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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/) 2021-07-16T00:09:31,592 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 2021-07-16T00:09:31,593 Skipping link: not a file: https://pypi.org/simple/cyvcf2/ 2021-07-16T00:09:31,605 Given no hashes to check 1 links for project 'cyvcf2': discarding no candidates 2021-07-16T00:09:31,628 Collecting cyvcf2==0.11.7 2021-07-16T00:09:31,630 Created temporary directory: /tmp/pip-unpack-vlrxggeg 2021-07-16T00:09:31,673 Downloading cyvcf2-0.11.7.tar.gz (1.1 MB) 2021-07-16T00:09:32,408 Added cyvcf2==0.11.7 from https://files.pythonhosted.org/packages/69/7f/2f256704fdb1f00c78e45ee937a371a4ea16e7f883bd301f3337bdad10ee/cyvcf2-0.11.7.tar.gz#sha256=a4b6229b89a0a1043684c65cbdd702c366a8800dc3591fb44c4b5a08640cbeec to build tracker '/tmp/pip-req-tracker-4fpx_y2r' 2021-07-16T00:09:32,409 Running setup.py (path:/tmp/pip-wheel-0nowjldb/cyvcf2_e683a955768740f9833ba3c58b91031b/setup.py) egg_info for package cyvcf2 2021-07-16T00:09:32,410 Created temporary directory: /tmp/pip-pip-egg-info-lj18njxu 2021-07-16T00:09:32,410 Running command python setup.py egg_info 2021-07-16T00:09:35,207 running egg_info 2021-07-16T00:09:35,210 creating /tmp/pip-pip-egg-info-lj18njxu/cyvcf2.egg-info 2021-07-16T00:09:35,211 writing /tmp/pip-pip-egg-info-lj18njxu/cyvcf2.egg-info/PKG-INFO 2021-07-16T00:09:35,215 writing dependency_links to /tmp/pip-pip-egg-info-lj18njxu/cyvcf2.egg-info/dependency_links.txt 2021-07-16T00:09:35,216 writing entry points to /tmp/pip-pip-egg-info-lj18njxu/cyvcf2.egg-info/entry_points.txt 2021-07-16T00:09:35,218 writing requirements to /tmp/pip-pip-egg-info-lj18njxu/cyvcf2.egg-info/requires.txt 2021-07-16T00:09:35,219 writing top-level names to /tmp/pip-pip-egg-info-lj18njxu/cyvcf2.egg-info/top_level.txt 2021-07-16T00:09:35,220 writing manifest file '/tmp/pip-pip-egg-info-lj18njxu/cyvcf2.egg-info/SOURCES.txt' 2021-07-16T00:09:35,697 reading manifest file '/tmp/pip-pip-egg-info-lj18njxu/cyvcf2.egg-info/SOURCES.txt' 2021-07-16T00:09:35,699 reading manifest template 'MANIFEST.in' 2021-07-16T00:09:35,716 adding license file 'LICENSE' 2021-07-16T00:09:35,725 writing manifest file '/tmp/pip-pip-egg-info-lj18njxu/cyvcf2.egg-info/SOURCES.txt' 2021-07-16T00:09:35,859 Source in /tmp/pip-wheel-0nowjldb/cyvcf2_e683a955768740f9833ba3c58b91031b has version 0.11.7, which satisfies requirement cyvcf2==0.11.7 from https://files.pythonhosted.org/packages/69/7f/2f256704fdb1f00c78e45ee937a371a4ea16e7f883bd301f3337bdad10ee/cyvcf2-0.11.7.tar.gz#sha256=a4b6229b89a0a1043684c65cbdd702c366a8800dc3591fb44c4b5a08640cbeec 2021-07-16T00:09:35,860 Removed cyvcf2==0.11.7 from https://files.pythonhosted.org/packages/69/7f/2f256704fdb1f00c78e45ee937a371a4ea16e7f883bd301f3337bdad10ee/cyvcf2-0.11.7.tar.gz#sha256=a4b6229b89a0a1043684c65cbdd702c366a8800dc3591fb44c4b5a08640cbeec from build tracker '/tmp/pip-req-tracker-4fpx_y2r' 2021-07-16T00:09:35,865 Created temporary directory: /tmp/pip-unpack-uq0kec71 2021-07-16T00:09:35,866 Building wheels for collected packages: cyvcf2 2021-07-16T00:09:35,870 Created temporary directory: /tmp/pip-wheel-d0sfns_d 2021-07-16T00:09:35,871 Building wheel for cyvcf2 (setup.py): started 2021-07-16T00:09:35,871 Destination directory: /tmp/pip-wheel-d0sfns_d 2021-07-16T00:09:35,871 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-0nowjldb/cyvcf2_e683a955768740f9833ba3c58b91031b/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-0nowjldb/cyvcf2_e683a955768740f9833ba3c58b91031b/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-d0sfns_d 2021-07-16T00:09:37,613 running bdist_wheel 2021-07-16T00:09:37,855 running build 2021-07-16T00:09:37,855 running build_py 2021-07-16T00:09:38,022 creating build 2021-07-16T00:09:38,022 creating build/lib.linux-armv7l-3.9 2021-07-16T00:09:38,023 creating build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,024 copying cyvcf2/cli.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,027 copying cyvcf2/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,029 copying cyvcf2/__main__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,031 creating build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,032 copying cyvcf2/tests/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,034 copying cyvcf2/tests/test_cli.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,036 copying cyvcf2/tests/test_hemi.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,038 copying cyvcf2/tests/test_reader.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,041 running egg_info 2021-07-16T00:09:38,057 writing cyvcf2.egg-info/PKG-INFO 2021-07-16T00:09:38,059 writing dependency_links to cyvcf2.egg-info/dependency_links.txt 2021-07-16T00:09:38,061 writing entry points to cyvcf2.egg-info/entry_points.txt 2021-07-16T00:09:38,062 writing requirements to cyvcf2.egg-info/requires.txt 2021-07-16T00:09:38,063 writing top-level names to cyvcf2.egg-info/top_level.txt 2021-07-16T00:09:38,107 reading manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-16T00:09:38,114 reading manifest template 'MANIFEST.in' 2021-07-16T00:09:38,127 adding license file 'LICENSE' 2021-07-16T00:09:38,137 writing manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-16T00:09:38,145 copying cyvcf2/cyvcf2.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,202 copying cyvcf2/cyvcf2.pxd -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,205 copying cyvcf2/cyvcf2.pyx -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,209 copying cyvcf2/helpers.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,212 copying cyvcf2/helpers.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,214 copying cyvcf2/relatedness.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,217 copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,220 copying cyvcf2/tests/decomposed.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,223 copying cyvcf2/tests/empty.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,225 copying cyvcf2/tests/issue_44.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,228 copying cyvcf2/tests/no-seq-len.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,230 copying cyvcf2/tests/no-seq-names.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,233 copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,238 copying cyvcf2/tests/seg.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,240 copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,243 copying cyvcf2/tests/test-diff.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,246 copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,248 copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,263 copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,266 copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,268 copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,271 copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,273 copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,275 copying cyvcf2/tests/test.bug.117.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,277 copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,280 copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,283 copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,285 copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,288 copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,295 copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,297 copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,301 copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-16T00:09:38,305 running build_ext 2021-07-16T00:09:38,312 building 'cyvcf2.cyvcf2' extension 2021-07-16T00:09:38,313 creating build/temp.linux-armv7l-3.9 2021-07-16T00:09:38,314 creating build/temp.linux-armv7l-3.9/cyvcf2 2021-07-16T00:09:38,315 creating build/temp.linux-armv7l-3.9/htslib 2021-07-16T00:09:38,316 creating build/temp.linux-armv7l-3.9/htslib/cram 2021-07-16T00:09:38,318 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 2021-07-16T00:09:38,836 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-16T00:09:38,837 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-16T00:09:38,837 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-16T00:09:38,837 from cyvcf2/cyvcf2.c:599: 2021-07-16T00:09:38,837 /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] 2021-07-16T00:09:38,837 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-16T00:09:38,838 | ^~~~~~~ 2021-07-16T00:09:38,915 In file included from htslib/htslib/vcf.h:42, 2021-07-16T00:09:38,915 from cyvcf2/helpers.h:1, 2021-07-16T00:09:38,916 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:38,916 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:09:38,916 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] 2021-07-16T00:09:38,916 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:09:38,917 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:38,917 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:09:38,917 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] 2021-07-16T00:09:38,917 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:09:38,918 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:38,933 In file included from cyvcf2/cyvcf2.c:604: 2021-07-16T00:09:38,933 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:09:38,934 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:09:38,934 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:09:38,934 | ^ 2021-07-16T00:09:39,105 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: 2021-07-16T00:09:39,109 cyvcf2/cyvcf2.c:7934:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:39,109 7934 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); 2021-07-16T00:09:39,110 | ~~~~~~~~~~~~^~~~~ 2021-07-16T00:09:39,110 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,110 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,110 htslib/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:39,110 443 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-16T00:09:39,110 | ~~~~~~~~~~~^ 2021-07-16T00:09:39,114 cyvcf2/cyvcf2.c:7976:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:39,114 7976 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-16T00:09:39,114 | ~~~~~~~~~~~~^~~~~ 2021-07-16T00:09:39,114 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,115 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,115 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:39,115 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-16T00:09:39,115 | ~~~~~~~~~~~^ 2021-07-16T00:09:39,123 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: 2021-07-16T00:09:39,128 cyvcf2/cyvcf2.c:8492:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:39,128 8492 | __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); 2021-07-16T00:09:39,128 | ~~~~~~~~~~~~^~~~~ 2021-07-16T00:09:39,128 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,129 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,129 htslib/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:39,129 315 | int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); 2021-07-16T00:09:39,129 | ~~~~~~~~~~~^~~ 2021-07-16T00:09:39,137 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: 2021-07-16T00:09:39,141 cyvcf2/cyvcf2.c:8790:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:39,142 8790 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); 2021-07-16T00:09:39,142 | ~~~~~~~~~~~~^~~~~ 2021-07-16T00:09:39,142 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,142 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,143 htslib/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:39,143 443 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-16T00:09:39,143 | ~~~~~~~~~~~^ 2021-07-16T00:09:39,147 cyvcf2/cyvcf2.c:8843:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:39,147 8843 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-16T00:09:39,148 | ~~~~~~~~~~~~^~~~~ 2021-07-16T00:09:39,148 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,148 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,148 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:39,149 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-16T00:09:39,149 | ~~~~~~~~~~~^ 2021-07-16T00:09:39,155 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_20generator’: 2021-07-16T00:09:39,157 cyvcf2/cyvcf2.c:9263:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:39,157 9263 | __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); 2021-07-16T00:09:39,158 htslib/htslib/vcf.h:796:103: note: in definition of macro ‘bcf_itr_querys’ 2021-07-16T00:09:39,158 796 | #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) 2021-07-16T00:09:39,158 | ^~~ 2021-07-16T00:09:39,158 In file included from htslib/htslib/vcf.h:39, 2021-07-16T00:09:39,158 from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,159 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,159 htslib/htslib/hts.h:675:97: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:39,159 675 | 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); 2021-07-16T00:09:39,159 | ~~~~~~^~~ 2021-07-16T00:09:39,177 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_26generator2’: 2021-07-16T00:09:39,182 cyvcf2/cyvcf2.c:10548:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:39,183 10548 | __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, 418, __pyx_L1_error) 2021-07-16T00:09:39,183 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-16T00:09:39,184 cyvcf2/cyvcf2.c:2913:107: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:39,184 2913 | static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ 2021-07-16T00:09:39,184 | ^~~~~~~~~~~ 2021-07-16T00:09:39,256 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_37__dealloc__’: 2021-07-16T00:09:39,263 cyvcf2/cyvcf2.c:12204:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:39,263 12204 | bcf_hdr_destroy(__pyx_v_self->hdr); 2021-07-16T00:09:39,263 | ~~~~~~~~~~~~^~~~~ 2021-07-16T00:09:39,263 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,264 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,264 