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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/) 2021-07-15T17:14:23,486 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 2021-07-15T17:14:23,486 Skipping link: not a file: https://pypi.org/simple/cyvcf2/ 2021-07-15T17:14:23,504 Given no hashes to check 1 links for project 'cyvcf2': discarding no candidates 2021-07-15T17:14:23,538 Collecting cyvcf2==0.11.6 2021-07-15T17:14:23,541 Created temporary directory: /tmp/pip-unpack-ndln_cdz 2021-07-15T17:14:24,349 Downloading cyvcf2-0.11.6.tar.gz (1.1 MB) 2021-07-15T17:14:25,742 Added cyvcf2==0.11.6 from https://files.pythonhosted.org/packages/9a/21/e35e64f3a19ca916caae59e368da8b3c2d939c0a18c98fd7a701d86fa93a/cyvcf2-0.11.6.tar.gz#sha256=59de422bf54f8439cdd039230bf40ebed3d1284727f88e1a71e1baba0ff56d48 to build tracker '/tmp/pip-req-tracker-fkijbdg_' 2021-07-15T17:14:25,743 Running setup.py (path:/tmp/pip-wheel-469fczxb/cyvcf2_9dd8788865af4848b2060a87f69315a1/setup.py) egg_info for package cyvcf2 2021-07-15T17:14:25,744 Created temporary directory: /tmp/pip-pip-egg-info-c19s82a4 2021-07-15T17:14:25,745 Running command python setup.py egg_info 2021-07-15T17:14:32,450 Collecting coloredlogs 2021-07-15T17:14:32,496 Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB) 2021-07-15T17:14:32,955 Collecting humanfriendly>=9.1 2021-07-15T17:14:32,969 Using cached humanfriendly-9.2-py2.py3-none-any.whl (86 kB) 2021-07-15T17:14:34,516 WARNING: Error parsing requirements for six: [Errno 2] No such file or directory: '/home/piwheels/.local/lib/python3.9/site-packages/six-1.16.0.dist-info/METADATA' 2021-07-15T17:14:38,943 Installing collected packages: humanfriendly, coloredlogs 2021-07-15T17:14:39,492 Successfully installed coloredlogs-15.0.1 humanfriendly-9.2 2021-07-15T17:14:41,217 running egg_info 2021-07-15T17:14:41,220 creating /tmp/pip-pip-egg-info-c19s82a4/cyvcf2.egg-info 2021-07-15T17:14:41,222 writing /tmp/pip-pip-egg-info-c19s82a4/cyvcf2.egg-info/PKG-INFO 2021-07-15T17:14:41,226 writing dependency_links to /tmp/pip-pip-egg-info-c19s82a4/cyvcf2.egg-info/dependency_links.txt 2021-07-15T17:14:41,228 writing entry points to /tmp/pip-pip-egg-info-c19s82a4/cyvcf2.egg-info/entry_points.txt 2021-07-15T17:14:41,230 writing requirements to /tmp/pip-pip-egg-info-c19s82a4/cyvcf2.egg-info/requires.txt 2021-07-15T17:14:41,231 writing top-level names to /tmp/pip-pip-egg-info-c19s82a4/cyvcf2.egg-info/top_level.txt 2021-07-15T17:14:41,234 writing manifest file '/tmp/pip-pip-egg-info-c19s82a4/cyvcf2.egg-info/SOURCES.txt' 2021-07-15T17:14:41,423 reading manifest file '/tmp/pip-pip-egg-info-c19s82a4/cyvcf2.egg-info/SOURCES.txt' 2021-07-15T17:14:41,425 reading manifest template 'MANIFEST.in' 2021-07-15T17:14:41,441 adding license file 'LICENSE' 2021-07-15T17:14:41,450 writing manifest file '/tmp/pip-pip-egg-info-c19s82a4/cyvcf2.egg-info/SOURCES.txt' 2021-07-15T17:14:41,621 Source in /tmp/pip-wheel-469fczxb/cyvcf2_9dd8788865af4848b2060a87f69315a1 has version 0.11.6, which satisfies requirement cyvcf2==0.11.6 from https://files.pythonhosted.org/packages/9a/21/e35e64f3a19ca916caae59e368da8b3c2d939c0a18c98fd7a701d86fa93a/cyvcf2-0.11.6.tar.gz#sha256=59de422bf54f8439cdd039230bf40ebed3d1284727f88e1a71e1baba0ff56d48 2021-07-15T17:14:41,623 Removed cyvcf2==0.11.6 from https://files.pythonhosted.org/packages/9a/21/e35e64f3a19ca916caae59e368da8b3c2d939c0a18c98fd7a701d86fa93a/cyvcf2-0.11.6.tar.gz#sha256=59de422bf54f8439cdd039230bf40ebed3d1284727f88e1a71e1baba0ff56d48 from build tracker '/tmp/pip-req-tracker-fkijbdg_' 2021-07-15T17:14:41,640 Created temporary directory: /tmp/pip-unpack-a0e6bpao 2021-07-15T17:14:41,641 Building wheels for collected packages: cyvcf2 2021-07-15T17:14:41,647 Created temporary directory: /tmp/pip-wheel-6g18e6kc 2021-07-15T17:14:41,648 Building wheel for cyvcf2 (setup.py): started 2021-07-15T17:14:41,648 Destination directory: /tmp/pip-wheel-6g18e6kc 2021-07-15T17:14:41,649 Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-469fczxb/cyvcf2_9dd8788865af4848b2060a87f69315a1/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-469fczxb/cyvcf2_9dd8788865af4848b2060a87f69315a1/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-6g18e6kc 2021-07-15T17:14:44,847 running bdist_wheel 2021-07-15T17:14:44,877 running build 2021-07-15T17:14:44,877 running build_py 2021-07-15T17:14:45,146 creating build 2021-07-15T17:14:45,147 creating build/lib.linux-armv7l-3.9 2021-07-15T17:14:45,148 creating build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,150 copying cyvcf2/cli.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,155 copying cyvcf2/__main__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,158 copying cyvcf2/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,163 creating build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,165 copying cyvcf2/tests/test_cli.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,169 copying cyvcf2/tests/test_hemi.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,172 copying cyvcf2/tests/test_reader.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,177 copying cyvcf2/tests/__init__.py -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,179 running egg_info 2021-07-15T17:14:45,226 writing cyvcf2.egg-info/PKG-INFO 2021-07-15T17:14:45,230 writing dependency_links to cyvcf2.egg-info/dependency_links.txt 2021-07-15T17:14:45,233 writing entry points to cyvcf2.egg-info/entry_points.txt 2021-07-15T17:14:45,234 writing requirements to cyvcf2.egg-info/requires.txt 2021-07-15T17:14:45,236 writing top-level names to cyvcf2.egg-info/top_level.txt 2021-07-15T17:14:45,246 reading manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-15T17:14:45,252 reading manifest template 'MANIFEST.in' 2021-07-15T17:14:45,269 adding license file 'LICENSE' 2021-07-15T17:14:45,279 writing manifest file 'cyvcf2.egg-info/SOURCES.txt' 2021-07-15T17:14:45,287 copying cyvcf2/cyvcf2.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,360 copying cyvcf2/cyvcf2.pxd -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,364 copying cyvcf2/cyvcf2.pyx -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,370 copying cyvcf2/helpers.c -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,374 copying cyvcf2/helpers.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,377 copying cyvcf2/relatedness.h -> build/lib.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,380 copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,384 copying cyvcf2/tests/decomposed.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,387 copying cyvcf2/tests/empty.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,390 copying cyvcf2/tests/issue_44.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,394 copying cyvcf2/tests/no-seq-len.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,397 copying cyvcf2/tests/no-seq-names.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,400 copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,406 copying cyvcf2/tests/seg.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,409 copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,413 copying cyvcf2/tests/test-diff.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,416 copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,420 copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,438 copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,442 copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,446 copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,452 copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,455 copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,459 copying cyvcf2/tests/test.bug.117.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,462 copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,467 copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,471 copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,474 copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,479 copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,487 copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,491 copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,495 copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-armv7l-3.9/cyvcf2/tests 2021-07-15T17:14:45,502 running build_ext 2021-07-15T17:14:45,675 skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date) 2021-07-15T17:14:45,686 building 'cyvcf2.cyvcf2' extension 2021-07-15T17:14:45,688 creating build/temp.linux-armv7l-3.9 2021-07-15T17:14:45,688 creating build/temp.linux-armv7l-3.9/cyvcf2 2021-07-15T17:14:45,690 creating build/temp.linux-armv7l-3.9/htslib 2021-07-15T17:14:45,691 creating build/temp.linux-armv7l-3.9/htslib/cram 2021-07-15T17:14:45,694 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 2021-07-15T17:14:46,576 In file included from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1969, 2021-07-15T17:14:46,576 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2021-07-15T17:14:46,576 from /home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2021-07-15T17:14:46,577 from cyvcf2/cyvcf2.c:599: 2021-07-15T17:14:46,577 /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] 2021-07-15T17:14:46,577 17 | #warning "Using deprecated NumPy API, disable it with " \ 2021-07-15T17:14:46,578 | ^~~~~~~ 2021-07-15T17:14:46,663 In file included from htslib/htslib/vcf.h:42, 2021-07-15T17:14:46,664 from cyvcf2/helpers.h:1, 2021-07-15T17:14:46,664 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:46,665 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:14:46,665 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] 2021-07-15T17:14:46,666 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:14:46,666 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:46,666 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:14:46,667 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] 2021-07-15T17:14:46,667 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:14:46,667 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:46,705 In file included from cyvcf2/cyvcf2.c:604: 2021-07-15T17:14:46,705 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:14:46,706 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:14:46,707 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:14:46,707 | ^ 2021-07-15T17:14:46,987 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’: 2021-07-15T17:14:46,992 cyvcf2/cyvcf2.c:7934:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:46,992 7934 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2); 2021-07-15T17:14:46,992 | ~~~~~~~~~~~~^~~~~ 2021-07-15T17:14:46,993 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:46,993 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:46,994 htslib/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:46,994 443 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-15T17:14:46,994 | ~~~~~~~~~~~^ 2021-07-15T17:14:46,999 cyvcf2/cyvcf2.c:7976:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:47,000 7976 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-15T17:14:47,000 | ~~~~~~~~~~~~^~~~~ 2021-07-15T17:14:47,015 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:47,016 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:47,016 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:47,017 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-15T17:14:47,017 | ~~~~~~~~~~~^ 2021-07-15T17:14:47,030 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’: 2021-07-15T17:14:47,035 cyvcf2/cyvcf2.c:8492:49: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:47,035 8492 | __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0); 2021-07-15T17:14:47,036 | ~~~~~~~~~~~~^~~~~ 2021-07-15T17:14:47,055 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:47,056 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:47,056 htslib/htslib/vcf.h:315:40: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:47,057 315 | int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file); 2021-07-15T17:14:47,057 | ~~~~~~~~~~~^~~ 2021-07-15T17:14:47,069 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’: 2021-07-15T17:14:47,074 cyvcf2/cyvcf2.c:8790:44: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:47,075 8790 | __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4); 2021-07-15T17:14:47,075 | ~~~~~~~~~~~~^~~~~ 2021-07-15T17:14:47,085 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:47,086 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:47,086 htslib/htslib/vcf.h:443:35: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:47,086 443 | int bcf_hdr_append(bcf_hdr_t *h, const char *line); 2021-07-15T17:14:47,087 | ~~~~~~~~~~~^ 2021-07-15T17:14:47,093 cyvcf2/cyvcf2.c:8843:42: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:47,093 8843 | __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr); 2021-07-15T17:14:47,094 | ~~~~~~~~~~~~^~~~~ 2021-07-15T17:14:47,094 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:47,095 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:47,095 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:47,095 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-15T17:14:47,096 | ~~~~~~~~~~~^ 2021-07-15T17:14:47,117 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_20generator’: 2021-07-15T17:14:47,120 cyvcf2/cyvcf2.c:9263:115: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:47,120 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); 2021-07-15T17:14:47,121 htslib/htslib/vcf.h:796:103: note: in definition of macro ‘bcf_itr_querys’ 2021-07-15T17:14:47,121 796 | #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec) 2021-07-15T17:14:47,121 | ^~~ 2021-07-15T17:14:47,122 In file included from htslib/htslib/vcf.h:39, 2021-07-15T17:14:47,122 from cyvcf2/helpers.h:1, 2021-07-15T17:14:47,123 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:47,123 htslib/htslib/hts.h:675:97: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:47,124 675 | 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); 2021-07-15T17:14:47,124 | ~~~~~~^~~ 2021-07-15T17:14:47,154 cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_26generator2’: 2021-07-15T17:14:47,160 cyvcf2/cyvcf2.c:10548:163: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:47,160 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) 2021-07-15T17:14:47,161 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2021-07-15T17:14:47,163 cyvcf2/cyvcf2.c:2913:107: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:47,163 2913 | static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/ 2021-07-15T17:14:47,163 | ^~~~~~~~~~~ 2021-07-15T17:14:47,256 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_37__dealloc__’: 2021-07-15T17:14:47,263 cyvcf2/cyvcf2.c:12204:33: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:47,263 12204 | bcf_hdr_destroy(__pyx_v_self->hdr); 2021-07-15T17:14:47,263 | ~~~~~~~~~~~~^~~~~ 2021-07-15T17:14:47,264 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:47,265 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:47,265 htslib/htslib/vcf.h:261:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:47,265 261 | void bcf_hdr_destroy(bcf_hdr_t *h); 2021-07-15T17:14:47,266 | ~~~~~~~~~~~^ 2021-07-15T17:14:47,273 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’: 2021-07-15T17:14:47,280 cyvcf2/cyvcf2.c:12685:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations] 2021-07-15T17:14:47,280 12685 | __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen)); 2021-07-15T17:14:47,280 | ^~~~~~~~~ 2021-07-15T17:14:47,281 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:47,282 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:47,282 htslib/htslib/vcf.h:439:11: note: declared here 2021-07-15T17:14:47,282 439 | char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len) 2021-07-15T17:14:47,283 | ^~~~~~~~~~~~~~~~ 2021-07-15T17:14:47,288 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’: 2021-07-15T17:14:47,296 cyvcf2/cyvcf2.c:12979:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-15T17:14:47,296 12979 | __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-15T17:14:47,296 | ^ 2021-07-15T17:14:47,304 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:47,304 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:47,305 cyvcf2/cyvcf2.c:13088:75: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:47,305 13088 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-15T17:14:47,306 htslib/htslib/vcf.h:799:112: note: in definition of macro ‘bcf_index_seqnames’ 2021-07-15T17:14:47,306 799 | #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr)) 2021-07-15T17:14:47,306 | ^~~ 2021-07-15T17:14:47,307 In file included from htslib/htslib/vcf.h:39, 2021-07-15T17:14:47,307 from cyvcf2/helpers.h:1, 2021-07-15T17:14:47,307 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:47,308 htslib/htslib/hts.h:677:92: note: expected ‘void *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:47,308 677 | 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 2021-07-15T17:14:47,308 | ~~~~~~^~~ 2021-07-15T17:14:47,317 cyvcf2/cyvcf2.c:13088:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-15T17:14:47,317 13088 | __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n)); 2021-07-15T17:14:47,318 | ^ 2021-07-15T17:14:47,326 cyvcf2/cyvcf2.c:13171:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types] 2021-07-15T17:14:47,326 13171 | __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n)); 2021-07-15T17:14:47,327 | ^ 2021-07-15T17:14:48,490 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’: 2021-07-15T17:14:48,502 cyvcf2/cyvcf2.c:24200:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:14:48,503 24200 | for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) { 2021-07-15T17:14:48,503 | ^ 2021-07-15T17:14:48,671 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’: 2021-07-15T17:14:48,685 cyvcf2/cyvcf2.c:26211:17: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:48,685 26211 | __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id); 2021-07-15T17:14:48,685 | ^ 2021-07-15T17:14:49,097 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’: 2021-07-15T17:14:49,115 cyvcf2/cyvcf2.c:33773:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:14:49,115 33773 | for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { 2021-07-15T17:14:49,116 | ^ 2021-07-15T17:14:49,123 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’: 2021-07-15T17:14:49,140 cyvcf2/cyvcf2.c:34038:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:14:49,141 34038 | for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { 2021-07-15T17:14:49,141 | ^ 2021-07-15T17:14:49,145 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’: 2021-07-15T17:14:49,163 cyvcf2/cyvcf2.c:34252:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:14:49,163 34252 | for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { 2021-07-15T17:14:49,164 | ^ 2021-07-15T17:14:49,182 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] 2021-07-15T17:14:49,182 34310 | __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0); 2021-07-15T17:14:49,183 | ^~ 2021-07-15T17:14:49,257 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’: 2021-07-15T17:14:49,275 cyvcf2/cyvcf2.c:36422:13: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,276 36422 | __pyx_v_h = __pyx_t_6; 2021-07-15T17:14:49,276 | ^ 2021-07-15T17:14:49,387 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’: 2021-07-15T17:14:49,407 cyvcf2/cyvcf2.c:39465:16: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,407 39465 | __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key); 2021-07-15T17:14:49,408 | ^ 2021-07-15T17:14:49,422 cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’: 2021-07-15T17:14:49,442 cyvcf2/cyvcf2.c:40448:18: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,443 40448 | __pyx_v_i->hdr = __pyx_t_4; 2021-07-15T17:14:49,443 | ^ 2021-07-15T17:14:49,460 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’: 2021-07-15T17:14:49,482 cyvcf2/cyvcf2.c:41102:35: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,482 41102 | (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr)); 2021-07-15T17:14:49,482 | ~~~~~~~~~~~~^~~~~ 2021-07-15T17:14:49,483 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:49,483 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:49,483 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:49,483 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-15T17:14:49,484 | ~~~~~~~~~~~^ 2021-07-15T17:14:49,503 cyvcf2/cyvcf2.c:41130:47: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,503 41130 | (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); 2021-07-15T17:14:49,504 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-15T17:14:49,504 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:49,505 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:49,505 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:49,505 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-15T17:14:49,506 | ~~~~~~~~~~~^ 2021-07-15T17:14:49,514 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2from_string’: 2021-07-15T17:14:49,536 cyvcf2/cyvcf2.c:41457:55: warning: passing argument 1 of ‘bcf_hdr_parse’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,536 41457 | __pyx_t_2 = ((bcf_hdr_parse(__pyx_v_self->__pyx_base.hdr, __pyx_t_7) != 0) != 0); 2021-07-15T17:14:49,536 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-15T17:14:49,537 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:49,537 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:49,537 htslib/htslib/vcf.h:478:34: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:49,538 478 | int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt); 2021-07-15T17:14:49,538 | ~~~~~~~~~~~^~~ 2021-07-15T17:14:49,558 cyvcf2/cyvcf2.c:41493:54: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,558 41493 | __pyx_t_2 = ((bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr) != 0) != 0); 2021-07-15T17:14:49,558 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-15T17:14:49,559 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:49,559 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:49,559 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:49,560 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-15T17:14:49,560 | ~~~~~~~~~~~^ 2021-07-15T17:14:49,566 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_6write_header’: 2021-07-15T17:14:49,608 cyvcf2/cyvcf2.c:41871:78: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,608 41871 | (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr)); 2021-07-15T17:14:49,609 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-15T17:14:49,609 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:49,609 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:49,610 htslib/htslib/vcf.h:320:47: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:49,610 320 | int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h); 2021-07-15T17:14:49,610 | ~~~~~~~~~~~^ 2021-07-15T17:14:49,612 cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_8write_record’: 2021-07-15T17:14:49,634 cyvcf2/cyvcf2.c:42043:60: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,634 42043 | __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0); 2021-07-15T17:14:49,635 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-15T17:14:49,635 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:49,635 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:49,636 htslib/htslib/vcf.h:482:37: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:49,636 482 | int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec); 2021-07-15T17:14:49,636 | ~~~~~~~~~~~^~~ 2021-07-15T17:14:49,656 cyvcf2/cyvcf2.c:42081:49: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,657 42081 | (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr)); 2021-07-15T17:14:49,657 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-15T17:14:49,658 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:49,658 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:49,658 htslib/htslib/vcf.h:479:33: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:49,658 479 | int bcf_hdr_sync(bcf_hdr_t *h); 2021-07-15T17:14:49,659 | ~~~~~~~~~~~^ 2021-07-15T17:14:49,679 cyvcf2/cyvcf2.c:42140:100: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2021-07-15T17:14:49,680 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) 2021-07-15T17:14:49,680 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~ 2021-07-15T17:14:49,681 In file included from cyvcf2/helpers.h:1, 2021-07-15T17:14:49,681 from cyvcf2/cyvcf2.c:602: 2021-07-15T17:14:49,681 htslib/htslib/vcf.h:370:43: note: expected ