htslib/htslib/vcf.h:39, 2021-07-14T07:11:31,409 from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,409 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,410 htslib/htslib/hts.h:675:97: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:31,410 675 | 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); 2021-07-14T07:11:31,410 | ~~~~~~^~~ 2021-07-14T07:11:31,427 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_24generator2’: 2021-07-14T07:11:31,432 cyvcf2/cyvcf2.c:10309:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:31,432 10309 | __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) 2021-07-14T07:11:31,432 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-14T07:11:31,433 cyvcf2/cyvcf2.c:2892:107: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:31,434 2892 | static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ 2021-07-14T07:11:31,434 | ^~~~~~~~~~~ 2021-07-14T07:11:31,501 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_35__dealloc__’: 2021-07-14T07:11:31,507 cyvcf2/cyvcf2.c:11992:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:31,508 11992 | bcf_hdr_destroy(__pyx_v_self->hdr); 2021-07-14T07:11:31,508 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:11:31,508 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,508 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,508 htslib/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:31,508 261 | void bcf_hdr_destroy(bcf_hdr_t *h); 2021-07-14T07:11:31,509 | ~~~~~~~~~~~^ 2021-07-14T07:11:31,512 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: 2021-07-14T07:11:31,518 cyvcf2/cyvcf2.c:12482:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 2021-07-14T07:11:31,518 12482 | __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); 2021-07-14T07:11:31,518 | ^~~~~~~~~ 2021-07-14T07:11:31,518 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,519 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,519 htslib/htslib/vcf.h:439:11: note: declared here 2021-07-14T07:11:31,519 439 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) 2021-07-14T07:11:31,519 | ^~~~~~~~~~~~~~~~ 2021-07-14T07:11:31,521 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: 2021-07-14T07:11:31,528 cyvcf2/cyvcf2.c:12741:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-14T07:11:31,528 12741 | __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-14T07:11:31,528 | ^ 2021-07-14T07:11:31,533 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,533 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,533 cyvcf2/cyvcf2.c:12850:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:31,533 12850 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-14T07:11:31,533 htslib/htslib/vcf.h:799:112: note: in definition of macro ‘bcf_index_seqnames’ 2021-07-14T07:11:31,534 799 | #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) 2021-07-14T07:11:31,534 | ^~~ 2021-07-14T07:11:31,534 In file included from htslib/htslib/vcf.h:39, 2021-07-14T07:11:31,534 from cyvcf2/helpers.h:1, 2021-07-14T07:11:31,534 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:31,534 htslib/htslib/hts.h:677:92: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:31,534 677 | 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 2021-07-14T07:11:31,534 | ~~~~~~^~~ 2021-07-14T07:11:31,541 cyvcf2/cyvcf2.c:12850:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-14T07:11:31,541 12850 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-14T07:11:31,541 | ^ 2021-07-14T07:11:31,548 cyvcf2/cyvcf2.c:12933:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-14T07:11:31,548 12933 | __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); 2021-07-14T07:11:31,548 | ^ 2021-07-14T07:11:32,130 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’: 2021-07-14T07:11:32,141 cyvcf2/cyvcf2.c:22394:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:11:32,142 22394 | for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) { 2021-07-14T07:11:32,142 | ^ 2021-07-14T07:11:32,243 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’: 2021-07-14T07:11:32,256 cyvcf2/cyvcf2.c:24438:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,256 24438 | __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id); 2021-07-14T07:11:32,256 | ^ 2021-07-14T07:11:32,523 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’: 2021-07-14T07:11:32,539 cyvcf2/cyvcf2.c:31921:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:11:32,540 31921 | for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-07-14T07:11:32,540 | ^ 2021-07-14T07:11:32,544 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’: 2021-07-14T07:11:32,560 cyvcf2/cyvcf2.c:32192:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:11:32,560 32192 | for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2021-07-14T07:11:32,560 | ^ 2021-07-14T07:11:32,563 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’: 2021-07-14T07:11:32,580 cyvcf2/cyvcf2.c:32407:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:11:32,580 32407 | for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2021-07-14T07:11:32,580 | ^ 2021-07-14T07:11:32,598 cyvcf2/cyvcf2.c:32465:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-14T07:11:32,598 32465 | __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0); 2021-07-14T07:11:32,598 | ^~ 2021-07-14T07:11:32,624 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: 2021-07-14T07:11:32,642 cyvcf2/cyvcf2.c:34619:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,642 34619 | __pyx_v_h = __pyx_t_6; 2021-07-14T07:11:32,642 | ^ 2021-07-14T07:11:32,723 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: 2021-07-14T07:11:32,742 cyvcf2/cyvcf2.c:37722:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,742 37722 | __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); 2021-07-14T07:11:32,742 | ^ 2021-07-14T07:11:32,750 cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: 2021-07-14T07:11:32,770 cyvcf2/cyvcf2.c:38717:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,770 38717 | __pyx_v_i->hdr = __pyx_t_4; 2021-07-14T07:11:32,771 | ^ 2021-07-14T07:11:32,781 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: 2021-07-14T07:11:32,801 cyvcf2/cyvcf2.c:39383:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,801 39383 | (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); 2021-07-14T07:11:32,801 | ~~~~~~~~~~~~^~~~~ 2021-07-14T07:11:32,802 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:32,802 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:32,802 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:32,802 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:11:32,802 | ~~~~~~~~~~~^ 2021-07-14T07:11:32,821 cyvcf2/cyvcf2.c:39411:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,822 39411 | (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); 2021-07-14T07:11:32,822 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:11:32,822 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:32,822 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:32,822 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:32,822 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:11:32,822 | ~~~~~~~~~~~^ 2021-07-14T07:11:32,823 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2write_header’: 2021-07-14T07:11:32,842 cyvcf2/cyvcf2.c:39479:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,842 39479 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); 2021-07-14T07:11:32,843 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:11:32,843 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:32,843 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:32,843 htslib/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:32,843 320 | int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); 2021-07-14T07:11:32,843 | ~~~~~~~~~~~^ 2021-07-14T07:11:32,845 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_4write_record’: 2021-07-14T07:11:32,865 cyvcf2/cyvcf2.c:39657:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,865 39657 | __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); 2021-07-14T07:11:32,866 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:11:32,866 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:32,866 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:32,866 htslib/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:32,866 482 | int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); 2021-07-14T07:11:32,866 | ~~~~~~~~~~~^~~ 2021-07-14T07:11:32,886 cyvcf2/cyvcf2.c:39695:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,887 39695 | (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); 2021-07-14T07:11:32,887 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:11:32,887 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:32,887 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:32,887 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:32,887 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-14T07:11:32,887 | ~~~~~~~~~~~^ 2021-07-14T07:11:32,908 cyvcf2/cyvcf2.c:39754:100: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-14T07:11:32,908 39754 | __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, 2082, __pyx_L1_error) 2021-07-14T07:11:32,908 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-14T07:11:32,908 In file included from cyvcf2/helpers.h:1, 2021-07-14T07:11:32,908 from cyvcf2/cyvcf2.c:622: 2021-07-14T07:11:32,908 htslib/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-14T07:11:32,909 370 | int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); 2021-07-14T07:11:32,909 | ~~~~~~~~~~~^ 2021-07-14T07:11:36,427 At top level: 2021-07-14T07:11:36,431 cyvcf2/cyvcf2.c:6524:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] 2021-07-14T07:11:36,431 6524 | static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { 2021-07-14T07:11:36,432 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:29,837 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 2021-07-14T07:12:29,986 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:12:29,986 from cyvcf2/helpers.h:1, 2021-07-14T07:12:29,987 from cyvcf2/helpers.c:1: 2021-07-14T07:12:29,987 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:29,988 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] 2021-07-14T07:12:29,988 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:29,988 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:29,989 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:29,989 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] 2021-07-14T07:12:29,989 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:29,989 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:30,206 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 2021-07-14T07:12:30,350 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:12:30,350 from htslib/htslib/synced_bcf_reader.h:60, 2021-07-14T07:12:30,350 from htslib/bcf_sr_sort.h:37, 2021-07-14T07:12:30,351 from htslib/bcf_sr_sort.c:29: 2021-07-14T07:12:30,351 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:30,351 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] 2021-07-14T07:12:30,351 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:30,351 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:30,352 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:30,352 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] 2021-07-14T07:12:30,352 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:30,352 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:30,375 htslib/bcf_sr_sort.c: In function ‘kbs_bitwise_or’: 2021-07-14T07:12:30,375 htslib/bcf_sr_sort.c:69:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:30,376 69 | for (i=0; in; i++) dst->b[i] |= src->b[i]; 2021-07-14T07:12:30,376 | ^ 2021-07-14T07:12:30,382 htslib/bcf_sr_sort.c: In function ‘bcf_sr_sort_set’: 2021-07-14T07:12:30,383 htslib/bcf_sr_sort.c:363:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:30,383 363 | for (k=0; k < kh_end(hash); k++) 2021-07-14T07:12:30,383 | ^ 2021-07-14T07:12:30,383 htslib/bcf_sr_sort.c:366:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:30,383 366 | for (k=0; k < kh_end(hash); k++) 2021-07-14T07:12:30,383 | ^ 2021-07-14T07:12:32,088 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 2021-07-14T07:12:32,277 In file included from htslib/bgzf.c:44: 2021-07-14T07:12:32,277 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:12:32,278 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:32,278 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:12:32,278 | ^ 2021-07-14T07:12:32,282 In file included from htslib/bgzf.c:46: 2021-07-14T07:12:32,282 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:32,283 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] 2021-07-14T07:12:32,283 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:32,283 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:32,284 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:32,284 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] 2021-07-14T07:12:32,284 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:32,284 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:32,313 htslib/bgzf.c: In function ‘bgzf_read’: 2021-07-14T07:12:32,314 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] 2021-07-14T07:12:32,314 983 | while (bytes_read < length) { 2021-07-14T07:12:32,314 | ^ 2021-07-14T07:12:32,315 htslib/bgzf.c:996:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:32,315 996 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-14T07:12:32,316 | ^ 2021-07-14T07:12:32,316 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] 2021-07-14T07:12:32,316 996 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-14T07:12:32,317 | ^~~~~~~~~ 2021-07-14T07:12:32,319 htslib/bgzf.c: In function ‘bgzf_mt_writer’: 2021-07-14T07:12:32,320 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] 2021-07-14T07:12:32,320 1107 | if (hwrite(fp->fp, j->comp_data, j->comp_len) != j->comp_len) { 2021-07-14T07:12:32,320 | ^~ 2021-07-14T07:12:32,332 htslib/bgzf.c: In function ‘bgzf_block_write’: 2021-07-14T07:12:32,333 htslib/bgzf.c:1594:41: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:32,333 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; 2021-07-14T07:12:32,333 | ^ 2021-07-14T07:12:32,335 htslib/bgzf.c:1602:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-14T07:12:32,335 1602 | if (fp->block_offset == ublock_size) { 2021-07-14T07:12:32,335 | ^~ 2021-07-14T07:12:32,354 htslib/bgzf.c: In function ‘bgzf_useek’: 2021-07-14T07:12:32,355 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] 2021-07-14T07:12:32,356 2049 | if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1; 2021-07-14T07:12:32,356 | ^ 2021-07-14T07:12:32,357 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] 2021-07-14T07:12:32,357 2050 | else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1; 2021-07-14T07:12:32,357 | ^~ 2021-07-14T07:12:34,542 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 2021-07-14T07:12:34,758 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:34,758 from htslib/cram/misc.h:66, 2021-07-14T07:12:34,758 from htslib/cram/cram_io.h:46, 2021-07-14T07:12:34,759 from htslib/cram/cram.h:48, 2021-07-14T07:12:34,759 from htslib/cram/cram_codecs.c:45: 2021-07-14T07:12:34,759 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:34,759 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] 2021-07-14T07:12:34,760 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:34,760 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:34,760 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:34,761 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] 2021-07-14T07:12:34,761 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:34,761 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:34,767 In file included from htslib/cram/cram.h:48, 2021-07-14T07:12:34,767 from htslib/cram/cram_codecs.c:45: 2021-07-14T07:12:34,767 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:12:34,768 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] 2021-07-14T07:12:34,768 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:12:34,768 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:34,777 In file included from htslib/cram/cram.h:52, 2021-07-14T07:12:34,777 from htslib/cram/cram_codecs.c:45: 2021-07-14T07:12:34,777 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:12:34,778 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] 2021-07-14T07:12:34,778 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:12:34,778 | ^~ 2021-07-14T07:12:34,779 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:34,779 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:12:34,779 | ^ 2021-07-14T07:12:34,782 htslib/cram/cram_codecs.c: In function ‘get_one_bits_MSB’: 2021-07-14T07:12:34,783 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] 2021-07-14T07:12:34,783 79 | if (block->byte >= block->uncomp_size) 2021-07-14T07:12:34,783 | ^~ 2021-07-14T07:12:34,784 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] 2021-07-14T07:12:34,784 86 | if (block->byte == block->uncomp_size && (b&1)) 2021-07-14T07:12:34,784 | ^~ 2021-07-14T07:12:34,784 htslib/cram/cram_codecs.c: In function ‘get_zero_bits_MSB’: 2021-07-14T07:12:34,785 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] 2021-07-14T07:12:34,785 97 | if (block->byte >= block->uncomp_size) 2021-07-14T07:12:34,785 | ^~ 2021-07-14T07:12:34,786 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] 2021-07-14T07:12:34,786 104 | if (block->byte == block->uncomp_size && !(b&1)) 2021-07-14T07:12:34,786 | ^~ 2021-07-14T07:12:34,796 htslib/cram/cram_codecs.c: In function ‘cram_beta_decode_init’: 2021-07-14T07:12:34,796 htslib/cram/cram_codecs.c:555:47: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:34,796 555 | || c->beta.nbits < 0 || c->beta.nbits > 8 * sizeof(int)) { 2021-07-14T07:12:34,796 | ^ 2021-07-14T07:12:34,807 htslib/cram/cram_codecs.c: In function ‘cram_huffman_decode_init’: 2021-07-14T07:12:34,807 htslib/cram/cram_codecs.c:976:16: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:34,808 976 | if (ncodes >= SIZE_MAX / sizeof(*codes)) { 2021-07-14T07:12:34,808 | ^~ 2021-07-14T07:12:34,810 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] 2021-07-14T07:12:34,811 1044 | if (val > max_val) 2021-07-14T07:12:34,811 | ^ 2021-07-14T07:12:34,830 htslib/cram/cram_codecs.c: In function ‘cram_byte_array_stop_decode_block’: 2021-07-14T07:12:34,831 htslib/cram/cram_codecs.c:1643:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:34,831 1643 | if (cp_end - cp < out->alloc - out->byte) { 2021-07-14T07:12:34,831 | ^ 2021-07-14T07:12:37,374 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 2021-07-14T07:12:37,639 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:37,639 from htslib/cram/misc.h:66, 2021-07-14T07:12:37,639 from htslib/cram/cram_io.h:46, 2021-07-14T07:12:37,639 from htslib/cram/cram.h:48, 2021-07-14T07:12:37,639 from htslib/cram/cram_decode.c:49: 2021-07-14T07:12:37,639 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:37,640 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] 2021-07-14T07:12:37,640 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:37,641 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:37,641 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:37,642 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] 2021-07-14T07:12:37,642 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:37,642 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:37,648 In file included from htslib/cram/cram.h:48, 2021-07-14T07:12:37,648 from htslib/cram/cram_decode.c:49: 2021-07-14T07:12:37,648 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:12:37,649 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] 2021-07-14T07:12:37,649 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:12:37,650 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:37,657 In file included from htslib/cram/cram.h:52, 2021-07-14T07:12:37,657 from htslib/cram/cram_decode.c:49: 2021-07-14T07:12:37,658 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:12:37,658 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] 2021-07-14T07:12:37,658 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:12:37,658 | ^~ 2021-07-14T07:12:37,659 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:37,659 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:12:37,659 | ^ 2021-07-14T07:12:37,665 htslib/cram/cram_decode.c: In function ‘cram_decode_TD’: 2021-07-14T07:12:37,665 htslib/cram/cram_decode.c:102:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:37,665 102 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-14T07:12:37,665 | ^ 2021-07-14T07:12:37,666 htslib/cram/cram_decode.c:114:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:37,666 114 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-14T07:12:37,666 | ^ 2021-07-14T07:12:37,667 htslib/cram/cram_decode.c: In function ‘cram_decode_compression_header’: 2021-07-14T07:12:37,667 htslib/cram/cram_decode.c:156:33: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:37,668 156 | hdr->num_landmarks >= SIZE_MAX / sizeof(int32_t))) { 2021-07-14T07:12:37,668 | ^~ 2021-07-14T07:12:37,686 htslib/cram/cram_decode.c: In function ‘cram_dependent_data_series’: 2021-07-14T07:12:37,687 htslib/cram/cram_decode.c:800:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:37,687 800 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-14T07:12:37,687 | ^ 2021-07-14T07:12:37,690 htslib/cram/cram_decode.c:894:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:37,690 894 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-14T07:12:37,690 | ^ 2021-07-14T07:12:37,695 htslib/cram/cram_decode.c: In function ‘cram_decode_slice_header’: 2021-07-14T07:12:37,696 htslib/cram/cram_decode.c:1114:30: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:37,696 1114 | hdr->num_content_ids >= SIZE_MAX / sizeof(int32_t)) { 2021-07-14T07:12:37,696 | ^~ 2021-07-14T07:12:37,702 htslib/cram/cram_decode.c: In function ‘cram_decode_seq’: 2021-07-14T07:12:37,703 htslib/cram/cram_decode.c:1286:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:37,703 1286 | if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) { 2021-07-14T07:12:37,703 | ^ 2021-07-14T07:12:37,708 htslib/cram/cram_decode.c:1437:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:37,708 1437 | if (cr->ref_id < 0 || ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-14T07:12:37,708 | ^~ 2021-07-14T07:12:37,712 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] 2021-07-14T07:12:37,712 1483 | if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) { 2021-07-14T07:12:37,712 | ^~ 2021-07-14T07:12:37,714 htslib/cram/cram_decode.c:1494:54: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:37,714 1494 | if (bfd->ref[cr->ref_id].len >= ref_pos) { 2021-07-14T07:12:37,715 | ^~ 2021-07-14T07:12:37,720 htslib/cram/cram_decode.c:1587:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:37,720 1587 | if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-14T07:12:37,721 | ^~ 2021-07-14T07:12:37,725 htslib/cram/cram_decode.c:1660:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:37,726 1660 | if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-14T07:12:37,726 | ^~ 2021-07-14T07:12:37,732 htslib/cram/cram_decode.c:1767:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:37,732 1767 | if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) { 2021-07-14T07:12:37,732 | ^ 2021-07-14T07:12:37,759 htslib/cram/cram_decode.c: In function ‘cram_decode_slice’: 2021-07-14T07:12:37,760 htslib/cram/cram_decode.c:2403:20: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:37,761 2403 | bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap)) 2021-07-14T07:12:37,761 | ^~ 2021-07-14T07:12:43,559 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 2021-07-14T07:12:43,819 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:43,819 from htslib/cram/misc.h:66, 2021-07-14T07:12:43,819 from htslib/cram/cram_io.h:46, 2021-07-14T07:12:43,819 from htslib/cram/cram.h:48, 2021-07-14T07:12:43,819 from htslib/cram/cram_encode.c:43: 2021-07-14T07:12:43,820 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:43,820 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] 2021-07-14T07:12:43,820 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:43,820 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:43,820 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:43,820 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] 2021-07-14T07:12:43,820 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:43,821 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:43,826 In file included from htslib/cram/cram.h:48, 2021-07-14T07:12:43,826 from htslib/cram/cram_encode.c:43: 2021-07-14T07:12:43,826 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:12:43,826 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] 2021-07-14T07:12:43,826 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:12:43,826 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:43,834 In file included from htslib/cram/cram.h:52, 2021-07-14T07:12:43,834 from htslib/cram/cram_encode.c:43: 2021-07-14T07:12:43,834 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:12:43,834 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] 2021-07-14T07:12:43,834 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:12:43,835 | ^~ 2021-07-14T07:12:43,835 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:43,835 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:12:43,835 | ^ 2021-07-14T07:12:43,868 htslib/cram/cram_encode.c: In function ‘cram_encode_slice’: 2021-07-14T07:12:43,869 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] 2021-07-14T07:12:43,869 1044 | for (id = 1; id < s->hdr->num_blocks; id++) { 2021-07-14T07:12:43,869 | ^ 2021-07-14T07:12:43,872 htslib/cram/cram_encode.c: In function ‘lossy_read_names’: 2021-07-14T07:12:43,873 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] 2021-07-14T07:12:43,873 1168 | if (u.counts.e != e) { 2021-07-14T07:12:43,873 | ^~ 2021-07-14T07:12:43,874 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] 2021-07-14T07:12:43,874 1198 | if (kh_val(names, k) == -1) 2021-07-14T07:12:43,874 | ^~ 2021-07-14T07:12:43,914 htslib/cram/cram_encode.c: In function ‘process_one_read’: 2021-07-14T07:12:43,915 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] 2021-07-14T07:12:43,915 2636 | while (cr->cigar + cr->ncigar >= s->cigar_alloc) { 2021-07-14T07:12:43,916 | ^~ 2021-07-14T07:12:43,917 htslib/cram/cram_encode.c:2666:44: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:43,917 2666 | int end = cig_len+apos < c->ref_end 2021-07-14T07:12:43,917 | ^ 2021-07-14T07:12:43,918 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] 2021-07-14T07:12:43,919 2667 | ? cig_len : c->ref_end - apos; 2021-07-14T07:12:43,919 | ^~~~~~~~~~~~~~~~~ 2021-07-14T07:12:43,923 htslib/cram/cram_encode.c:2710:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:43,923 2710 | if (l < cig_len && cr->len) { 2021-07-14T07:12:43,923 | ^ 2021-07-14T07:12:43,925 htslib/cram/cram_encode.c:2718:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:43,925 2718 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-14T07:12:43,925 | ^ 2021-07-14T07:12:43,926 htslib/cram/cram_encode.c:2727:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:43,926 2727 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-14T07:12:43,926 | ^ 2021-07-14T07:12:43,930 htslib/cram/cram_encode.c:2759:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:43,930 2759 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-14T07:12:43,930 | ^ 2021-07-14T07:12:43,932 htslib/cram/cram_encode.c:2776:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:43,933 2776 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-14T07:12:43,933 | ^ 2021-07-14T07:12:43,934 htslib/cram/cram_encode.c:2780:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:43,934 2780 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-14T07:12:43,934 | ^ 2021-07-14T07:12:43,938 htslib/cram/cram_encode.c:2834:17: warning: unused variable ‘brg’ [-Wunused-variable] 2021-07-14T07:12:43,939 2834 | SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); 2021-07-14T07:12:43,939 | ^~~ 2021-07-14T07:12:43,954 htslib/cram/cram_encode.c: In function ‘cram_put_bam_seq’: 2021-07-14T07:12:43,956 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] 2021-07-14T07:12:43,956 3077 | (c->s_num_bases >= fd->bases_per_slice)) { 2021-07-14T07:12:43,956 | ^~ 2021-07-14T07:12:43,958 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] 2021-07-14T07:12:43,958 3100 | c->s_num_bases >= fd->bases_per_slice) { 2021-07-14T07:12:43,958 | ^~ 2021-07-14T07:12:49,089 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 2021-07-14T07:12:49,179 In file included from htslib/cram/cram_external.c:43: 2021-07-14T07:12:49,179 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:12:49,179 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:49,179 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:12:49,179 | ^ 2021-07-14T07:12:49,299 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:49,299 from htslib/cram/misc.h:66, 2021-07-14T07:12:49,299 from htslib/cram/cram_io.h:46, 2021-07-14T07:12:49,299 from htslib/cram/cram.h:48, 2021-07-14T07:12:49,299 from htslib/cram/cram_external.c:44: 2021-07-14T07:12:49,300 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:49,300 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] 2021-07-14T07:12:49,300 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:49,300 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:49,300 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:49,300 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] 2021-07-14T07:12:49,300 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:49,301 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:49,305 In file included from htslib/cram/cram.h:48, 2021-07-14T07:12:49,305 from htslib/cram/cram_external.c:44: 2021-07-14T07:12:49,305 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:12:49,306 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] 2021-07-14T07:12:49,306 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:12:49,306 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:49,313 In file included from htslib/cram/cram.h:52, 2021-07-14T07:12:49,314 from htslib/cram/cram_external.c:44: 2021-07-14T07:12:49,314 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:12:49,314 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] 2021-07-14T07:12:49,314 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:12:49,314 | ^~ 2021-07-14T07:12:49,314 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:49,315 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:12:49,315 | ^ 2021-07-14T07:12:49,689 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 2021-07-14T07:12:49,874 In file included from htslib/cram/cram_index.c:64: 2021-07-14T07:12:49,875 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:12:49,875 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:49,875 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:12:49,875 | ^ 2021-07-14T07:12:49,964 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:49,964 from htslib/cram/misc.h:66, 2021-07-14T07:12:49,964 from htslib/cram/cram_io.h:46, 2021-07-14T07:12:49,965 from htslib/cram/cram.h:48, 2021-07-14T07:12:49,965 from htslib/cram/cram_index.c:66: 2021-07-14T07:12:49,965 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:49,965 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] 2021-07-14T07:12:49,965 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:49,965 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:49,966 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:49,966 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] 2021-07-14T07:12:49,966 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:49,966 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:49,970 In file included from htslib/cram/cram.h:48, 2021-07-14T07:12:49,971 from htslib/cram/cram_index.c:66: 2021-07-14T07:12:49,971 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:12:49,971 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] 2021-07-14T07:12:49,971 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:12:49,971 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:49,980 In file included from htslib/cram/cram.h:52, 2021-07-14T07:12:49,980 from htslib/cram/cram_index.c:66: 2021-07-14T07:12:49,980 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:12:49,980 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] 2021-07-14T07:12:49,981 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:12:49,981 | ^~ 2021-07-14T07:12:49,981 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:49,981 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:12:49,981 | ^ 2021-07-14T07:12:49,993 htslib/cram/cram_index.c: In function ‘cram_index_build’: 2021-07-14T07:12:49,993 htslib/cram/cram_index.c:587:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] 2021-07-14T07:12:49,993 587 | off_t cpos, spos, hpos; 2021-07-14T07:12:49,994 | ^~~~ 2021-07-14T07:12:50,739 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 2021-07-14T07:12:51,008 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:51,008 from htslib/cram/misc.h:66, 2021-07-14T07:12:51,009 from htslib/cram/cram_io.h:46, 2021-07-14T07:12:51,009 from htslib/cram/cram.h:48, 2021-07-14T07:12:51,009 from htslib/cram/cram_io.c:77: 2021-07-14T07:12:51,009 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:51,009 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] 2021-07-14T07:12:51,009 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:51,010 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:51,010 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:51,010 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] 2021-07-14T07:12:51,010 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:51,010 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:51,015 In file included from htslib/cram/cram.h:48, 2021-07-14T07:12:51,016 from htslib/cram/cram_io.c:77: 2021-07-14T07:12:51,016 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:12:51,016 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] 2021-07-14T07:12:51,016 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:12:51,016 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:51,023 In file included from htslib/cram/cram.h:52, 2021-07-14T07:12:51,024 from htslib/cram/cram_io.c:77: 2021-07-14T07:12:51,024 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:12:51,024 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] 2021-07-14T07:12:51,024 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:12:51,024 | ^~ 2021-07-14T07:12:51,025 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:51,025 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:12:51,025 | ^ 2021-07-14T07:12:51,031 In file included from htslib/cram/cram_io.c:94: 2021-07-14T07:12:51,031 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:12:51,031 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:51,031 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:12:51,031 | ^ 2021-07-14T07:12:51,047 htslib/cram/cram_io.c: In function ‘itf8_decode_crc’: 2021-07-14T07:12:51,047 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] 2021-07-14T07:12:51,047 241 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:12:51,047 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:51,100 htslib/cram/cram_io.c: In function ‘expand_cache_path’: 2021-07-14T07:12:51,101 htslib/cram/cram_io.c:1920:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:51,101 1920 | if (cp-dir >= sz) return -1; 2021-07-14T07:12:51,101 | ^~ 2021-07-14T07:12:51,104 In file included from htslib/cram/cram_io.h:46, 2021-07-14T07:12:51,104 from htslib/cram/cram.h:48, 2021-07-14T07:12:51,104 from htslib/cram/cram_io.c:77: 2021-07-14T07:12:51,105 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:51,105 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:12:51,105 | ^ 2021-07-14T07:12:51,105 htslib/cram/cram_io.c:1938:17: note: in expansion of macro ‘MIN’ 2021-07-14T07:12:51,105 1938 | l = MIN(l, strlen(fn)); 2021-07-14T07:12:51,105 | ^~~ 2021-07-14T07:12:51,106 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] 2021-07-14T07:12:51,106 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:12:51,106 | ^~~ 2021-07-14T07:12:51,106 htslib/cram/cram_io.c:1938:17: note: in expansion of macro ‘MIN’ 2021-07-14T07:12:51,106 1938 | l = MIN(l, strlen(fn)); 2021-07-14T07:12:51,106 | ^~~ 2021-07-14T07:12:51,107 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] 2021-07-14T07:12:51,107 1940 | if (l >= sz) return -1; 2021-07-14T07:12:51,107 | ^~ 2021-07-14T07:12:51,159 htslib/cram/cram_io.c: In function ‘cram_read_container’: 2021-07-14T07:12:51,160 htslib/cram/cram_io.c:2882:50: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:51,160 2882 | if (c2.num_landmarks < 0 || c2.num_landmarks >= SIZE_MAX / sizeof(int32_t)) 2021-07-14T07:12:51,161 | ^~ 2021-07-14T07:12:51,255 In file included from htslib/cram/cram.h:48, 2021-07-14T07:12:51,255 from htslib/cram/cram_io.c:77: 2021-07-14T07:12:51,255 htslib/cram/cram_io.c: In function ‘cram_write_SAM_hdr’: 2021-07-14T07:12:51,257 htslib/cram/cram_io.h:511:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:51,258 511 | while((b)->alloc <= (l)) { \ 2021-07-14T07:12:51,258 | ^~ 2021-07-14T07:12:51,258 htslib/cram/cram_io.c:3925:13: note: in expansion of macro ‘BLOCK_RESIZE’ 2021-07-14T07:12:51,258 3925 | BLOCK_RESIZE(b, padded_length); 2021-07-14T07:12:51,258 | ^~~~~~~~~~~~ 2021-07-14T07:12:55,255 In file included from /usr/include/string.h:495, 2021-07-14T07:12:55,256 from htslib/cram/cram_io.c:53: 2021-07-14T07:12:55,256 In function ‘strncpy’, 2021-07-14T07:12:55,256 inlined from ‘full_path’ at htslib/cram/cram_io.c:3748:13, 2021-07-14T07:12:55,256 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-14T07:12:55,257 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-14T07:12:55,257 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-14T07:12:55,257 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:55,257 In function ‘strncpy’, 2021-07-14T07:12:55,257 inlined from ‘full_path’ at htslib/cram/cram_io.c:3740:9, 2021-07-14T07:12:55,257 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-14T07:12:55,257 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-14T07:12:55,257 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-14T07:12:55,258 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:55,536 In function ‘strncpy’, 2021-07-14T07:12:55,536 inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4126:9: 2021-07-14T07:12:55,536 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 2021-07-14T07:12:55,536 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-14T07:12:55,536 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:56,305 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 2021-07-14T07:12:56,510 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:56,510 from htslib/cram/misc.h:66, 2021-07-14T07:12:56,510 from htslib/cram/cram_io.h:46, 2021-07-14T07:12:56,510 from htslib/cram/cram.h:48, 2021-07-14T07:12:56,511 from htslib/cram/cram_samtools.c:37: 2021-07-14T07:12:56,511 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:56,511 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] 2021-07-14T07:12:56,511 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:56,511 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:56,511 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:56,512 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] 2021-07-14T07:12:56,512 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:56,512 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:56,516 In file included from htslib/cram/cram.h:48, 2021-07-14T07:12:56,516 from htslib/cram/cram_samtools.c:37: 2021-07-14T07:12:56,517 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:12:56,517 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] 2021-07-14T07:12:56,517 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:12:56,517 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:56,524 In file included from htslib/cram/cram.h:52, 2021-07-14T07:12:56,525 from htslib/cram/cram_samtools.c:37: 2021-07-14T07:12:56,525 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:12:56,525 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] 2021-07-14T07:12:56,525 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:12:56,525 | ^~ 2021-07-14T07:12:56,525 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:56,525 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:12:56,526 | ^ 2021-07-14T07:12:56,529 htslib/cram/cram_samtools.c: In function ‘bam_construct_seq’: 2021-07-14T07:12:56,529 htslib/cram/cram_samtools.c:85:19: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:56,529 85 | if (b->m_data < bam_len) { 2021-07-14T07:12:56,529 | ^ 2021-07-14T07:12:56,701 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 2021-07-14T07:12:56,965 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:56,965 from htslib/cram/misc.h:66, 2021-07-14T07:12:56,965 from htslib/cram/cram_io.h:46, 2021-07-14T07:12:56,965 from htslib/cram/cram.h:48, 2021-07-14T07:12:56,966 from htslib/cram/cram_stats.c:43: 2021-07-14T07:12:56,966 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:56,966 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] 2021-07-14T07:12:56,966 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:56,966 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:56,966 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:56,966 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] 2021-07-14T07:12:56,967 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:56,967 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:56,972 In file included from htslib/cram/cram.h:48, 2021-07-14T07:12:56,972 from htslib/cram/cram_stats.c:43: 2021-07-14T07:12:56,972 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:12:56,972 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] 2021-07-14T07:12:56,973 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:12:56,973 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:56,980 In file included from htslib/cram/cram.h:52, 2021-07-14T07:12:56,980 from htslib/cram/cram_stats.c:43: 2021-07-14T07:12:56,980 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:12:56,980 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] 2021-07-14T07:12:56,981 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:12:56,981 | ^~ 2021-07-14T07:12:56,981 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:12:56,981 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:12:56,981 | ^ 2021-07-14T07:12:57,312 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 2021-07-14T07:12:57,388 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:57,388 from htslib/cram/misc.h:66, 2021-07-14T07:12:57,388 from htslib/cram/files.c:34: 2021-07-14T07:12:57,388 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:57,389 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] 2021-07-14T07:12:57,389 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:57,389 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:57,389 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:57,389 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] 2021-07-14T07:12:57,389 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:57,390 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:57,504 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 2021-07-14T07:12:57,660 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:57,660 from htslib/cram/mFILE.c:44: 2021-07-14T07:12:57,660 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:57,660 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] 2021-07-14T07:12:57,661 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:57,661 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:57,661 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:57,661 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] 2021-07-14T07:12:57,661 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:57,662 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:57,667 htslib/cram/mFILE.c: In function ‘mfload’: 2021-07-14T07:12:57,668 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] 2021-07-14T07:12:57,668 103 | } while (!feof(fp) && (fn == NULL || used < sb.st_size)); 2021-07-14T07:12:57,668 | ^ 2021-07-14T07:12:57,673 htslib/cram/mFILE.c: In function ‘mftruncate’: 2021-07-14T07:12:57,673 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] 2021-07-14T07:12:57,673 476 | mf->size = offset != -1 ? offset : mf->offset; 2021-07-14T07:12:57,673 | ^~~~~~ 2021-07-14T07:12:58,107 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 2021-07-14T07:12:58,259 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:58,259 from htslib/cram/open_trace_file.c:74: 2021-07-14T07:12:58,259 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:58,259 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] 2021-07-14T07:12:58,260 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:58,260 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:58,260 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:58,260 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] 2021-07-14T07:12:58,260 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:58,260 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:58,265 In file included from htslib/cram/open_trace_file.c:81: 2021-07-14T07:12:58,266 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:12:58,266 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:12:58,266 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:12:58,266 | ^ 2021-07-14T07:12:58,270 In file included from htslib/cram/open_trace_file.c:80: 2021-07-14T07:12:58,271 htslib/cram/open_trace_file.c: In function ‘expand_path’: 2021-07-14T07:12:58,271 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-14T07:12:58,271 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:12:58,271 | ^ 2021-07-14T07:12:58,272 htslib/cram/open_trace_file.c:251:29: note: in expansion of macro ‘MIN’ 2021-07-14T07:12:58,272 251 | path_end += MIN(strlen(file), l); 2021-07-14T07:12:58,272 | ^~~ 2021-07-14T07:12:58,272 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] 2021-07-14T07:12:58,272 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:12:58,272 | ^~~ 2021-07-14T07:12:58,272 htslib/cram/open_trace_file.c:251:29: note: in expansion of macro ‘MIN’ 2021-07-14T07:12:58,273 251 | path_end += MIN(strlen(file), l); 2021-07-14T07:12:58,273 | ^~~ 2021-07-14T07:12:58,273 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-14T07:12:58,273 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:12:58,273 | ^ 2021-07-14T07:12:58,273 htslib/cram/open_trace_file.c:252:29: note: in expansion of macro ‘MIN’ 2021-07-14T07:12:58,273 252 | file += MIN(strlen(file), l); 2021-07-14T07:12:58,274 | ^~~ 2021-07-14T07:12:58,274 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] 2021-07-14T07:12:58,274 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-14T07:12:58,274 | ^~~ 2021-07-14T07:12:58,274 htslib/cram/open_trace_file.c:252:29: note: in expansion of macro ‘MIN’ 2021-07-14T07:12:58,274 252 | file += MIN(strlen(file), l); 2021-07-14T07:12:58,275 | ^~~ 2021-07-14T07:12:58,650 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 2021-07-14T07:12:58,770 In file included from htslib/cram/os.h:80, 2021-07-14T07:12:58,770 from htslib/cram/misc.h:66, 2021-07-14T07:12:58,770 from htslib/cram/pooled_alloc.c:38: 2021-07-14T07:12:58,770 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:12:58,771 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] 2021-07-14T07:12:58,772 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:12:58,772 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:58,772 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:12:58,773 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] 2021-07-14T07:12:58,773 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:12:58,773 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:12:58,887 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 2021-07-14T07:12:59,032 htslib/cram/rANS_static.c: In function ‘rans_compress_O0’: 2021-07-14T07:12:59,033 htslib/cram/rANS_static.c:86:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:59,033 86 | for (i = 0; i < in_size; i++) { 2021-07-14T07:12:59,033 | ^ 2021-07-14T07:12:59,038 htslib/cram/rANS_static.c: In function ‘rans_compress_O1’: 2021-07-14T07:12:59,038 htslib/cram/rANS_static.c:388:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:12:59,039 388 | for (last_i=i=0; ih, type, &new))) 2021-07-14T07:13:00,524 | ^~ 2021-07-14T07:13:00,527 htslib/cram/sam_header.c: In function ‘sam_hdr_vadd’: 2021-07-14T07:13:00,528 htslib/cram/sam_header.c:451:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:00,528 451 | if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new))) 2021-07-14T07:13:00,528 | ^~ 2021-07-14T07:13:00,537 htslib/cram/sam_header.c: In function ‘sam_hdr_rebuild’: 2021-07-14T07:13:00,538 htslib/cram/sam_header.c:821:31: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:00,538 821 | if (kh_key(hdr->h, k) == K("HD")) 2021-07-14T07:13:00,538 | ^~ 2021-07-14T07:13:02,606 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 2021-07-14T07:13:02,825 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 2021-07-14T07:13:03,575 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 2021-07-14T07:13:03,737 In file included from htslib/faidx.c:40: 2021-07-14T07:13:03,737 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:03,737 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:03,737 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:03,738 | ^ 2021-07-14T07:13:03,772 htslib/faidx.c: In function ‘fai_retrieve’: 2021-07-14T07:13:03,773 htslib/faidx.c:711:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-14T07:13:03,773 711 | while ( l < end - beg && (c=bgzf_getc(fai->bgzf))>=0 ) 2021-07-14T07:13:03,773 | ^ 2021-07-14T07:13:03,777 htslib/faidx.c: In function ‘fai_get_val’: 2021-07-14T07:13:03,778 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] 2021-07-14T07:13:03,778 789 | end = i < k? strtol(s + i, &ep, 10) : val->len; 2021-07-14T07:13:03,778 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:03,779 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] 2021-07-14T07:13:03,779 801 | if (beg >= val->len) beg = val->len; 2021-07-14T07:13:03,779 | ^~ 2021-07-14T07:13:03,780 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] 2021-07-14T07:13:03,780 802 | if (end >= val->len) end = val->len; 2021-07-14T07:13:03,780 | ^~ 2021-07-14T07:13:03,783 htslib/faidx.c: In function ‘faidx_adjust_position’: 2021-07-14T07:13:03,783 htslib/faidx.c:882:22: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:03,783 882 | else if(val->len <= *p_beg_i) 2021-07-14T07:13:03,784 | ^~ 2021-07-14T07:13:03,785 htslib/faidx.c:887:22: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:03,785 887 | else if(val->len <= *p_end_i) 2021-07-14T07:13:03,785 | ^~ 2021-07-14T07:13:05,251 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 2021-07-14T07:13:05,396 In file included from htslib/hfile.c:36: 2021-07-14T07:13:05,396 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:05,396 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:05,397 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:05,397 | ^ 2021-07-14T07:13:05,412 htslib/hfile.c: In function ‘hfile_set_blksize’: 2021-07-14T07:13:05,413 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] 2021-07-14T07:13:05,413 200 | if (bufsiz < curr_used) 2021-07-14T07:13:05,413 | ^ 2021-07-14T07:13:05,416 htslib/hfile.c: In function ‘hseek’: 2021-07-14T07:13:05,417 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] 2021-07-14T07:13:05,417 436 | if (offset > 0 || -offset > length) { 2021-07-14T07:13:05,417 | ^ 2021-07-14T07:13:05,488 htslib/hfile.c: In function ‘find_scheme_handler’: 2021-07-14T07:13:05,489 htslib/hfile.c:1004:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:13:05,489 1004 | for (i = 0; i < sizeof scheme; i++) 2021-07-14T07:13:05,489 | ^ 2021-07-14T07:13:05,490 htslib/hfile.c:1011:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-14T07:13:05,490 1011 | if (i <= 1 || i >= sizeof scheme) return NULL; 2021-07-14T07:13:05,490 | ^~ 2021-07-14T07:13:06,486 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 2021-07-14T07:13:06,625 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:13:06,625 from htslib/hfile_gcs.c:35: 2021-07-14T07:13:06,626 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:06,626 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:06,626 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:06,626 | ^ 2021-07-14T07:13:06,956 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 2021-07-14T07:13:07,078 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:13:07,078 from htslib/hfile_libcurl.c:37: 2021-07-14T07:13:07,078 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:07,078 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:07,078 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:07,079 | ^ 2021-07-14T07:13:08,974 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 2021-07-14T07:13:09,090 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:13:09,090 from htslib/hfile_net.c:30: 2021-07-14T07:13:09,091 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:09,091 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:09,091 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:09,092 | ^ 2021-07-14T07:13:09,209 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 2021-07-14T07:13:09,335 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:13:09,335 from htslib/hfile_s3.c:33: 2021-07-14T07:13:09,336 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:09,336 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:09,336 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:09,336 | ^ 2021-07-14T07:13:10,434 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 2021-07-14T07:13:10,677 In file included from htslib/cram/os.h:80, 2021-07-14T07:13:10,678 from htslib/cram/misc.h:66, 2021-07-14T07:13:10,678 from htslib/cram/cram_io.h:46, 2021-07-14T07:13:10,678 from htslib/cram/cram.h:48, 2021-07-14T07:13:10,678 from htslib/hts.c:41: 2021-07-14T07:13:10,678 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:13:10,678 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] 2021-07-14T07:13:10,679 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:13:10,679 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:10,679 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:13:10,679 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] 2021-07-14T07:13:10,679 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:13:10,679 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:10,684 In file included from htslib/cram/cram.h:48, 2021-07-14T07:13:10,684 from htslib/hts.c:41: 2021-07-14T07:13:10,684 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:13:10,684 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] 2021-07-14T07:13:10,684 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:13:10,685 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:10,692 In file included from htslib/cram/cram.h:52, 2021-07-14T07:13:10,693 from htslib/hts.c:41: 2021-07-14T07:13:10,693 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:13:10,693 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] 2021-07-14T07:13:10,693 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:13:10,693 | ^~ 2021-07-14T07:13:10,694 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:10,694 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:13:10,694 | ^ 2021-07-14T07:13:10,698 In file included from htslib/hts.c:42: 2021-07-14T07:13:10,698 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:10,698 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:10,698 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:10,698 | ^ 2021-07-14T07:13:10,760 htslib/hts.c: In function ‘hts_idx_init’: 2021-07-14T07:13:10,761 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] 2021-07-14T07:13:10,761 1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; 2021-07-14T07:13:10,761 | ^~~ 2021-07-14T07:13:10,763 htslib/hts.c: In function ‘update_loff’: 2021-07-14T07:13:10,764 htslib/hts.c:1420:34: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:10,764 1420 | if ( kh_key(bidx, k) < idx->n_bins ) 2021-07-14T07:13:10,764 | ^ 2021-07-14T07:13:10,765 htslib/hts.c: In function ‘compress_binning’: 2021-07-14T07:13:10,766 htslib/hts.c:1447:55: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:10,766 1447 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue; 2021-07-14T07:13:10,766 | ^~ 2021-07-14T07:13:10,768 htslib/hts.c:1472:51: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:10,768 1472 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue; 2021-07-14T07:13:10,768 | ^~ 2021-07-14T07:13:10,792 htslib/hts.c: In function ‘hts_idx_load_local’: 2021-07-14T07:13:10,793 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] 2021-07-14T07:13:10,793 1832 | if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail; 2021-07-14T07:13:10,793 | ^~ 2021-07-14T07:13:10,797 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] 2021-07-14T07:13:10,797 1859 | if (bgzf_read(fp, idx->meta + 28, n) != n) goto fail; 2021-07-14T07:13:10,797 | ^~ 2021-07-14T07:13:10,815 htslib/hts.c: In function ‘hts_itr_multi_bam’: 2021-07-14T07:13:10,816 htslib/hts.c:2230:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:10,816 2230 | for(j=0; jcount; j++) { 2021-07-14T07:13:10,816 | ^ 2021-07-14T07:13:10,822 htslib/hts.c: In function ‘hts_itr_multi_cram’: 2021-07-14T07:13:10,823 htslib/hts.c:2341:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:10,823 2341 | for (j=0; j < curr_reg->count; j++) { 2021-07-14T07:13:10,823 | ^ 2021-07-14T07:13:10,845 htslib/hts.c: In function ‘hts_itr_multi_next’: 2021-07-14T07:13:10,846 htslib/hts.c:2737:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-14T07:13:10,846 2737 | if (beg > iter->off[iter->i].max) { 2021-07-14T07:13:10,846 | ^ 2021-07-14T07:13:10,847 htslib/hts.c:2741:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:10,848 2741 | if (beg > iter->reg_list[cr].max_end) 2021-07-14T07:13:10,848 | ^ 2021-07-14T07:13:10,849 htslib/hts.c:2744:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:10,849 2744 | for (i = ci; i < iter->reg_list[cr].count; i++) { 2021-07-14T07:13:10,850 | ^ 2021-07-14T07:13:10,851 htslib/hts.c:2745:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:10,851 2745 | if (end > iter->reg_list[cr].intervals[i].beg && iter->reg_list[cr].intervals[i].end > beg) { 2021-07-14T07:13:10,851 | ^ 2021-07-14T07:13:10,852 htslib/hts.c:2745:98: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:10,852 2745 | if (end > iter->reg_list[cr].intervals[i].beg && iter->reg_list[cr].intervals[i].end > beg) { 2021-07-14T07:13:10,853 | ^ 2021-07-14T07:13:10,855 htslib/hts.c: In function ‘test_and_fetch’: 2021-07-14T07:13:10,856 htslib/hts.c:2798:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:10,856 2798 | if (fwrite(buf, 1, l, local_fp) != l) { 2021-07-14T07:13:10,856 | ^~ 2021-07-14T07:13:10,863 htslib/hts.c: In function ‘hts_log’: 2021-07-14T07:13:10,864 htslib/hts.c:2967:18: warning: comparison of integer expressions of different signedness: ‘enum htsLogLevel’ and ‘int’ [-Wsign-compare] 2021-07-14T07:13:10,865 2967 | if (severity <= hts_verbose) { 2021-07-14T07:13:10,865 | ^~ 2021-07-14T07:13:16,272 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 2021-07-14T07:13:16,417 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 2021-07-14T07:13:16,851 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 2021-07-14T07:13:17,614 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 2021-07-14T07:13:17,773 htslib/kstring.c: In function ‘kvsprintf’: 2021-07-14T07:13:17,773 htslib/kstring.c:156:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:17,773 156 | if (l + 1 > s->m - s->l) { 2021-07-14T07:13:17,773 | ^ 2021-07-14T07:13:18,338 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 2021-07-14T07:13:18,440 In file included from htslib/md5.c:53: 2021-07-14T07:13:18,440 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:13:18,440 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] 2021-07-14T07:13:18,440 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:13:18,440 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:18,441 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:13:18,441 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] 2021-07-14T07:13:18,441 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:13:18,441 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:18,903 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 2021-07-14T07:13:19,049 In file included from htslib/hfile_internal.h:30, 2021-07-14T07:13:19,049 from htslib/multipart.c:34: 2021-07-14T07:13:19,049 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:19,049 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:19,049 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:19,049 | ^ 2021-07-14T07:13:19,424 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/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 2021-07-14T07:13:19,589 htslib/probaln.c: In function ‘probaln_glocal’: 2021-07-14T07:13:19,589 htslib/probaln.c:177:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:19,589 177 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-14T07:13:19,590 | ^~ 2021-07-14T07:13:19,591 htslib/probaln.c:201:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:19,591 201 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-14T07:13:19,592 | ^~ 2021-07-14T07:13:19,594 htslib/probaln.c:239:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:19,594 239 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-14T07:13:19,594 | ^~ 2021-07-14T07:13:20,130 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 2021-07-14T07:13:20,276 htslib/realn.c: In function ‘sam_cap_mapq’: 2021-07-14T07:13:20,276 htslib/realn.c:47:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:20,277 47 | for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { 2021-07-14T07:13:20,277 | ^ 2021-07-14T07:13:20,278 htslib/realn.c: In function ‘realn_check_tag’: 2021-07-14T07:13:20,278 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] 2021-07-14T07:13:20,279 96 | if (b->core.l_qseq != strlen((const char *) tg + 1)) { 2021-07-14T07:13:20,279 | ^~ 2021-07-14T07:13:20,280 htslib/realn.c: In function ‘sam_prob_realn’: 2021-07-14T07:13:20,281 htslib/realn.c:158:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:20,281 158 | for (k = 0; k < c->n_cigar; ++k) { 2021-07-14T07:13:20,281 | ^ 2021-07-14T07:13:20,282 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] 2021-07-14T07:13:20,282 188 | if (extend_baq && lref < c->l_qseq) 2021-07-14T07:13:20,282 | ^ 2021-07-14T07:13:20,283 htslib/realn.c:221:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:20,283 221 | for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { 2021-07-14T07:13:20,283 | ^ 2021-07-14T07:13:20,284 htslib/realn.c:247:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:20,284 247 | for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { 2021-07-14T07:13:20,284 | ^ 2021-07-14T07:13:20,886 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 2021-07-14T07:13:21,042 htslib/regidx.c: In function ‘regidx_insert’: 2021-07-14T07:13:21,043 htslib/regidx.c:156:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:21,043 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-14T07:13:21,043 | ^ 2021-07-14T07:13:21,043 htslib/regidx.c:156:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:21,043 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-14T07:13:21,043 | ^~ 2021-07-14T07:13:21,044 htslib/regidx.c:156:89: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:21,044 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-14T07:13:21,044 | ^ 2021-07-14T07:13:21,779 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/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 2021-07-14T07:13:22,014 In file included from htslib/cram/os.h:80, 2021-07-14T07:13:22,015 from htslib/cram/misc.h:66, 2021-07-14T07:13:22,015 from htslib/cram/cram_io.h:46, 2021-07-14T07:13:22,015 from htslib/cram/cram.h:48, 2021-07-14T07:13:22,015 from htslib/sam.c:37: 2021-07-14T07:13:22,015 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:13:22,015 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] 2021-07-14T07:13:22,015 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:13:22,016 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:22,016 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:13:22,016 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] 2021-07-14T07:13:22,016 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:13:22,016 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:22,020 In file included from htslib/cram/cram.h:48, 2021-07-14T07:13:22,021 from htslib/sam.c:37: 2021-07-14T07:13:22,021 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-14T07:13:22,021 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] 2021-07-14T07:13:22,021 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-14T07:13:22,021 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:22,029 In file included from htslib/cram/cram.h:52, 2021-07-14T07:13:22,030 from htslib/sam.c:37: 2021-07-14T07:13:22,030 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-14T07:13:22,030 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] 2021-07-14T07:13:22,030 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-14T07:13:22,030 | ^~ 2021-07-14T07:13:22,030 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:22,031 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-14T07:13:22,031 | ^ 2021-07-14T07:13:22,042 In file included from htslib/sam.c:39: 2021-07-14T07:13:22,042 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:22,042 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,043 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:22,043 | ^ 2021-07-14T07:13:22,048 htslib/sam.c: In function ‘bam_hdr_read’: 2021-07-14T07:13:22,048 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] 2021-07-14T07:13:22,048 155 | if (bytes != h->l_text) goto read_err; 2021-07-14T07:13:22,049 | ^~ 2021-07-14T07:13:22,052 htslib/sam.c: In function ‘possibly_expand_bam_data’: 2021-07-14T07:13:22,052 htslib/sam.c:323:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:22,052 323 | if (new_len > INT32_MAX || new_len < b->l_data) { 2021-07-14T07:13:22,052 | ^ 2021-07-14T07:13:22,055 htslib/sam.c: In function ‘bam_tag2cigar’: 2021-07-14T07:13:22,055 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] 2021-07-14T07:13:22,055 408 | if (bam_cigar_op(cigar0[0]) != BAM_CSOFT_CLIP || bam_cigar_oplen(cigar0[0]) != c->l_qseq) return 0; 2021-07-14T07:13:22,055 | ^~ 2021-07-14T07:13:22,062 htslib/sam.c: In function ‘bam_write1’: 2021-07-14T07:13:22,063 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] 2021-07-14T07:13:22,063 564 | return ok? 4 + block_len : -1; 2021-07-14T07:13:22,063 | ^~ 2021-07-14T07:13:22,079 htslib/sam.c: In function ‘sam_hdr_write’: 2021-07-14T07:13:22,079 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] 2021-07-14T07:13:22,079 1108 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-14T07:13:22,079 | ^~ 2021-07-14T07:13:22,081 htslib/sam.c: In function ‘sam_hdr_change_HD’: 2021-07-14T07:13:22,081 htslib/sam.c:1143:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:22,082 1143 | && strlen(val) == end - beg - 4) 2021-07-14T07:13:22,082 | ^~ 2021-07-14T07:13:22,088 htslib/sam.c: In function ‘sam_parse1’: 2021-07-14T07:13:22,088 htslib/sam.c:1262:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,089 1262 | for (i = 0; i < c->n_cigar; ++i, ++q) { 2021-07-14T07:13:22,089 | ^ 2021-07-14T07:13:22,096 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] 2021-07-14T07:13:22,096 1392 | _parse_err(bytes / size != n 2021-07-14T07:13:22,096 | ^~ 2021-07-14T07:13:22,097 htslib/sam.c:1202:40: note: in definition of macro ‘_parse_err’ 2021-07-14T07:13:22,097 1202 | #define _parse_err(cond, msg) do { if (cond) { hts_log_error(msg); goto err_ret; } } while (0) 2021-07-14T07:13:22,097 | ^~~~ 2021-07-14T07:13:22,100 htslib/sam.c: In function ‘sam_format1’: 2021-07-14T07:13:22,101 htslib/sam.c:1495:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,101 1495 | for (i = 0; i < c->n_cigar; ++i) { 2021-07-14T07:13:22,101 | ^ 2021-07-14T07:13:22,106 htslib/sam.c:1586:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,106 1586 | if ((end - s) / sub_type_size < n) 2021-07-14T07:13:22,107 | ^ 2021-07-14T07:13:22,107 htslib/sam.c:1589:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,108 1589 | for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if" 2021-07-14T07:13:22,108 | ^ 2021-07-14T07:13:22,109 htslib/sam.c: In function ‘sam_write1’: 2021-07-14T07:13:22,110 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] 2021-07-14T07:13:22,110 1633 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-14T07:13:22,110 | ^~ 2021-07-14T07:13:22,110 htslib/sam.c: In function ‘bam_aux_append’: 2021-07-14T07:13:22,111 htslib/sam.c:1695:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:22,111 1695 | if (new_len > INT32_MAX || new_len < b->l_data) goto nomem; 2021-07-14T07:13:22,111 | ^ 2021-07-14T07:13:22,114 htslib/sam.c: In function ‘skip_aux’: 2021-07-14T07:13:22,114 htslib/sam.c:1737:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,115 1737 | if (size == 0 || end - s < size * n) return NULL; 2021-07-14T07:13:22,115 | ^ 2021-07-14T07:13:22,148 htslib/sam.c: In function ‘resolve_cigar2’: 2021-07-14T07:13:22,149 htslib/sam.c:2287:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,149 2287 | for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) { 2021-07-14T07:13:22,149 | ^ 2021-07-14T07:13:22,152 htslib/sam.c:2309:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,152 2309 | for (k = s->k + 1; k < c->n_cigar; ++k) { 2021-07-14T07:13:22,153 | ^ 2021-07-14T07:13:22,154 htslib/sam.c:2323:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,154 2323 | if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation 2021-07-14T07:13:22,154 | ^ 2021-07-14T07:13:22,155 htslib/sam.c:2328:50: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,156 2328 | else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding 2021-07-14T07:13:22,156 | ^ 2021-07-14T07:13:22,157 htslib/sam.c:2330:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:22,157 2330 | for (k = s->k + 2; k < c->n_cigar; ++k) { 2021-07-14T07:13:22,157 | ^ 2021-07-14T07:13:28,564 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 2021-07-14T07:13:28,731 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:13:28,731 from htslib/htslib/synced_bcf_reader.h:60, 2021-07-14T07:13:28,731 from htslib/synced_bcf_reader.c:34: 2021-07-14T07:13:28,732 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:13:28,732 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] 2021-07-14T07:13:28,732 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:13:28,732 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:28,732 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:13:28,732 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] 2021-07-14T07:13:28,733 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:13:28,733 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:28,783 htslib/synced_bcf_reader.c: In function ‘_regions_add’: 2021-07-14T07:13:28,783 htslib/synced_bcf_reader.c:801:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:28,783 801 | if ( start < creg->regs[i].start ) max = i - 1; 2021-07-14T07:13:28,783 | ^ 2021-07-14T07:13:28,783 htslib/synced_bcf_reader.c:802:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:28,784 802 | else if ( start > creg->regs[i].start ) min = i + 1; 2021-07-14T07:13:28,784 | ^ 2021-07-14T07:13:28,784 htslib/synced_bcf_reader.c:805:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:28,784 805 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-14T07:13:28,784 | ^~ 2021-07-14T07:13:28,784 htslib/synced_bcf_reader.c:805:68: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:28,785 805 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-14T07:13:28,785 | ^~ 2021-07-14T07:13:30,589 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 2021-07-14T07:13:30,753 In file included from htslib/tbx.c:35: 2021-07-14T07:13:30,753 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:13:30,754 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] 2021-07-14T07:13:30,754 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:13:30,754 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:30,754 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:13:30,754 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] 2021-07-14T07:13:30,754 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:13:30,755 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:30,776 htslib/tbx.c: In function ‘tbx_index_load2’: 2021-07-14T07:13:30,776 htslib/tbx.c:321:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:30,776 321 | for (; p - nm < l_nm; p += strlen(p) + 1) { 2021-07-14T07:13:30,776 | ^ 2021-07-14T07:13:31,275 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/textutils.c -o build/temp.linux-armv7l-3.9/htslib/textutils.o 2021-07-14T07:13:31,380 In file included from htslib/textutils.c:30: 2021-07-14T07:13:31,380 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:31,381 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:31,381 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:31,381 | ^ 2021-07-14T07:13:32,031 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 2021-07-14T07:13:32,767 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 2021-07-14T07:13:32,910 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:13:32,910 from htslib/vcf.c:38: 2021-07-14T07:13:32,911 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:13:32,911 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] 2021-07-14T07:13:32,911 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:13:32,911 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:32,911 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:13:32,912 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] 2021-07-14T07:13:32,912 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:13:32,912 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:32,948 In file included from htslib/vcf.c:41: 2021-07-14T07:13:32,949 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-14T07:13:32,949 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:32,949 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-14T07:13:32,949 | ^ 2021-07-14T07:13:32,975 htslib/vcf.c: In function ‘bcf_hdr_sync’: 2021-07-14T07:13:32,975 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] 2021-07-14T07:13:32,976 149 | if ( h->n[i] < kh_size(d) ) 2021-07-14T07:13:32,976 | ^ 2021-07-14T07:13:32,986 htslib/vcf.c: In function ‘bcf_hdr_register_hrec’: 2021-07-14T07:13:32,986 htslib/vcf.c:499:18: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:32,987 499 | if (type == -1) { 2021-07-14T07:13:32,987 | ^~ 2021-07-14T07:13:32,987 htslib/vcf.c:504:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:32,987 504 | if (var == -1) { 2021-07-14T07:13:32,987 | ^~ 2021-07-14T07:13:32,999 htslib/vcf.c: In function ‘bcf_hdr_read’: 2021-07-14T07:13:32,999 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] 2021-07-14T07:13:32,999 917 | if (bgzf_read(fp, htxt, hlen) != hlen) goto fail; 2021-07-14T07:13:32,999 | ^~ 2021-07-14T07:13:33,001 htslib/vcf.c: In function ‘bcf_hdr_write’: 2021-07-14T07:13:33,001 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] 2021-07-14T07:13:33,002 948 | if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1; 2021-07-14T07:13:33,002 | ^~ 2021-07-14T07:13:33,004 htslib/vcf.c: In function ‘bcf_read1_core’: 2021-07-14T07:13:33,005 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] 2021-07-14T07:13:33,005 1033 | if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -2; 2021-07-14T07:13:33,005 | ^~ 2021-07-14T07:13:33,006 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] 2021-07-14T07:13:33,006 1034 | if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -2; 2021-07-14T07:13:33,006 | ^~ 2021-07-14T07:13:33,007 htslib/vcf.c: In function ‘bcf_dec_typed_int1_safe’: 2021-07-14T07:13:33,008 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] 2021-07-14T07:13:33,008 1058 | *val = v < 0x8000 ? v : -((int32_t) (0xffff - v)) - 1; 2021-07-14T07:13:33,008 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:33,009 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] 2021-07-14T07:13:33,009 1063 | *val = v < 0x80000000UL ? v : -((int32_t) (0xffffffffUL - v)) - 1; 2021-07-14T07:13:33,009 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:33,011 htslib/vcf.c: In function ‘bcf_record_check’: 2021-07-14T07:13:33,011 htslib/vcf.c:1125:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:33,011 1125 | if (end - ptr < bytes) goto bad_shared; 2021-07-14T07:13:33,012 | ^ 2021-07-14T07:13:33,013 htslib/vcf.c:1138:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:33,013 1138 | if (end - ptr < bytes) goto bad_shared; 2021-07-14T07:13:33,013 | ^ 2021-07-14T07:13:33,014 htslib/vcf.c:1151:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:33,014 1151 | if (end - ptr < bytes) goto bad_shared; 2021-07-14T07:13:33,014 | ^ 2021-07-14T07:13:33,015 htslib/vcf.c:1152:23: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-14T07:13:33,015 1152 | for (i = 0; i < num; i++) { 2021-07-14T07:13:33,015 | ^ 2021-07-14T07:13:33,017 htslib/vcf.c:1179:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:33,017 1179 | if (end - ptr < bytes) goto bad_shared; 2021-07-14T07:13:33,017 | ^ 2021-07-14T07:13:33,018 htslib/vcf.c:1202:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:33,019 1202 | if (end - ptr < bytes) goto bad_indiv; 2021-07-14T07:13:33,019 | ^ 2021-07-14T07:13:33,030 htslib/vcf.c: In function ‘bcf_write’: 2021-07-14T07:13:33,031 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] 2021-07-14T07:13:33,031 1533 | if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1; 2021-07-14T07:13:33,031 | ^~ 2021-07-14T07:13:33,032 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] 2021-07-14T07:13:33,032 1534 | if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1; 2021-07-14T07:13:33,032 | ^~ 2021-07-14T07:13:33,050 htslib/vcf.c: In function ‘vcf_parse_format’: 2021-07-14T07:13:33,051 htslib/vcf.c:1970:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:13:33,051 1970 | if (fmt[j].max_l < l) fmt[j].max_l = l; 2021-07-14T07:13:33,051 | ^ 2021-07-14T07:13:33,055 htslib/vcf.c:2000:33: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2021-07-14T07:13:33,056 2000 | f->size = f->is_gt? f->max_g << 2 : f->max_l; 2021-07-14T07:13:33,056 | ^~~~~~~~~~~~~ 2021-07-14T07:13:33,095 htslib/vcf.c: In function ‘vcf_write_line’: 2021-07-14T07:13:33,096 htslib/vcf.c:2611:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:33,097 2611 | return ret==line->l ? 0 : -1; 2021-07-14T07:13:33,097 | ^~ 2021-07-14T07:13:33,098 htslib/vcf.c: In function ‘vcf_write’: 2021-07-14T07:13:33,099 htslib/vcf.c:2624:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:33,099 2624 | return ret==fp->line.l ? 0 : -1; 2021-07-14T07:13:33,099 | ^~ 2021-07-14T07:13:33,132 htslib/vcf.c: In function ‘bcf_hdr_set_samples’: 2021-07-14T07:13:33,134 htslib/vcf.c:3136:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-14T07:13:33,134 3136 | for (k = kh_begin(d); k != kh_end(d); ++k) 2021-07-14T07:13:33,134 | ^~ 2021-07-14T07:13:33,181 htslib/vcf.c: In function ‘_bcf1_sync_alleles’: 2021-07-14T07:13:33,183 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] 2021-07-14T07:13:33,183 3586 | line->rlen = end_info ? end_info->v1.i - line->pos : strlen(line->d.allele[0]); 2021-07-14T07:13:33,184 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:33,195 htslib/vcf.c: In function ‘bcf_get_info_values’: 2021-07-14T07:13:33,196 htslib/vcf.c:3716:49: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:13:33,196 3716 | if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2; // expected different type 2021-07-14T07:13:33,197 | ^~ 2021-07-14T07:13:33,212 htslib/vcf.c: In function ‘bcf_get_format_values’: 2021-07-14T07:13:33,214 htslib/vcf.c:3819:53: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-14T07:13:33,214 3819 | else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2; // expected different type 2021-07-14T07:13:33,214 | ^~ 2021-07-14T07:13:41,987 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 2021-07-14T07:13:42,135 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:13:42,135 from htslib/htslib/vcf_sweep.h:30, 2021-07-14T07:13:42,135 from htslib/vcf_sweep.c:27: 2021-07-14T07:13:42,135 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:13:42,135 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] 2021-07-14T07:13:42,136 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:13:42,136 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:42,136 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:13:42,136 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] 2021-07-14T07:13:42,136 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:13:42,136 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:42,173 htslib/vcf_sweep.c: In function ‘bcf_sweep_fwd’: 2021-07-14T07:13:42,173 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] 2021-07-14T07:13:42,173 164 | if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size ) 2021-07-14T07:13:42,174 | ^ 2021-07-14T07:13:42,369 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 2021-07-14T07:13:42,516 In file included from htslib/htslib/vcf.h:42, 2021-07-14T07:13:42,516 from htslib/htslib/vcfutils.h:29, 2021-07-14T07:13:42,517 from htslib/vcfutils.c:27: 2021-07-14T07:13:42,517 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-14T07:13:42,517 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] 2021-07-14T07:13:42,518 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-14T07:13:42,518 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:42,518 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-14T07:13:42,519 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] 2021-07-14T07:13:42,519 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-14T07:13:42,519 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-14T07:13:44,833 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 2021-07-14T07:13:45,557 installing to build/bdist.linux-armv7l/wheel 2021-07-14T07:13:45,557 running install 2021-07-14T07:13:45,558 running install_lib 2021-07-14T07:13:45,562 creating build/bdist.linux-armv7l 2021-07-14T07:13:45,563 creating build/bdist.linux-armv7l/wheel 2021-07-14T07:13:45,564 creating build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,565 copying build/lib.linux-armv7l-3.9/cyvcf2/cli.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,568 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,678 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,681 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,687 creating build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,687 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,690 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,692 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,694 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,696 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,698 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/issue_44.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,699 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,717 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,720 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,722 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,724 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,726 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,727 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,730 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,736 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,738 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-alt-repr.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,740 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,743 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/empty.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,744 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,746 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/seg.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,748 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,752 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,755 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_cli.pyc -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,757 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/decomposed.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,759 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_alt_freqs.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,762 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,765 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,768 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,770 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,773 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-14T07:13:45,775 copying build/lib.linux-armv7l-3.9/cyvcf2/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,777 copying build/lib.linux-armv7l-3.9/cyvcf2/__main__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,778 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,780 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,782 copying build/lib.linux-armv7l-3.9/cyvcf2/relatedness.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,784 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-14T07:13:45,849 running install_egg_info 2021-07-14T07:13:45,855 Copying cyvcf2.egg-info to build/bdist.linux-armv7l/wheel/cyvcf2-0.10.7-py3.9.egg-info 2021-07-14T07:13:45,869 running install_scripts 2021-07-14T07:13:45,911 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-14T07:13:45,915 creating build/bdist.linux-armv7l/wheel/cyvcf2-0.10.7.dist-info/WHEEL 2021-07-14T07:13:45,918 creating '/tmp/pip-wheel-e0zr5ctz/cyvcf2-0.10.7-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-14T07:13:45,921 adding 'cyvcf2/__init__.py' 2021-07-14T07:13:45,922 adding 'cyvcf2/__main__.py' 2021-07-14T07:13:45,924 adding 'cyvcf2/cli.py' 2021-07-14T07:13:46,125 adding 'cyvcf2/cyvcf2.c' 2021-07-14T07:13:47,488 adding 'cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so' 2021-07-14T07:13:47,541 adding 'cyvcf2/cyvcf2.pxd' 2021-07-14T07:13:47,550 adding 'cyvcf2/cyvcf2.pyx' 2021-07-14T07:13:47,552 adding 'cyvcf2/helpers.c' 2021-07-14T07:13:47,553 adding 'cyvcf2/helpers.h' 2021-07-14T07:13:47,555 adding 'cyvcf2/relatedness.h' 2021-07-14T07:13:47,557 adding 'cyvcf2/tests/__init__.py' 2021-07-14T07:13:47,558 adding 'cyvcf2/tests/__init__.pyc' 2021-07-14T07:13:47,559 adding 'cyvcf2/tests/bug.vcf.gz' 2021-07-14T07:13:47,560 adding 'cyvcf2/tests/decomposed.vcf' 2021-07-14T07:13:47,561 adding 'cyvcf2/tests/empty.vcf' 2021-07-14T07:13:47,563 adding 'cyvcf2/tests/issue_44.vcf' 2021-07-14T07:13:47,568 adding 'cyvcf2/tests/o.vcf.gz' 2021-07-14T07:13:47,569 adding 'cyvcf2/tests/seg.vcf.gz' 2021-07-14T07:13:47,571 adding 'cyvcf2/tests/test-alt-repr.vcf' 2021-07-14T07:13:47,572 adding 'cyvcf2/tests/test-format-string.vcf' 2021-07-14T07:13:47,615 adding 'cyvcf2/tests/test-haploidX.vcf' 2021-07-14T07:13:47,622 adding 'cyvcf2/tests/test-hemi.vcf' 2021-07-14T07:13:47,623 adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz' 2021-07-14T07:13:47,624 adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi' 2021-07-14T07:13:47,625 adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz' 2021-07-14T07:13:47,626 adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi' 2021-07-14T07:13:47,628 adding 'cyvcf2/tests/test.comp_het.3.vcf' 2021-07-14T07:13:47,630 adding 'cyvcf2/tests/test.snpeff.bcf' 2021-07-14T07:13:47,631 adding 'cyvcf2/tests/test.snpeff.bcf.csi' 2021-07-14T07:13:47,633 adding 'cyvcf2/tests/test.snpeff.vcf' 2021-07-14T07:13:47,653 adding 'cyvcf2/tests/test.vcf.gz' 2021-07-14T07:13:47,656 adding 'cyvcf2/tests/test.vcf.gz.tbi' 2021-07-14T07:13:47,657 adding 'cyvcf2/tests/test_cli.py' 2021-07-14T07:13:47,658 adding 'cyvcf2/tests/test_cli.pyc' 2021-07-14T07:13:47,660 adding 'cyvcf2/tests/test_gt_alt_freqs.vcf' 2021-07-14T07:13:47,662 adding 'cyvcf2/tests/test_gt_bases.vcf.gz' 2021-07-14T07:13:47,663 adding 'cyvcf2/tests/test_hemi.py' 2021-07-14T07:13:47,664 adding 'cyvcf2/tests/test_hemi.pyc' 2021-07-14T07:13:47,667 adding 'cyvcf2/tests/test_reader.py' 2021-07-14T07:13:47,674 adding 'cyvcf2/tests/test_reader.pyc' 2021-07-14T07:13:47,676 adding 'cyvcf2-0.10.7.dist-info/LICENSE' 2021-07-14T07:13:47,678 adding 'cyvcf2-0.10.7.dist-info/METADATA' 2021-07-14T07:13:47,679 adding 'cyvcf2-0.10.7.dist-info/WHEEL' 2021-07-14T07:13:47,680 adding 'cyvcf2-0.10.7.dist-info/entry_points.txt' 2021-07-14T07:13:47,680 adding 'cyvcf2-0.10.7.dist-info/top_level.txt' 2021-07-14T07:13:47,682 adding 'cyvcf2-0.10.7.dist-info/RECORD' 2021-07-14T07:13:47,739 removing build/bdist.linux-armv7l/wheel 2021-07-14T07:13:48,300 Building wheel for cyvcf2 (setup.py): finished with status 'done' 2021-07-14T07:13:48,343 Created wheel for cyvcf2: filename=cyvcf2-0.10.7-cp39-cp39-linux_armv7l.whl size=3232766 sha256=ada328301a0f65be0500d1d18f14ee5f27ad092363afd6f53577fe9141dd06ed 2021-07-14T07:13:48,344 Stored in directory: /tmp/pip-ephem-wheel-cache-h8z_z7b4/wheels/f5/1a/3e/494157faca9c4605e7067c1e452a414a104bf76ea17ad720bd 2021-07-14T07:13:48,357 Successfully built cyvcf2 2021-07-14T07:13:48,456 Removed build tracker: '/tmp/pip-req-tracker-z01i9hmt'