htslib/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:39,264 261 | void bcf_hdr_destroy(bcf_hdr_t *h); 2021-07-16T00:09:39,264 | ~~~~~~~~~~~^ 2021-07-16T00:09:39,267 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: 2021-07-16T00:09:39,274 cyvcf2/cyvcf2.c:12685:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 2021-07-16T00:09:39,274 12685 | __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); 2021-07-16T00:09:39,274 | ^~~~~~~~~ 2021-07-16T00:09:39,274 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,275 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,275 htslib/htslib/vcf.h:439:11: note: declared here 2021-07-16T00:09:39,275 439 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) 2021-07-16T00:09:39,275 | ^~~~~~~~~~~~~~~~ 2021-07-16T00:09:39,278 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: 2021-07-16T00:09:39,284 cyvcf2/cyvcf2.c:12979:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-16T00:09:39,284 12979 | __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-16T00:09:39,285 | ^ 2021-07-16T00:09:39,290 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,290 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,290 cyvcf2/cyvcf2.c:13088:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:39,290 13088 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-16T00:09:39,291 htslib/htslib/vcf.h:799:112: note: in definition of macro ‘bcf_index_seqnames’ 2021-07-16T00:09:39,291 799 | #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) 2021-07-16T00:09:39,291 | ^~~ 2021-07-16T00:09:39,291 In file included from htslib/htslib/vcf.h:39, 2021-07-16T00:09:39,291 from cyvcf2/helpers.h:1, 2021-07-16T00:09:39,291 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:39,292 htslib/htslib/hts.h:677:92: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:39,292 677 | 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 2021-07-16T00:09:39,292 | ~~~~~~^~~ 2021-07-16T00:09:39,298 cyvcf2/cyvcf2.c:13088:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-16T00:09:39,298 13088 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-16T00:09:39,298 | ^ 2021-07-16T00:09:39,305 cyvcf2/cyvcf2.c:13171:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-16T00:09:39,306 13171 | __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); 2021-07-16T00:09:39,306 | ^ 2021-07-16T00:09:39,941 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’: 2021-07-16T00:09:39,954 cyvcf2/cyvcf2.c:24200:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:09:39,954 24200 | for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) { 2021-07-16T00:09:39,954 | ^ 2021-07-16T00:09:40,062 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’: 2021-07-16T00:09:40,075 cyvcf2/cyvcf2.c:26211:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,076 26211 | __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id); 2021-07-16T00:09:40,076 | ^ 2021-07-16T00:09:40,369 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’: 2021-07-16T00:09:40,386 cyvcf2/cyvcf2.c:33773:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:09:40,386 33773 | for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-07-16T00:09:40,387 | ^ 2021-07-16T00:09:40,391 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’: 2021-07-16T00:09:40,409 cyvcf2/cyvcf2.c:34038:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:09:40,409 34038 | for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2021-07-16T00:09:40,409 | ^ 2021-07-16T00:09:40,412 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’: 2021-07-16T00:09:40,430 cyvcf2/cyvcf2.c:34252:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:09:40,430 34252 | for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2021-07-16T00:09:40,430 | ^ 2021-07-16T00:09:40,448 cyvcf2/cyvcf2.c:34310:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘Py_ssize_t’ {aka ‘int’} [-Wsign-compare] 2021-07-16T00:09:40,449 34310 | __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0); 2021-07-16T00:09:40,449 | ^~ 2021-07-16T00:09:40,475 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: 2021-07-16T00:09:40,494 cyvcf2/cyvcf2.c:36422:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,494 36422 | __pyx_v_h = __pyx_t_6; 2021-07-16T00:09:40,494 | ^ 2021-07-16T00:09:40,579 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: 2021-07-16T00:09:40,599 cyvcf2/cyvcf2.c:39465:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,599 39465 | __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); 2021-07-16T00:09:40,599 | ^ 2021-07-16T00:09:40,608 cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: 2021-07-16T00:09:40,628 cyvcf2/cyvcf2.c:40448:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,628 40448 | __pyx_v_i->hdr = __pyx_t_4; 2021-07-16T00:09:40,629 | ^ 2021-07-16T00:09:40,639 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: 2021-07-16T00:09:40,660 cyvcf2/cyvcf2.c:41102:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,661 41102 | (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); 2021-07-16T00:09:40,661 | ~~~~~~~~~~~~^~~~~ 2021-07-16T00:09:40,661 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:40,661 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:40,661 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:40,662 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-16T00:09:40,662 | ~~~~~~~~~~~^ 2021-07-16T00:09:40,682 cyvcf2/cyvcf2.c:41130:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,682 41130 | (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); 2021-07-16T00:09:40,682 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-16T00:09:40,683 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:40,683 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:40,683 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:40,683 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-16T00:09:40,684 | ~~~~~~~~~~~^ 2021-07-16T00:09:40,689 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2from_string’: 2021-07-16T00:09:40,710 cyvcf2/cyvcf2.c:41457:55: warning: passing argument 1 of ‘bcf_hdr_parse’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,710 41457 | __pyx_t_2 = ((bcf_hdr_parse(__pyx_v_self->__pyx_base.hdr, __pyx_t_7) != 0) != 0); 2021-07-16T00:09:40,710 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-16T00:09:40,711 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:40,711 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:40,711 htslib/htslib/vcf.h:478:34: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:40,711 478 | int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt); 2021-07-16T00:09:40,711 | ~~~~~~~~~~~^~~ 2021-07-16T00:09:40,732 cyvcf2/cyvcf2.c:41493:54: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,732 41493 | __pyx_t_2 = ((bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr) != 0) != 0); 2021-07-16T00:09:40,732 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-16T00:09:40,733 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:40,733 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:40,733 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:40,733 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-16T00:09:40,733 | ~~~~~~~~~~~^ 2021-07-16T00:09:40,738 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_6write_header’: 2021-07-16T00:09:40,759 cyvcf2/cyvcf2.c:41871:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,759 41871 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); 2021-07-16T00:09:40,760 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-16T00:09:40,760 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:40,760 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:40,760 htslib/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:40,761 320 | int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); 2021-07-16T00:09:40,761 | ~~~~~~~~~~~^ 2021-07-16T00:09:40,762 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_8write_record’: 2021-07-16T00:09:40,784 cyvcf2/cyvcf2.c:42043:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,784 42043 | __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); 2021-07-16T00:09:40,784 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-16T00:09:40,784 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:40,785 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:40,785 htslib/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:40,785 482 | int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); 2021-07-16T00:09:40,785 | ~~~~~~~~~~~^~~ 2021-07-16T00:09:40,806 cyvcf2/cyvcf2.c:42081:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,807 42081 | (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); 2021-07-16T00:09:40,807 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-16T00:09:40,807 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:40,808 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:40,808 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:40,808 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-16T00:09:40,808 | ~~~~~~~~~~~^ 2021-07-16T00:09:40,829 cyvcf2/cyvcf2.c:42140:100: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-16T00:09:40,829 42140 | __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, 2251, __pyx_L1_error) 2021-07-16T00:09:40,829 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-16T00:09:40,830 In file included from cyvcf2/helpers.h:1, 2021-07-16T00:09:40,830 from cyvcf2/cyvcf2.c:602: 2021-07-16T00:09:40,830 htslib/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-16T00:09:40,830 370 | int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); 2021-07-16T00:09:40,831 | ~~~~~~~~~~~^ 2021-07-16T00:09:41,784 cyvcf2/cyvcf2.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-16T00:09:41,816 cyvcf2/cyvcf2.c:63586:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:41,816 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:41,817 | ^ 2021-07-16T00:09:41,817 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:41,817 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:41,817 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:41,817 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-16T00:09:41,818 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-16T00:09:41,818 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:41,855 cyvcf2/cyvcf2.c:63586:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:41,856 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:41,856 | ^ 2021-07-16T00:09:41,856 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:41,856 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:41,856 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:41,856 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-16T00:09:41,857 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-16T00:09:41,857 | ^~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:41,894 cyvcf2/cyvcf2.c:63586:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:41,895 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:41,895 | ^ 2021-07-16T00:09:41,895 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:41,896 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:41,896 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:41,896 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-16T00:09:41,896 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-16T00:09:41,896 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:41,934 cyvcf2/cyvcf2.c:63586:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:41,934 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:41,934 | ^ 2021-07-16T00:09:41,934 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:41,935 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:41,935 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:41,935 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-16T00:09:41,935 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-16T00:09:41,935 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:41,973 cyvcf2/cyvcf2.c:63586:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:41,973 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:41,973 | ^ 2021-07-16T00:09:41,973 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:41,974 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:41,974 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:41,974 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-16T00:09:41,974 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-16T00:09:41,974 | ^~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:42,012 cyvcf2/cyvcf2.c:63586:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:42,012 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:42,013 | ^ 2021-07-16T00:09:42,013 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:42,013 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:42,013 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:42,013 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-16T00:09:42,013 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-16T00:09:42,013 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:42,057 cyvcf2/cyvcf2.c:63602:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:42,058 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:42,058 | ^ 2021-07-16T00:09:42,058 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:42,058 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:42,058 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:42,059 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-16T00:09:42,059 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-16T00:09:42,059 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:42,097 cyvcf2/cyvcf2.c:63602:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:42,097 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:42,097 | ^ 2021-07-16T00:09:42,097 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:42,097 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:42,098 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:42,098 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-16T00:09:42,098 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-16T00:09:42,098 | ^~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:42,136 cyvcf2/cyvcf2.c:63602:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:42,136 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:42,136 | ^ 2021-07-16T00:09:42,137 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:42,137 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:42,137 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:42,137 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-16T00:09:42,137 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-16T00:09:42,137 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:42,175 cyvcf2/cyvcf2.c:63602:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:42,175 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:42,176 | ^ 2021-07-16T00:09:42,176 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:42,176 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:42,176 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:42,176 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-16T00:09:42,176 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-16T00:09:42,177 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:42,214 cyvcf2/cyvcf2.c:63602:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:42,215 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:42,215 | ^ 2021-07-16T00:09:42,215 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:42,215 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:42,215 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:42,215 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-16T00:09:42,216 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-16T00:09:42,216 | ^~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:42,254 cyvcf2/cyvcf2.c:63602:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:42,254 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-16T00:09:42,254 | ^ 2021-07-16T00:09:42,254 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:42,254 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:42,255 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:42,255 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-16T00:09:42,255 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-16T00:09:42,255 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:42,585 cyvcf2/cyvcf2.c: In function ‘__Pyx_decode_c_bytes’: 2021-07-16T00:09:42,617 cyvcf2/cyvcf2.c:64591:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:42,618 64591 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-16T00:09:42,618 | ^~~~~~ 2021-07-16T00:09:42,618 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:42,618 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:42,618 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:42,618 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-16T00:09:42,619 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-16T00:09:42,619 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:43,284 cyvcf2/cyvcf2.c: In function ‘__Pyx_decode_c_string’: 2021-07-16T00:09:43,318 cyvcf2/cyvcf2.c:66444:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-16T00:09:43,318 66444 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-16T00:09:43,318 | ^~~~~~ 2021-07-16T00:09:43,318 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-16T00:09:43,319 from /usr/include/python3.9/Python.h:97, 2021-07-16T00:09:43,319 from cyvcf2/cyvcf2.c:4: 2021-07-16T00:09:43,319 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-16T00:09:43,319 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-16T00:09:43,319 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:09:45,399 At top level: 2021-07-16T00:09:45,403 cyvcf2/cyvcf2.c:6618:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] 2021-07-16T00:09:45,404 6618 | static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { 2021-07-16T00:09:45,404 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:10:55,586 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 2021-07-16T00:10:55,762 In file included from htslib/htslib/vcf.h:42, 2021-07-16T00:10:55,762 from cyvcf2/helpers.h:1, 2021-07-16T00:10:55,762 from cyvcf2/helpers.c:1: 2021-07-16T00:10:55,763 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:10:55,763 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] 2021-07-16T00:10:55,763 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:10:55,763 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:10:55,764 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:10:55,764 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] 2021-07-16T00:10:55,764 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:10:55,764 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:10:56,008 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 2021-07-16T00:10:56,159 In file included from htslib/htslib/vcf.h:42, 2021-07-16T00:10:56,160 from htslib/htslib/synced_bcf_reader.h:60, 2021-07-16T00:10:56,160 from htslib/bcf_sr_sort.h:37, 2021-07-16T00:10:56,160 from htslib/bcf_sr_sort.c:29: 2021-07-16T00:10:56,160 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:10:56,161 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] 2021-07-16T00:10:56,161 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:10:56,161 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:10:56,161 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:10:56,161 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] 2021-07-16T00:10:56,162 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:10:56,162 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:10:56,187 htslib/bcf_sr_sort.c: In function ‘kbs_bitwise_or’: 2021-07-16T00:10:56,187 htslib/bcf_sr_sort.c:69:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:10:56,187 69 | for (i=0; in; i++) dst->b[i] |= src->b[i]; 2021-07-16T00:10:56,188 | ^ 2021-07-16T00:10:56,195 htslib/bcf_sr_sort.c: In function ‘bcf_sr_sort_set’: 2021-07-16T00:10:56,195 htslib/bcf_sr_sort.c:363:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:10:56,196 363 | for (k=0; k < kh_end(hash); k++) 2021-07-16T00:10:56,196 | ^ 2021-07-16T00:10:56,196 htslib/bcf_sr_sort.c:366:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:10:56,196 366 | for (k=0; k < kh_end(hash); k++) 2021-07-16T00:10:56,197 | ^ 2021-07-16T00:10:58,099 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 2021-07-16T00:10:58,319 In file included from htslib/bgzf.c:44: 2021-07-16T00:10:58,319 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:10:58,320 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:10:58,320 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:10:58,320 | ^ 2021-07-16T00:10:58,323 In file included from htslib/bgzf.c:46: 2021-07-16T00:10:58,323 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:10:58,324 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] 2021-07-16T00:10:58,324 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:10:58,324 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:10:58,325 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:10:58,325 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] 2021-07-16T00:10:58,325 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:10:58,326 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:10:58,357 htslib/bgzf.c: In function ‘bgzf_read’: 2021-07-16T00:10:58,358 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] 2021-07-16T00:10:58,358 983 | while (bytes_read < length) { 2021-07-16T00:10:58,358 | ^ 2021-07-16T00:10:58,359 htslib/bgzf.c:996:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:10:58,359 996 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-16T00:10:58,359 | ^ 2021-07-16T00:10:58,360 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] 2021-07-16T00:10:58,360 996 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-16T00:10:58,360 | ^~~~~~~~~ 2021-07-16T00:10:58,362 htslib/bgzf.c: In function ‘bgzf_mt_writer’: 2021-07-16T00:10:58,363 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] 2021-07-16T00:10:58,363 1107 | if (hwrite(fp->fp, j->comp_data, j->comp_len) != j->comp_len) { 2021-07-16T00:10:58,363 | ^~ 2021-07-16T00:10:58,375 htslib/bgzf.c: In function ‘bgzf_block_write’: 2021-07-16T00:10:58,376 htslib/bgzf.c:1594:41: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:10:58,376 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; 2021-07-16T00:10:58,377 | ^ 2021-07-16T00:10:58,378 htslib/bgzf.c:1602:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-16T00:10:58,378 1602 | if (fp->block_offset == ublock_size) { 2021-07-16T00:10:58,378 | ^~ 2021-07-16T00:10:58,399 htslib/bgzf.c: In function ‘bgzf_useek’: 2021-07-16T00:10:58,400 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] 2021-07-16T00:10:58,400 2049 | if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1; 2021-07-16T00:10:58,400 | ^ 2021-07-16T00:10:58,401 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] 2021-07-16T00:10:58,401 2050 | else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1; 2021-07-16T00:10:58,401 | ^~ 2021-07-16T00:11:00,837 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 htslib/cram/cram_codecs.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_codecs.o 2021-07-16T00:11:01,111 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:01,112 from htslib/cram/misc.h:66, 2021-07-16T00:11:01,112 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:01,112 from htslib/cram/cram.h:48, 2021-07-16T00:11:01,112 from htslib/cram/cram_codecs.c:45: 2021-07-16T00:11:01,112 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:01,112 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] 2021-07-16T00:11:01,112 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:01,113 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:01,113 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:01,113 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] 2021-07-16T00:11:01,113 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:01,113 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:01,119 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:01,120 from htslib/cram/cram_codecs.c:45: 2021-07-16T00:11:01,120 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:01,120 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] 2021-07-16T00:11:01,120 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:01,120 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:01,130 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:01,131 from htslib/cram/cram_codecs.c:45: 2021-07-16T00:11:01,131 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:01,131 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] 2021-07-16T00:11:01,131 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:01,131 | ^~ 2021-07-16T00:11:01,132 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:01,132 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:01,132 | ^ 2021-07-16T00:11:01,134 htslib/cram/cram_codecs.c: In function ‘get_one_bits_MSB’: 2021-07-16T00:11:01,135 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] 2021-07-16T00:11:01,135 79 | if (block->byte >= block->uncomp_size) 2021-07-16T00:11:01,135 | ^~ 2021-07-16T00:11:01,135 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] 2021-07-16T00:11:01,135 86 | if (block->byte == block->uncomp_size && (b&1)) 2021-07-16T00:11:01,136 | ^~ 2021-07-16T00:11:01,136 htslib/cram/cram_codecs.c: In function ‘get_zero_bits_MSB’: 2021-07-16T00:11:01,136 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] 2021-07-16T00:11:01,136 97 | if (block->byte >= block->uncomp_size) 2021-07-16T00:11:01,136 | ^~ 2021-07-16T00:11:01,136 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] 2021-07-16T00:11:01,136 104 | if (block->byte == block->uncomp_size && !(b&1)) 2021-07-16T00:11:01,137 | ^~ 2021-07-16T00:11:01,148 htslib/cram/cram_codecs.c: In function ‘cram_beta_decode_init’: 2021-07-16T00:11:01,148 htslib/cram/cram_codecs.c:555:47: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:01,148 555 | || c->beta.nbits < 0 || c->beta.nbits > 8 * sizeof(int)) { 2021-07-16T00:11:01,149 | ^ 2021-07-16T00:11:01,162 htslib/cram/cram_codecs.c: In function ‘cram_huffman_decode_init’: 2021-07-16T00:11:01,162 htslib/cram/cram_codecs.c:976:16: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:01,162 976 | if (ncodes >= SIZE_MAX / sizeof(*codes)) { 2021-07-16T00:11:01,162 | ^~ 2021-07-16T00:11:01,165 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] 2021-07-16T00:11:01,165 1044 | if (val > max_val) 2021-07-16T00:11:01,166 | ^ 2021-07-16T00:11:01,191 htslib/cram/cram_codecs.c: In function ‘cram_byte_array_stop_decode_block’: 2021-07-16T00:11:01,192 htslib/cram/cram_codecs.c:1643:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:01,192 1643 | if (cp_end - cp < out->alloc - out->byte) { 2021-07-16T00:11:01,192 | ^ 2021-07-16T00:11:04,285 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 2021-07-16T00:11:04,574 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:04,575 from htslib/cram/misc.h:66, 2021-07-16T00:11:04,575 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:04,575 from htslib/cram/cram.h:48, 2021-07-16T00:11:04,575 from htslib/cram/cram_decode.c:49: 2021-07-16T00:11:04,575 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:04,575 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] 2021-07-16T00:11:04,576 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:04,576 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:04,576 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:04,576 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] 2021-07-16T00:11:04,576 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:04,576 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:04,582 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:04,582 from htslib/cram/cram_decode.c:49: 2021-07-16T00:11:04,582 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:04,582 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] 2021-07-16T00:11:04,583 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:04,583 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:04,590 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:04,591 from htslib/cram/cram_decode.c:49: 2021-07-16T00:11:04,591 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:04,591 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] 2021-07-16T00:11:04,591 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:04,591 | ^~ 2021-07-16T00:11:04,591 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:04,592 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:04,592 | ^ 2021-07-16T00:11:04,596 htslib/cram/cram_decode.c: In function ‘cram_decode_TD’: 2021-07-16T00:11:04,597 htslib/cram/cram_decode.c:102:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:04,597 102 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-16T00:11:04,597 | ^ 2021-07-16T00:11:04,597 htslib/cram/cram_decode.c:114:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:04,597 114 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-16T00:11:04,598 | ^ 2021-07-16T00:11:04,598 htslib/cram/cram_decode.c: In function ‘cram_decode_compression_header’: 2021-07-16T00:11:04,598 htslib/cram/cram_decode.c:156:33: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:04,598 156 | hdr->num_landmarks >= SIZE_MAX / sizeof(int32_t))) { 2021-07-16T00:11:04,598 | ^~ 2021-07-16T00:11:04,618 htslib/cram/cram_decode.c: In function ‘cram_dependent_data_series’: 2021-07-16T00:11:04,618 htslib/cram/cram_decode.c:800:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:04,618 800 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-16T00:11:04,618 | ^ 2021-07-16T00:11:04,620 htslib/cram/cram_decode.c:894:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:04,621 894 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-16T00:11:04,621 | ^ 2021-07-16T00:11:04,626 htslib/cram/cram_decode.c: In function ‘cram_decode_slice_header’: 2021-07-16T00:11:04,626 htslib/cram/cram_decode.c:1114:30: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:04,626 1114 | hdr->num_content_ids >= SIZE_MAX / sizeof(int32_t)) { 2021-07-16T00:11:04,627 | ^~ 2021-07-16T00:11:04,632 htslib/cram/cram_decode.c: In function ‘cram_decode_seq’: 2021-07-16T00:11:04,633 htslib/cram/cram_decode.c:1286:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:04,633 1286 | if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) { 2021-07-16T00:11:04,633 | ^ 2021-07-16T00:11:04,638 htslib/cram/cram_decode.c:1437:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:04,638 1437 | if (cr->ref_id < 0 || ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-16T00:11:04,638 | ^~ 2021-07-16T00:11:04,642 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] 2021-07-16T00:11:04,642 1483 | if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) { 2021-07-16T00:11:04,642 | ^~ 2021-07-16T00:11:04,644 htslib/cram/cram_decode.c:1494:54: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:04,644 1494 | if (bfd->ref[cr->ref_id].len >= ref_pos) { 2021-07-16T00:11:04,644 | ^~ 2021-07-16T00:11:04,650 htslib/cram/cram_decode.c:1587:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:04,650 1587 | if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-16T00:11:04,650 | ^~ 2021-07-16T00:11:04,655 htslib/cram/cram_decode.c:1660:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:04,655 1660 | if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-16T00:11:04,655 | ^~ 2021-07-16T00:11:04,661 htslib/cram/cram_decode.c:1767:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:04,661 1767 | if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) { 2021-07-16T00:11:04,662 | ^ 2021-07-16T00:11:04,690 htslib/cram/cram_decode.c: In function ‘cram_decode_slice’: 2021-07-16T00:11:04,691 htslib/cram/cram_decode.c:2403:20: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:04,692 2403 | bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap)) 2021-07-16T00:11:04,692 | ^~ 2021-07-16T00:11:11,148 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 2021-07-16T00:11:11,438 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:11,438 from htslib/cram/misc.h:66, 2021-07-16T00:11:11,438 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:11,439 from htslib/cram/cram.h:48, 2021-07-16T00:11:11,439 from htslib/cram/cram_encode.c:43: 2021-07-16T00:11:11,439 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:11,439 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] 2021-07-16T00:11:11,439 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:11,439 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:11,439 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:11,440 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] 2021-07-16T00:11:11,440 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:11,440 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:11,445 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:11,445 from htslib/cram/cram_encode.c:43: 2021-07-16T00:11:11,446 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:11,446 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] 2021-07-16T00:11:11,446 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:11,446 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:11,454 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:11,454 from htslib/cram/cram_encode.c:43: 2021-07-16T00:11:11,454 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:11,454 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] 2021-07-16T00:11:11,454 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:11,455 | ^~ 2021-07-16T00:11:11,455 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:11,455 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:11,455 | ^ 2021-07-16T00:11:11,492 htslib/cram/cram_encode.c: In function ‘cram_encode_slice’: 2021-07-16T00:11:11,493 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] 2021-07-16T00:11:11,493 1044 | for (id = 1; id < s->hdr->num_blocks; id++) { 2021-07-16T00:11:11,493 | ^ 2021-07-16T00:11:11,497 htslib/cram/cram_encode.c: In function ‘lossy_read_names’: 2021-07-16T00:11:11,497 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] 2021-07-16T00:11:11,498 1168 | if (u.counts.e != e) { 2021-07-16T00:11:11,498 | ^~ 2021-07-16T00:11:11,499 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] 2021-07-16T00:11:11,499 1198 | if (kh_val(names, k) == -1) 2021-07-16T00:11:11,499 | ^~ 2021-07-16T00:11:11,544 htslib/cram/cram_encode.c: In function ‘process_one_read’: 2021-07-16T00:11:11,545 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] 2021-07-16T00:11:11,545 2636 | while (cr->cigar + cr->ncigar >= s->cigar_alloc) { 2021-07-16T00:11:11,545 | ^~ 2021-07-16T00:11:11,547 htslib/cram/cram_encode.c:2666:44: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:11,547 2666 | int end = cig_len+apos < c->ref_end 2021-07-16T00:11:11,547 | ^ 2021-07-16T00:11:11,548 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] 2021-07-16T00:11:11,548 2667 | ? cig_len : c->ref_end - apos; 2021-07-16T00:11:11,549 | ^~~~~~~~~~~~~~~~~ 2021-07-16T00:11:11,553 htslib/cram/cram_encode.c:2710:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:11,553 2710 | if (l < cig_len && cr->len) { 2021-07-16T00:11:11,553 | ^ 2021-07-16T00:11:11,555 htslib/cram/cram_encode.c:2718:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:11,555 2718 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-16T00:11:11,555 | ^ 2021-07-16T00:11:11,556 htslib/cram/cram_encode.c:2727:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:11,556 2727 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-16T00:11:11,557 | ^ 2021-07-16T00:11:11,560 htslib/cram/cram_encode.c:2759:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:11,561 2759 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-16T00:11:11,561 | ^ 2021-07-16T00:11:11,563 htslib/cram/cram_encode.c:2776:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:11,563 2776 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-16T00:11:11,563 | ^ 2021-07-16T00:11:11,564 htslib/cram/cram_encode.c:2780:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:11,564 2780 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-16T00:11:11,565 | ^ 2021-07-16T00:11:11,569 htslib/cram/cram_encode.c:2834:17: warning: unused variable ‘brg’ [-Wunused-variable] 2021-07-16T00:11:11,569 2834 | SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); 2021-07-16T00:11:11,569 | ^~~ 2021-07-16T00:11:11,587 htslib/cram/cram_encode.c: In function ‘cram_put_bam_seq’: 2021-07-16T00:11:11,589 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] 2021-07-16T00:11:11,589 3077 | (c->s_num_bases >= fd->bases_per_slice)) { 2021-07-16T00:11:11,589 | ^~ 2021-07-16T00:11:11,591 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] 2021-07-16T00:11:11,591 3100 | c->s_num_bases >= fd->bases_per_slice) { 2021-07-16T00:11:11,591 | ^~ 2021-07-16T00:11:17,311 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/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 2021-07-16T00:11:17,403 In file included from htslib/cram/cram_external.c:43: 2021-07-16T00:11:17,403 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:17,404 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:17,404 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:17,404 | ^ 2021-07-16T00:11:17,536 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:17,537 from htslib/cram/misc.h:66, 2021-07-16T00:11:17,537 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:17,537 from htslib/cram/cram.h:48, 2021-07-16T00:11:17,537 from htslib/cram/cram_external.c:44: 2021-07-16T00:11:17,537 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:17,537 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] 2021-07-16T00:11:17,538 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:17,538 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:17,538 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:17,538 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] 2021-07-16T00:11:17,538 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:17,538 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:17,543 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:17,543 from htslib/cram/cram_external.c:44: 2021-07-16T00:11:17,543 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:17,544 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] 2021-07-16T00:11:17,544 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:17,544 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:17,552 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:17,552 from htslib/cram/cram_external.c:44: 2021-07-16T00:11:17,552 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:17,552 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] 2021-07-16T00:11:17,552 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:17,552 | ^~ 2021-07-16T00:11:17,553 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:17,553 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:17,553 | ^ 2021-07-16T00:11:17,963 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 2021-07-16T00:11:18,174 In file included from htslib/cram/cram_index.c:64: 2021-07-16T00:11:18,174 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:18,174 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:18,175 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:18,175 | ^ 2021-07-16T00:11:18,272 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:18,272 from htslib/cram/misc.h:66, 2021-07-16T00:11:18,272 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:18,272 from htslib/cram/cram.h:48, 2021-07-16T00:11:18,273 from htslib/cram/cram_index.c:66: 2021-07-16T00:11:18,273 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:18,273 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] 2021-07-16T00:11:18,273 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:18,273 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:18,273 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:18,273 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] 2021-07-16T00:11:18,274 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:18,274 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:18,279 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:18,279 from htslib/cram/cram_index.c:66: 2021-07-16T00:11:18,279 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:18,279 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] 2021-07-16T00:11:18,280 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:18,280 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:18,289 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:18,289 from htslib/cram/cram_index.c:66: 2021-07-16T00:11:18,289 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:18,289 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] 2021-07-16T00:11:18,289 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:18,290 | ^~ 2021-07-16T00:11:18,290 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:18,290 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:18,290 | ^ 2021-07-16T00:11:18,302 htslib/cram/cram_index.c: In function ‘cram_index_build’: 2021-07-16T00:11:18,302 htslib/cram/cram_index.c:587:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] 2021-07-16T00:11:18,303 587 | off_t cpos, spos, hpos; 2021-07-16T00:11:18,304 | ^~~~ 2021-07-16T00:11:19,127 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 2021-07-16T00:11:19,560 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:19,561 from htslib/cram/misc.h:66, 2021-07-16T00:11:19,561 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:19,561 from htslib/cram/cram.h:48, 2021-07-16T00:11:19,561 from htslib/cram/cram_io.c:77: 2021-07-16T00:11:19,562 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:19,562 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] 2021-07-16T00:11:19,562 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:19,563 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:19,563 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:19,563 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] 2021-07-16T00:11:19,563 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:19,564 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:19,567 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:19,568 from htslib/cram/cram_io.c:77: 2021-07-16T00:11:19,568 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:19,568 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] 2021-07-16T00:11:19,568 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:19,569 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:19,576 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:19,576 from htslib/cram/cram_io.c:77: 2021-07-16T00:11:19,576 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:19,577 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] 2021-07-16T00:11:19,577 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:19,578 | ^~ 2021-07-16T00:11:19,578 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:19,578 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:19,578 | ^ 2021-07-16T00:11:19,583 In file included from htslib/cram/cram_io.c:94: 2021-07-16T00:11:19,584 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:19,584 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:19,584 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:19,585 | ^ 2021-07-16T00:11:19,598 htslib/cram/cram_io.c: In function ‘itf8_decode_crc’: 2021-07-16T00:11:19,598 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] 2021-07-16T00:11:19,598 241 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:19,599 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:19,650 htslib/cram/cram_io.c: In function ‘expand_cache_path’: 2021-07-16T00:11:19,651 htslib/cram/cram_io.c:1920:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:19,651 1920 | if (cp-dir >= sz) return -1; 2021-07-16T00:11:19,651 | ^~ 2021-07-16T00:11:19,653 In file included from htslib/cram/cram_io.h:46, 2021-07-16T00:11:19,654 from htslib/cram/cram.h:48, 2021-07-16T00:11:19,654 from htslib/cram/cram_io.c:77: 2021-07-16T00:11:19,654 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:19,654 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-16T00:11:19,654 | ^ 2021-07-16T00:11:19,655 htslib/cram/cram_io.c:1938:17: note: in expansion of macro ‘MIN’ 2021-07-16T00:11:19,655 1938 | l = MIN(l, strlen(fn)); 2021-07-16T00:11:19,655 | ^~~ 2021-07-16T00:11:19,655 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] 2021-07-16T00:11:19,655 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-16T00:11:19,656 | ^~~ 2021-07-16T00:11:19,656 htslib/cram/cram_io.c:1938:17: note: in expansion of macro ‘MIN’ 2021-07-16T00:11:19,656 1938 | l = MIN(l, strlen(fn)); 2021-07-16T00:11:19,656 | ^~~ 2021-07-16T00:11:19,657 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] 2021-07-16T00:11:19,657 1940 | if (l >= sz) return -1; 2021-07-16T00:11:19,657 | ^~ 2021-07-16T00:11:19,699 htslib/cram/cram_io.c: In function ‘cram_read_container’: 2021-07-16T00:11:19,700 htslib/cram/cram_io.c:2882:50: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:19,701 2882 | if (c2.num_landmarks < 0 || c2.num_landmarks >= SIZE_MAX / sizeof(int32_t)) 2021-07-16T00:11:19,701 | ^~ 2021-07-16T00:11:19,779 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:19,779 from htslib/cram/cram_io.c:77: 2021-07-16T00:11:19,779 htslib/cram/cram_io.c: In function ‘cram_write_SAM_hdr’: 2021-07-16T00:11:19,781 htslib/cram/cram_io.h:511:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:19,781 511 | while((b)->alloc <= (l)) { \ 2021-07-16T00:11:19,781 | ^~ 2021-07-16T00:11:19,782 htslib/cram/cram_io.c:3925:13: note: in expansion of macro ‘BLOCK_RESIZE’ 2021-07-16T00:11:19,782 3925 | BLOCK_RESIZE(b, padded_length); 2021-07-16T00:11:19,782 | ^~~~~~~~~~~~ 2021-07-16T00:11:24,321 In file included from /usr/include/string.h:495, 2021-07-16T00:11:24,322 from htslib/cram/cram_io.c:53: 2021-07-16T00:11:24,322 In function ‘strncpy’, 2021-07-16T00:11:24,322 inlined from ‘full_path’ at htslib/cram/cram_io.c:3748:13, 2021-07-16T00:11:24,323 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-16T00:11:24,323 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-16T00:11:24,323 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-16T00:11:24,323 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:24,324 In function ‘strncpy’, 2021-07-16T00:11:24,324 inlined from ‘full_path’ at htslib/cram/cram_io.c:3740:9, 2021-07-16T00:11:24,324 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-16T00:11:24,325 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-16T00:11:24,325 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-16T00:11:24,325 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:24,630 In function ‘strncpy’, 2021-07-16T00:11:24,630 inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4126:9: 2021-07-16T00:11:24,631 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 2021-07-16T00:11:24,631 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-16T00:11:24,631 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:25,542 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_samtools.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_samtools.o 2021-07-16T00:11:25,808 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:25,808 from htslib/cram/misc.h:66, 2021-07-16T00:11:25,808 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:25,809 from htslib/cram/cram.h:48, 2021-07-16T00:11:25,809 from htslib/cram/cram_samtools.c:37: 2021-07-16T00:11:25,809 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:25,810 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] 2021-07-16T00:11:25,810 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:25,810 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:25,811 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:25,812 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] 2021-07-16T00:11:25,812 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:25,812 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:25,820 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:25,820 from htslib/cram/cram_samtools.c:37: 2021-07-16T00:11:25,821 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:25,821 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] 2021-07-16T00:11:25,822 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:25,822 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:25,831 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:25,832 from htslib/cram/cram_samtools.c:37: 2021-07-16T00:11:25,832 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:25,832 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] 2021-07-16T00:11:25,833 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:25,833 | ^~ 2021-07-16T00:11:25,834 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:25,834 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:25,834 | ^ 2021-07-16T00:11:25,836 htslib/cram/cram_samtools.c: In function ‘bam_construct_seq’: 2021-07-16T00:11:25,836 htslib/cram/cram_samtools.c:85:19: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:25,836 85 | if (b->m_data < bam_len) { 2021-07-16T00:11:25,837 | ^ 2021-07-16T00:11:26,031 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/cram/cram_stats.c -o build/temp.linux-armv7l-3.9/htslib/cram/cram_stats.o 2021-07-16T00:11:26,376 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:26,376 from htslib/cram/misc.h:66, 2021-07-16T00:11:26,376 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:26,376 from htslib/cram/cram.h:48, 2021-07-16T00:11:26,377 from htslib/cram/cram_stats.c:43: 2021-07-16T00:11:26,377 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:26,377 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] 2021-07-16T00:11:26,377 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:26,377 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:26,378 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:26,378 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] 2021-07-16T00:11:26,378 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:26,378 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:26,386 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:26,386 from htslib/cram/cram_stats.c:43: 2021-07-16T00:11:26,386 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:26,386 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] 2021-07-16T00:11:26,387 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:26,387 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:26,397 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:26,397 from htslib/cram/cram_stats.c:43: 2021-07-16T00:11:26,397 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:26,397 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] 2021-07-16T00:11:26,398 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:26,398 | ^~ 2021-07-16T00:11:26,398 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:26,398 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:26,398 | ^ 2021-07-16T00:11:26,847 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 2021-07-16T00:11:26,924 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:26,924 from htslib/cram/misc.h:66, 2021-07-16T00:11:26,925 from htslib/cram/files.c:34: 2021-07-16T00:11:26,925 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:26,925 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] 2021-07-16T00:11:26,926 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:26,926 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:26,926 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:26,926 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] 2021-07-16T00:11:26,927 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:26,927 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:27,055 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 2021-07-16T00:11:27,227 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:27,228 from htslib/cram/mFILE.c:44: 2021-07-16T00:11:27,228 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:27,228 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] 2021-07-16T00:11:27,229 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:27,229 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:27,229 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:27,230 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] 2021-07-16T00:11:27,230 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:27,230 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:27,236 htslib/cram/mFILE.c: In function ‘mfload’: 2021-07-16T00:11:27,236 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] 2021-07-16T00:11:27,237 103 | } while (!feof(fp) && (fn == NULL || used < sb.st_size)); 2021-07-16T00:11:27,237 | ^ 2021-07-16T00:11:27,242 htslib/cram/mFILE.c: In function ‘mftruncate’: 2021-07-16T00:11:27,242 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] 2021-07-16T00:11:27,243 476 | mf->size = offset != -1 ? offset : mf->offset; 2021-07-16T00:11:27,243 | ^~~~~~ 2021-07-16T00:11:27,725 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 2021-07-16T00:11:27,917 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:27,917 from htslib/cram/open_trace_file.c:74: 2021-07-16T00:11:27,918 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:27,918 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] 2021-07-16T00:11:27,918 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:27,918 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:27,919 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:27,919 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] 2021-07-16T00:11:27,919 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:27,919 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:27,925 In file included from htslib/cram/open_trace_file.c:81: 2021-07-16T00:11:27,926 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:27,926 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:27,926 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:27,926 | ^ 2021-07-16T00:11:27,932 In file included from htslib/cram/open_trace_file.c:80: 2021-07-16T00:11:27,932 htslib/cram/open_trace_file.c: In function ‘expand_path’: 2021-07-16T00:11:27,932 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-16T00:11:27,933 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-16T00:11:27,933 | ^ 2021-07-16T00:11:27,933 htslib/cram/open_trace_file.c:251:29: note: in expansion of macro ‘MIN’ 2021-07-16T00:11:27,933 251 | path_end += MIN(strlen(file), l); 2021-07-16T00:11:27,933 | ^~~ 2021-07-16T00:11:27,933 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] 2021-07-16T00:11:27,933 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-16T00:11:27,934 | ^~~ 2021-07-16T00:11:27,934 htslib/cram/open_trace_file.c:251:29: note: in expansion of macro ‘MIN’ 2021-07-16T00:11:27,934 251 | path_end += MIN(strlen(file), l); 2021-07-16T00:11:27,934 | ^~~ 2021-07-16T00:11:27,934 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-16T00:11:27,934 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-16T00:11:27,934 | ^ 2021-07-16T00:11:27,934 htslib/cram/open_trace_file.c:252:29: note: in expansion of macro ‘MIN’ 2021-07-16T00:11:27,935 252 | file += MIN(strlen(file), l); 2021-07-16T00:11:27,935 | ^~~ 2021-07-16T00:11:27,935 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] 2021-07-16T00:11:27,935 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-16T00:11:27,935 | ^~~ 2021-07-16T00:11:27,935 htslib/cram/open_trace_file.c:252:29: note: in expansion of macro ‘MIN’ 2021-07-16T00:11:27,935 252 | file += MIN(strlen(file), l); 2021-07-16T00:11:27,936 | ^~~ 2021-07-16T00:11:28,356 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 2021-07-16T00:11:28,485 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:28,485 from htslib/cram/misc.h:66, 2021-07-16T00:11:28,486 from htslib/cram/pooled_alloc.c:38: 2021-07-16T00:11:28,486 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:28,486 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] 2021-07-16T00:11:28,486 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:28,486 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:28,486 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:28,487 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] 2021-07-16T00:11:28,487 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:28,487 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:28,600 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 2021-07-16T00:11:28,758 htslib/cram/rANS_static.c: In function ‘rans_compress_O0’: 2021-07-16T00:11:28,758 htslib/cram/rANS_static.c:86:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:28,758 86 | for (i = 0; i < in_size; i++) { 2021-07-16T00:11:28,758 | ^ 2021-07-16T00:11:28,764 htslib/cram/rANS_static.c: In function ‘rans_compress_O1’: 2021-07-16T00:11:28,764 htslib/cram/rANS_static.c:388:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:28,765 388 | for (last_i=i=0; ih, type, &new))) 2021-07-16T00:11:30,455 | ^~ 2021-07-16T00:11:30,457 htslib/cram/sam_header.c: In function ‘sam_hdr_vadd’: 2021-07-16T00:11:30,457 htslib/cram/sam_header.c:451:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:30,458 451 | if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new))) 2021-07-16T00:11:30,458 | ^~ 2021-07-16T00:11:30,467 htslib/cram/sam_header.c: In function ‘sam_hdr_rebuild’: 2021-07-16T00:11:30,467 htslib/cram/sam_header.c:821:31: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:30,468 821 | if (kh_key(hdr->h, k) == K("HD")) 2021-07-16T00:11:30,468 | ^~ 2021-07-16T00:11:32,727 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 2021-07-16T00:11:32,967 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 2021-07-16T00:11:33,807 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/faidx.c -o build/temp.linux-armv7l-3.9/htslib/faidx.o 2021-07-16T00:11:33,988 In file included from htslib/faidx.c:40: 2021-07-16T00:11:33,988 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:33,989 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:33,989 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:33,989 | ^ 2021-07-16T00:11:34,026 htslib/faidx.c: In function ‘fai_retrieve’: 2021-07-16T00:11:34,026 htslib/faidx.c:711:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-16T00:11:34,027 711 | while ( l < end - beg && (c=bgzf_getc(fai->bgzf))>=0 ) 2021-07-16T00:11:34,027 | ^ 2021-07-16T00:11:34,030 htslib/faidx.c: In function ‘fai_get_val’: 2021-07-16T00:11:34,031 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] 2021-07-16T00:11:34,031 789 | end = i < k? strtol(s + i, &ep, 10) : val->len; 2021-07-16T00:11:34,031 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:34,032 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] 2021-07-16T00:11:34,032 801 | if (beg >= val->len) beg = val->len; 2021-07-16T00:11:34,032 | ^~ 2021-07-16T00:11:34,032 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] 2021-07-16T00:11:34,033 802 | if (end >= val->len) end = val->len; 2021-07-16T00:11:34,033 | ^~ 2021-07-16T00:11:34,034 htslib/faidx.c: In function ‘faidx_adjust_position’: 2021-07-16T00:11:34,034 htslib/faidx.c:882:22: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:34,035 882 | else if(val->len <= *p_beg_i) 2021-07-16T00:11:34,035 | ^~ 2021-07-16T00:11:34,035 htslib/faidx.c:887:22: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:34,035 887 | else if(val->len <= *p_end_i) 2021-07-16T00:11:34,036 | ^~ 2021-07-16T00:11:35,674 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 2021-07-16T00:11:35,825 In file included from htslib/hfile.c:36: 2021-07-16T00:11:35,825 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:35,825 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:35,826 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:35,826 | ^ 2021-07-16T00:11:35,843 htslib/hfile.c: In function ‘hfile_set_blksize’: 2021-07-16T00:11:35,843 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] 2021-07-16T00:11:35,843 200 | if (bufsiz < curr_used) 2021-07-16T00:11:35,844 | ^ 2021-07-16T00:11:35,848 htslib/hfile.c: In function ‘hseek’: 2021-07-16T00:11:35,849 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] 2021-07-16T00:11:35,849 436 | if (offset > 0 || -offset > length) { 2021-07-16T00:11:35,849 | ^ 2021-07-16T00:11:36,006 htslib/hfile.c: In function ‘find_scheme_handler’: 2021-07-16T00:11:36,007 htslib/hfile.c:1004:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:36,007 1004 | for (i = 0; i < sizeof scheme; i++) 2021-07-16T00:11:36,007 | ^ 2021-07-16T00:11:36,008 htslib/hfile.c:1011:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-16T00:11:36,008 1011 | if (i <= 1 || i >= sizeof scheme) return NULL; 2021-07-16T00:11:36,009 | ^~ 2021-07-16T00:11:37,113 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 2021-07-16T00:11:37,266 In file included from htslib/hfile_internal.h:30, 2021-07-16T00:11:37,266 from htslib/hfile_gcs.c:35: 2021-07-16T00:11:37,266 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:37,266 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:37,267 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:37,267 | ^ 2021-07-16T00:11:37,633 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 2021-07-16T00:11:37,763 In file included from htslib/hfile_internal.h:30, 2021-07-16T00:11:37,764 from htslib/hfile_libcurl.c:37: 2021-07-16T00:11:37,764 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:37,764 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:37,764 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:37,765 | ^ 2021-07-16T00:11:39,857 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 2021-07-16T00:11:39,968 In file included from htslib/hfile_internal.h:30, 2021-07-16T00:11:39,969 from htslib/hfile_net.c:30: 2021-07-16T00:11:39,969 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:39,969 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:39,969 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:39,969 | ^ 2021-07-16T00:11:40,098 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 2021-07-16T00:11:40,233 In file included from htslib/hfile_internal.h:30, 2021-07-16T00:11:40,233 from htslib/hfile_s3.c:33: 2021-07-16T00:11:40,233 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:40,233 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:40,234 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:40,234 | ^ 2021-07-16T00:11:41,538 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/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 2021-07-16T00:11:41,814 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:41,815 from htslib/cram/misc.h:66, 2021-07-16T00:11:41,815 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:41,815 from htslib/cram/cram.h:48, 2021-07-16T00:11:41,815 from htslib/hts.c:41: 2021-07-16T00:11:41,815 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:41,815 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] 2021-07-16T00:11:41,816 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:41,816 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:41,816 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:41,816 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] 2021-07-16T00:11:41,816 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:41,816 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:41,821 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:41,821 from htslib/hts.c:41: 2021-07-16T00:11:41,822 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:41,822 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] 2021-07-16T00:11:41,822 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:41,822 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:41,831 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:41,831 from htslib/hts.c:41: 2021-07-16T00:11:41,831 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:41,831 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] 2021-07-16T00:11:41,831 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:41,832 | ^~ 2021-07-16T00:11:41,832 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:41,832 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:41,832 | ^ 2021-07-16T00:11:41,836 In file included from htslib/hts.c:42: 2021-07-16T00:11:41,836 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:41,837 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:41,837 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:41,837 | ^ 2021-07-16T00:11:41,909 htslib/hts.c: In function ‘hts_idx_init’: 2021-07-16T00:11:41,909 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] 2021-07-16T00:11:41,910 1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; 2021-07-16T00:11:41,910 | ^~~ 2021-07-16T00:11:41,912 htslib/hts.c: In function ‘update_loff’: 2021-07-16T00:11:41,912 htslib/hts.c:1420:34: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:41,913 1420 | if ( kh_key(bidx, k) < idx->n_bins ) 2021-07-16T00:11:41,913 | ^ 2021-07-16T00:11:41,914 htslib/hts.c: In function ‘compress_binning’: 2021-07-16T00:11:41,914 htslib/hts.c:1447:55: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:41,915 1447 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue; 2021-07-16T00:11:41,915 | ^~ 2021-07-16T00:11:41,917 htslib/hts.c:1472:51: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:41,918 1472 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue; 2021-07-16T00:11:41,918 | ^~ 2021-07-16T00:11:41,943 htslib/hts.c: In function ‘hts_idx_load_local’: 2021-07-16T00:11:41,944 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] 2021-07-16T00:11:41,944 1832 | if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail; 2021-07-16T00:11:41,945 | ^~ 2021-07-16T00:11:41,949 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] 2021-07-16T00:11:41,949 1859 | if (bgzf_read(fp, idx->meta + 28, n) != n) goto fail; 2021-07-16T00:11:41,949 | ^~ 2021-07-16T00:11:41,968 htslib/hts.c: In function ‘hts_itr_multi_bam’: 2021-07-16T00:11:41,969 htslib/hts.c:2230:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:41,969 2230 | for(j=0; jcount; j++) { 2021-07-16T00:11:41,970 | ^ 2021-07-16T00:11:41,976 htslib/hts.c: In function ‘hts_itr_multi_cram’: 2021-07-16T00:11:41,977 htslib/hts.c:2341:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:41,977 2341 | for (j=0; j < curr_reg->count; j++) { 2021-07-16T00:11:41,977 | ^ 2021-07-16T00:11:42,001 htslib/hts.c: In function ‘hts_itr_multi_next’: 2021-07-16T00:11:42,002 htslib/hts.c:2737:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-16T00:11:42,002 2737 | if (beg > iter->off[iter->i].max) { 2021-07-16T00:11:42,002 | ^ 2021-07-16T00:11:42,003 htslib/hts.c:2741:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:42,004 2741 | if (beg > iter->reg_list[cr].max_end) 2021-07-16T00:11:42,004 | ^ 2021-07-16T00:11:42,005 htslib/hts.c:2744:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:42,006 2744 | for (i = ci; i < iter->reg_list[cr].count; i++) { 2021-07-16T00:11:42,006 | ^ 2021-07-16T00:11:42,007 htslib/hts.c:2745:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:42,007 2745 | if (end > iter->reg_list[cr].intervals[i].beg && iter->reg_list[cr].intervals[i].end > beg) { 2021-07-16T00:11:42,007 | ^ 2021-07-16T00:11:42,008 htslib/hts.c:2745:98: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:42,009 2745 | if (end > iter->reg_list[cr].intervals[i].beg && iter->reg_list[cr].intervals[i].end > beg) { 2021-07-16T00:11:42,009 | ^ 2021-07-16T00:11:42,011 htslib/hts.c: In function ‘test_and_fetch’: 2021-07-16T00:11:42,013 htslib/hts.c:2798:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:42,013 2798 | if (fwrite(buf, 1, l, local_fp) != l) { 2021-07-16T00:11:42,013 | ^~ 2021-07-16T00:11:42,020 htslib/hts.c: In function ‘hts_log’: 2021-07-16T00:11:42,021 htslib/hts.c:2967:18: warning: comparison of integer expressions of different signedness: ‘enum htsLogLevel’ and ‘int’ [-Wsign-compare] 2021-07-16T00:11:42,021 2967 | if (severity <= hts_verbose) { 2021-07-16T00:11:42,022 | ^~ 2021-07-16T00:11:48,034 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 2021-07-16T00:11:48,208 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 2021-07-16T00:11:48,687 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 2021-07-16T00:11:49,597 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 2021-07-16T00:11:49,769 htslib/kstring.c: In function ‘kvsprintf’: 2021-07-16T00:11:49,770 htslib/kstring.c:156:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:49,770 156 | if (l + 1 > s->m - s->l) { 2021-07-16T00:11:49,770 | ^ 2021-07-16T00:11:50,396 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 2021-07-16T00:11:50,508 In file included from htslib/md5.c:53: 2021-07-16T00:11:50,508 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:50,509 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] 2021-07-16T00:11:50,509 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:50,509 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:50,510 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:50,510 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] 2021-07-16T00:11:50,510 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:50,510 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:51,022 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 2021-07-16T00:11:51,181 In file included from htslib/hfile_internal.h:30, 2021-07-16T00:11:51,181 from htslib/multipart.c:34: 2021-07-16T00:11:51,182 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:51,182 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:51,182 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:51,182 | ^ 2021-07-16T00:11:51,630 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 2021-07-16T00:11:51,810 htslib/probaln.c: In function ‘probaln_glocal’: 2021-07-16T00:11:51,810 htslib/probaln.c:177:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:51,810 177 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-16T00:11:51,811 | ^~ 2021-07-16T00:11:51,812 htslib/probaln.c:201:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:51,812 201 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-16T00:11:51,812 | ^~ 2021-07-16T00:11:51,815 htslib/probaln.c:239:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:51,816 239 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-16T00:11:51,816 | ^~ 2021-07-16T00:11:52,405 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 2021-07-16T00:11:52,565 htslib/realn.c: In function ‘sam_cap_mapq’: 2021-07-16T00:11:52,566 htslib/realn.c:47:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:52,566 47 | for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { 2021-07-16T00:11:52,566 | ^ 2021-07-16T00:11:52,570 htslib/realn.c: In function ‘realn_check_tag’: 2021-07-16T00:11:52,570 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] 2021-07-16T00:11:52,570 96 | if (b->core.l_qseq != strlen((const char *) tg + 1)) { 2021-07-16T00:11:52,571 | ^~ 2021-07-16T00:11:52,574 htslib/realn.c: In function ‘sam_prob_realn’: 2021-07-16T00:11:52,574 htslib/realn.c:158:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:52,575 158 | for (k = 0; k < c->n_cigar; ++k) { 2021-07-16T00:11:52,575 | ^ 2021-07-16T00:11:52,577 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] 2021-07-16T00:11:52,577 188 | if (extend_baq && lref < c->l_qseq) 2021-07-16T00:11:52,577 | ^ 2021-07-16T00:11:52,579 htslib/realn.c:221:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:52,579 221 | for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { 2021-07-16T00:11:52,579 | ^ 2021-07-16T00:11:52,580 htslib/realn.c:247:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:52,580 247 | for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { 2021-07-16T00:11:52,581 | ^ 2021-07-16T00:11:53,255 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/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 2021-07-16T00:11:53,428 htslib/regidx.c: In function ‘regidx_insert’: 2021-07-16T00:11:53,428 htslib/regidx.c:156:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:53,428 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-16T00:11:53,429 | ^ 2021-07-16T00:11:53,429 htslib/regidx.c:156:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:53,429 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-16T00:11:53,429 | ^~ 2021-07-16T00:11:53,430 htslib/regidx.c:156:89: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:53,430 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-16T00:11:53,430 | ^ 2021-07-16T00:11:54,252 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 2021-07-16T00:11:54,514 In file included from htslib/cram/os.h:80, 2021-07-16T00:11:54,514 from htslib/cram/misc.h:66, 2021-07-16T00:11:54,514 from htslib/cram/cram_io.h:46, 2021-07-16T00:11:54,514 from htslib/cram/cram.h:48, 2021-07-16T00:11:54,514 from htslib/sam.c:37: 2021-07-16T00:11:54,514 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:11:54,515 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] 2021-07-16T00:11:54,515 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:11:54,515 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:54,516 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:11:54,516 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] 2021-07-16T00:11:54,517 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:11:54,517 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:54,523 In file included from htslib/cram/cram.h:48, 2021-07-16T00:11:54,523 from htslib/sam.c:37: 2021-07-16T00:11:54,523 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-16T00:11:54,524 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] 2021-07-16T00:11:54,525 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-16T00:11:54,525 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:11:54,534 In file included from htslib/cram/cram.h:52, 2021-07-16T00:11:54,534 from htslib/sam.c:37: 2021-07-16T00:11:54,534 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-16T00:11:54,535 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] 2021-07-16T00:11:54,535 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-16T00:11:54,535 | ^~ 2021-07-16T00:11:54,536 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:54,536 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-16T00:11:54,536 | ^ 2021-07-16T00:11:54,549 In file included from htslib/sam.c:39: 2021-07-16T00:11:54,549 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:11:54,549 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,550 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:11:54,550 | ^ 2021-07-16T00:11:54,556 htslib/sam.c: In function ‘bam_hdr_read’: 2021-07-16T00:11:54,557 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] 2021-07-16T00:11:54,557 155 | if (bytes != h->l_text) goto read_err; 2021-07-16T00:11:54,557 | ^~ 2021-07-16T00:11:54,562 htslib/sam.c: In function ‘possibly_expand_bam_data’: 2021-07-16T00:11:54,562 htslib/sam.c:323:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:54,562 323 | if (new_len > INT32_MAX || new_len < b->l_data) { 2021-07-16T00:11:54,563 | ^ 2021-07-16T00:11:54,565 htslib/sam.c: In function ‘bam_tag2cigar’: 2021-07-16T00:11:54,566 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] 2021-07-16T00:11:54,566 408 | if (bam_cigar_op(cigar0[0]) != BAM_CSOFT_CLIP || bam_cigar_oplen(cigar0[0]) != c->l_qseq) return 0; 2021-07-16T00:11:54,566 | ^~ 2021-07-16T00:11:54,574 htslib/sam.c: In function ‘bam_write1’: 2021-07-16T00:11:54,575 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] 2021-07-16T00:11:54,575 564 | return ok? 4 + block_len : -1; 2021-07-16T00:11:54,575 | ^~ 2021-07-16T00:11:54,596 htslib/sam.c: In function ‘sam_hdr_write’: 2021-07-16T00:11:54,596 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] 2021-07-16T00:11:54,597 1108 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-16T00:11:54,597 | ^~ 2021-07-16T00:11:54,598 htslib/sam.c: In function ‘sam_hdr_change_HD’: 2021-07-16T00:11:54,599 htslib/sam.c:1143:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:54,599 1143 | && strlen(val) == end - beg - 4) 2021-07-16T00:11:54,599 | ^~ 2021-07-16T00:11:54,606 htslib/sam.c: In function ‘sam_parse1’: 2021-07-16T00:11:54,607 htslib/sam.c:1262:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,607 1262 | for (i = 0; i < c->n_cigar; ++i, ++q) { 2021-07-16T00:11:54,607 | ^ 2021-07-16T00:11:54,615 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] 2021-07-16T00:11:54,616 1392 | _parse_err(bytes / size != n 2021-07-16T00:11:54,616 | ^~ 2021-07-16T00:11:54,616 htslib/sam.c:1202:40: note: in definition of macro ‘_parse_err’ 2021-07-16T00:11:54,616 1202 | #define _parse_err(cond, msg) do { if (cond) { hts_log_error(msg); goto err_ret; } } while (0) 2021-07-16T00:11:54,617 | ^~~~ 2021-07-16T00:11:54,620 htslib/sam.c: In function ‘sam_format1’: 2021-07-16T00:11:54,621 htslib/sam.c:1495:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,621 1495 | for (i = 0; i < c->n_cigar; ++i) { 2021-07-16T00:11:54,622 | ^ 2021-07-16T00:11:54,627 htslib/sam.c:1586:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,627 1586 | if ((end - s) / sub_type_size < n) 2021-07-16T00:11:54,627 | ^ 2021-07-16T00:11:54,628 htslib/sam.c:1589:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,628 1589 | for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if" 2021-07-16T00:11:54,629 | ^ 2021-07-16T00:11:54,630 htslib/sam.c: In function ‘sam_write1’: 2021-07-16T00:11:54,631 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] 2021-07-16T00:11:54,631 1633 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-16T00:11:54,631 | ^~ 2021-07-16T00:11:54,631 htslib/sam.c: In function ‘bam_aux_append’: 2021-07-16T00:11:54,632 htslib/sam.c:1695:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:11:54,632 1695 | if (new_len > INT32_MAX || new_len < b->l_data) goto nomem; 2021-07-16T00:11:54,633 | ^ 2021-07-16T00:11:54,635 htslib/sam.c: In function ‘skip_aux’: 2021-07-16T00:11:54,636 htslib/sam.c:1737:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,636 1737 | if (size == 0 || end - s < size * n) return NULL; 2021-07-16T00:11:54,636 | ^ 2021-07-16T00:11:54,673 htslib/sam.c: In function ‘resolve_cigar2’: 2021-07-16T00:11:54,674 htslib/sam.c:2287:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,674 2287 | for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) { 2021-07-16T00:11:54,674 | ^ 2021-07-16T00:11:54,677 htslib/sam.c:2309:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,678 2309 | for (k = s->k + 1; k < c->n_cigar; ++k) { 2021-07-16T00:11:54,678 | ^ 2021-07-16T00:11:54,679 htslib/sam.c:2323:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,679 2323 | if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation 2021-07-16T00:11:54,680 | ^ 2021-07-16T00:11:54,681 htslib/sam.c:2328:50: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,681 2328 | else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding 2021-07-16T00:11:54,681 | ^ 2021-07-16T00:11:54,682 htslib/sam.c:2330:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:11:54,682 2330 | for (k = s->k + 2; k < c->n_cigar; ++k) { 2021-07-16T00:11:54,682 | ^ 2021-07-16T00:12:01,871 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 2021-07-16T00:12:02,066 In file included from htslib/htslib/vcf.h:42, 2021-07-16T00:12:02,066 from htslib/htslib/synced_bcf_reader.h:60, 2021-07-16T00:12:02,066 from htslib/synced_bcf_reader.c:34: 2021-07-16T00:12:02,067 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:12:02,068 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] 2021-07-16T00:12:02,068 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:12:02,068 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:02,069 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:12:02,070 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] 2021-07-16T00:12:02,070 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:12:02,070 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:02,133 htslib/synced_bcf_reader.c: In function ‘_regions_add’: 2021-07-16T00:12:02,134 htslib/synced_bcf_reader.c:801:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:02,134 801 | if ( start < creg->regs[i].start ) max = i - 1; 2021-07-16T00:12:02,135 | ^ 2021-07-16T00:12:02,135 htslib/synced_bcf_reader.c:802:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:02,136 802 | else if ( start > creg->regs[i].start ) min = i + 1; 2021-07-16T00:12:02,136 | ^ 2021-07-16T00:12:02,137 htslib/synced_bcf_reader.c:805:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:12:02,137 805 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-16T00:12:02,138 | ^~ 2021-07-16T00:12:02,138 htslib/synced_bcf_reader.c:805:68: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:12:02,139 805 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-16T00:12:02,139 | ^~ 2021-07-16T00:12:04,177 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 2021-07-16T00:12:04,356 In file included from htslib/tbx.c:35: 2021-07-16T00:12:04,356 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:12:04,356 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] 2021-07-16T00:12:04,356 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:12:04,357 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:04,357 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:12:04,357 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] 2021-07-16T00:12:04,357 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:12:04,357 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:04,380 htslib/tbx.c: In function ‘tbx_index_load2’: 2021-07-16T00:12:04,380 htslib/tbx.c:321:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:04,381 321 | for (; p - nm < l_nm; p += strlen(p) + 1) { 2021-07-16T00:12:04,381 | ^ 2021-07-16T00:12:04,937 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 2021-07-16T00:12:05,047 In file included from htslib/textutils.c:30: 2021-07-16T00:12:05,047 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:12:05,048 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:05,048 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:12:05,048 | ^ 2021-07-16T00:12:05,781 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 2021-07-16T00:12:06,615 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/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 2021-07-16T00:12:06,776 In file included from htslib/htslib/vcf.h:42, 2021-07-16T00:12:06,776 from htslib/vcf.c:38: 2021-07-16T00:12:06,777 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:12:06,777 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] 2021-07-16T00:12:06,777 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:12:06,777 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:06,778 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:12:06,778 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] 2021-07-16T00:12:06,778 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:12:06,778 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:06,819 In file included from htslib/vcf.c:41: 2021-07-16T00:12:06,820 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-16T00:12:06,820 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:06,820 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-16T00:12:06,820 | ^ 2021-07-16T00:12:06,849 htslib/vcf.c: In function ‘bcf_hdr_sync’: 2021-07-16T00:12:06,849 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] 2021-07-16T00:12:06,850 149 | if ( h->n[i] < kh_size(d) ) 2021-07-16T00:12:06,850 | ^ 2021-07-16T00:12:06,862 htslib/vcf.c: In function ‘bcf_hdr_register_hrec’: 2021-07-16T00:12:06,862 htslib/vcf.c:499:18: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:12:06,862 499 | if (type == -1) { 2021-07-16T00:12:06,862 | ^~ 2021-07-16T00:12:06,863 htslib/vcf.c:504:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:12:06,863 504 | if (var == -1) { 2021-07-16T00:12:06,863 | ^~ 2021-07-16T00:12:06,877 htslib/vcf.c: In function ‘bcf_hdr_read’: 2021-07-16T00:12:06,877 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] 2021-07-16T00:12:06,877 917 | if (bgzf_read(fp, htxt, hlen) != hlen) goto fail; 2021-07-16T00:12:06,877 | ^~ 2021-07-16T00:12:06,879 htslib/vcf.c: In function ‘bcf_hdr_write’: 2021-07-16T00:12:06,880 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] 2021-07-16T00:12:06,880 948 | if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1; 2021-07-16T00:12:06,880 | ^~ 2021-07-16T00:12:06,883 htslib/vcf.c: In function ‘bcf_read1_core’: 2021-07-16T00:12:06,884 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] 2021-07-16T00:12:06,884 1033 | if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -2; 2021-07-16T00:12:06,884 | ^~ 2021-07-16T00:12:06,884 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] 2021-07-16T00:12:06,885 1034 | if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -2; 2021-07-16T00:12:06,885 | ^~ 2021-07-16T00:12:06,886 htslib/vcf.c: In function ‘bcf_dec_typed_int1_safe’: 2021-07-16T00:12:06,886 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] 2021-07-16T00:12:06,887 1058 | *val = v < 0x8000 ? v : -((int32_t) (0xffff - v)) - 1; 2021-07-16T00:12:06,887 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:06,888 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] 2021-07-16T00:12:06,888 1063 | *val = v < 0x80000000UL ? v : -((int32_t) (0xffffffffUL - v)) - 1; 2021-07-16T00:12:06,888 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:06,890 htslib/vcf.c: In function ‘bcf_record_check’: 2021-07-16T00:12:06,891 htslib/vcf.c:1125:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:06,891 1125 | if (end - ptr < bytes) goto bad_shared; 2021-07-16T00:12:06,891 | ^ 2021-07-16T00:12:06,892 htslib/vcf.c:1138:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:06,892 1138 | if (end - ptr < bytes) goto bad_shared; 2021-07-16T00:12:06,893 | ^ 2021-07-16T00:12:06,894 htslib/vcf.c:1151:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:06,894 1151 | if (end - ptr < bytes) goto bad_shared; 2021-07-16T00:12:06,894 | ^ 2021-07-16T00:12:06,894 htslib/vcf.c:1152:23: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-16T00:12:06,895 1152 | for (i = 0; i < num; i++) { 2021-07-16T00:12:06,895 | ^ 2021-07-16T00:12:06,897 htslib/vcf.c:1179:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:06,897 1179 | if (end - ptr < bytes) goto bad_shared; 2021-07-16T00:12:06,897 | ^ 2021-07-16T00:12:06,899 htslib/vcf.c:1202:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:06,899 1202 | if (end - ptr < bytes) goto bad_indiv; 2021-07-16T00:12:06,899 | ^ 2021-07-16T00:12:06,912 htslib/vcf.c: In function ‘bcf_write’: 2021-07-16T00:12:06,913 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] 2021-07-16T00:12:06,913 1533 | if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1; 2021-07-16T00:12:06,914 | ^~ 2021-07-16T00:12:06,914 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] 2021-07-16T00:12:06,915 1534 | if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1; 2021-07-16T00:12:06,915 | ^~ 2021-07-16T00:12:06,934 htslib/vcf.c: In function ‘vcf_parse_format’: 2021-07-16T00:12:06,935 htslib/vcf.c:1970:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T00:12:06,936 1970 | if (fmt[j].max_l < l) fmt[j].max_l = l; 2021-07-16T00:12:06,936 | ^ 2021-07-16T00:12:06,940 htslib/vcf.c:2000:33: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2021-07-16T00:12:06,941 2000 | f->size = f->is_gt? f->max_g << 2 : f->max_l; 2021-07-16T00:12:06,941 | ^~~~~~~~~~~~~ 2021-07-16T00:12:06,984 htslib/vcf.c: In function ‘vcf_write_line’: 2021-07-16T00:12:06,986 htslib/vcf.c:2611:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:06,986 2611 | return ret==line->l ? 0 : -1; 2021-07-16T00:12:06,986 | ^~ 2021-07-16T00:12:06,987 htslib/vcf.c: In function ‘vcf_write’: 2021-07-16T00:12:06,989 htslib/vcf.c:2624:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:06,989 2624 | return ret==fp->line.l ? 0 : -1; 2021-07-16T00:12:06,989 | ^~ 2021-07-16T00:12:07,025 htslib/vcf.c: In function ‘bcf_hdr_set_samples’: 2021-07-16T00:12:07,027 htslib/vcf.c:3136:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-16T00:12:07,027 3136 | for (k = kh_begin(d); k != kh_end(d); ++k) 2021-07-16T00:12:07,027 | ^~ 2021-07-16T00:12:07,078 htslib/vcf.c: In function ‘_bcf1_sync_alleles’: 2021-07-16T00:12:07,080 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] 2021-07-16T00:12:07,080 3586 | line->rlen = end_info ? end_info->v1.i - line->pos : strlen(line->d.allele[0]); 2021-07-16T00:12:07,080 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:07,092 htslib/vcf.c: In function ‘bcf_get_info_values’: 2021-07-16T00:12:07,094 htslib/vcf.c:3716:49: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T00:12:07,094 3716 | if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2; // expected different type 2021-07-16T00:12:07,095 | ^~ 2021-07-16T00:12:07,111 htslib/vcf.c: In function ‘bcf_get_format_values’: 2021-07-16T00:12:07,112 htslib/vcf.c:3819:53: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-16T00:12:07,113 3819 | else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2; // expected different type 2021-07-16T00:12:07,113 | ^~ 2021-07-16T00:12:17,067 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 2021-07-16T00:12:17,245 In file included from htslib/htslib/vcf.h:42, 2021-07-16T00:12:17,245 from htslib/htslib/vcf_sweep.h:30, 2021-07-16T00:12:17,245 from htslib/vcf_sweep.c:27: 2021-07-16T00:12:17,246 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:12:17,246 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] 2021-07-16T00:12:17,246 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:12:17,246 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:17,247 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:12:17,247 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] 2021-07-16T00:12:17,247 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:12:17,247 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:17,299 htslib/vcf_sweep.c: In function ‘bcf_sweep_fwd’: 2021-07-16T00:12:17,299 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] 2021-07-16T00:12:17,300 164 | if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size ) 2021-07-16T00:12:17,300 | ^ 2021-07-16T00:12:17,555 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 2021-07-16T00:12:17,707 In file included from htslib/htslib/vcf.h:42, 2021-07-16T00:12:17,707 from htslib/htslib/vcfutils.h:29, 2021-07-16T00:12:17,707 from htslib/vcfutils.c:27: 2021-07-16T00:12:17,708 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-16T00:12:17,708 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] 2021-07-16T00:12:17,708 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-16T00:12:17,708 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:17,709 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-16T00:12:17,709 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] 2021-07-16T00:12:17,709 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-16T00:12:17,709 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-16T00:12:20,348 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 2021-07-16T00:12:21,169 installing to build/bdist.linux-armv7l/wheel 2021-07-16T00:12:21,169 running install 2021-07-16T00:12:21,171 running install_lib 2021-07-16T00:12:21,177 creating build/bdist.linux-armv7l 2021-07-16T00:12:21,177 creating build/bdist.linux-armv7l/wheel 2021-07-16T00:12:21,180 creating build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,181 copying build/lib.linux-armv7l-3.9/cyvcf2/cli.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,184 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,187 copying build/lib.linux-armv7l-3.9/cyvcf2/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,189 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,195 creating build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,196 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,199 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,201 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.bug.117.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,203 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,206 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/seg.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,208 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,210 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,240 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/issue_44.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,241 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,246 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,248 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,250 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,253 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,255 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,258 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,268 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,271 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,273 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,275 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/empty.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,276 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,278 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,281 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/decomposed.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,283 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,285 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_alt_freqs.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,289 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/no-seq-len.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,291 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,295 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-alt-repr.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,297 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-diff.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,299 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/no-seq-names.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,302 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-16T00:12:21,305 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,308 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,310 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,382 copying build/lib.linux-armv7l-3.9/cyvcf2/relatedness.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,385 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,520 copying build/lib.linux-armv7l-3.9/cyvcf2/__main__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-16T00:12:21,522 running install_egg_info 2021-07-16T00:12:21,528 Copying cyvcf2.egg-info to build/bdist.linux-armv7l/wheel/cyvcf2-0.11.7-py3.9.egg-info 2021-07-16T00:12:21,546 running install_scripts 2021-07-16T00:12:21,640 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-16T00:12:21,646 creating build/bdist.linux-armv7l/wheel/cyvcf2-0.11.7.dist-info/WHEEL 2021-07-16T00:12:21,649 creating '/tmp/pip-wheel-d0sfns_d/cyvcf2-0.11.7-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-16T00:12:21,652 adding 'cyvcf2/__init__.py' 2021-07-16T00:12:21,654 adding 'cyvcf2/__main__.py' 2021-07-16T00:12:21,656 adding 'cyvcf2/cli.py' 2021-07-16T00:12:21,875 adding 'cyvcf2/cyvcf2.c' 2021-07-16T00:12:23,370 adding 'cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so' 2021-07-16T00:12:23,427 adding 'cyvcf2/cyvcf2.pxd' 2021-07-16T00:12:23,436 adding 'cyvcf2/cyvcf2.pyx' 2021-07-16T00:12:23,439 adding 'cyvcf2/helpers.c' 2021-07-16T00:12:23,440 adding 'cyvcf2/helpers.h' 2021-07-16T00:12:23,442 adding 'cyvcf2/relatedness.h' 2021-07-16T00:12:23,445 adding 'cyvcf2/tests/__init__.py' 2021-07-16T00:12:23,447 adding 'cyvcf2/tests/bug.vcf.gz' 2021-07-16T00:12:23,448 adding 'cyvcf2/tests/decomposed.vcf' 2021-07-16T00:12:23,450 adding 'cyvcf2/tests/empty.vcf' 2021-07-16T00:12:23,451 adding 'cyvcf2/tests/issue_44.vcf' 2021-07-16T00:12:23,453 adding 'cyvcf2/tests/no-seq-len.vcf' 2021-07-16T00:12:23,454 adding 'cyvcf2/tests/no-seq-names.vcf' 2021-07-16T00:12:23,460 adding 'cyvcf2/tests/o.vcf.gz' 2021-07-16T00:12:23,462 adding 'cyvcf2/tests/seg.vcf.gz' 2021-07-16T00:12:23,464 adding 'cyvcf2/tests/test-alt-repr.vcf' 2021-07-16T00:12:23,465 adding 'cyvcf2/tests/test-diff.csi' 2021-07-16T00:12:23,467 adding 'cyvcf2/tests/test-format-string.vcf' 2021-07-16T00:12:23,511 adding 'cyvcf2/tests/test-haploidX.vcf' 2021-07-16T00:12:23,518 adding 'cyvcf2/tests/test-hemi.vcf' 2021-07-16T00:12:23,520 adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz' 2021-07-16T00:12:23,521 adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi' 2021-07-16T00:12:23,523 adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz' 2021-07-16T00:12:23,524 adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi' 2021-07-16T00:12:23,526 adding 'cyvcf2/tests/test.bug.117.vcf' 2021-07-16T00:12:23,528 adding 'cyvcf2/tests/test.comp_het.3.vcf' 2021-07-16T00:12:23,530 adding 'cyvcf2/tests/test.snpeff.bcf' 2021-07-16T00:12:23,532 adding 'cyvcf2/tests/test.snpeff.bcf.csi' 2021-07-16T00:12:23,534 adding 'cyvcf2/tests/test.snpeff.vcf' 2021-07-16T00:12:23,556 adding 'cyvcf2/tests/test.vcf.gz' 2021-07-16T00:12:23,559 adding 'cyvcf2/tests/test.vcf.gz.tbi' 2021-07-16T00:12:23,560 adding 'cyvcf2/tests/test_cli.py' 2021-07-16T00:12:23,563 adding 'cyvcf2/tests/test_gt_alt_freqs.vcf' 2021-07-16T00:12:23,565 adding 'cyvcf2/tests/test_gt_bases.vcf.gz' 2021-07-16T00:12:23,567 adding 'cyvcf2/tests/test_hemi.py' 2021-07-16T00:12:23,571 adding 'cyvcf2/tests/test_reader.py' 2021-07-16T00:12:23,574 adding 'cyvcf2-0.11.7.dist-info/LICENSE' 2021-07-16T00:12:23,575 adding 'cyvcf2-0.11.7.dist-info/METADATA' 2021-07-16T00:12:23,577 adding 'cyvcf2-0.11.7.dist-info/WHEEL' 2021-07-16T00:12:23,578 adding 'cyvcf2-0.11.7.dist-info/entry_points.txt' 2021-07-16T00:12:23,579 adding 'cyvcf2-0.11.7.dist-info/top_level.txt' 2021-07-16T00:12:23,581 adding 'cyvcf2-0.11.7.dist-info/RECORD' 2021-07-16T00:12:23,640 removing build/bdist.linux-armv7l/wheel 2021-07-16T00:12:23,830 Building wheel for cyvcf2 (setup.py): finished with status 'done' 2021-07-16T00:12:23,876 Created wheel for cyvcf2: filename=cyvcf2-0.11.7-cp39-cp39-linux_armv7l.whl size=3367308 sha256=78d19de313d5cb28845ab60a58cd04bca7256c5bd7b313d62da7d860c1d9c5b7 2021-07-16T00:12:23,877 Stored in directory: /tmp/pip-ephem-wheel-cache-vgjj51u8/wheels/ce/69/5a/9553f3eea4121aea3ef43ae58d62bdd5269db41e2f40365b91 2021-07-16T00:12:23,889 Successfully built cyvcf2 2021-07-16T00:12:24,010 Removed build tracker: '/tmp/pip-req-tracker-4fpx_y2r'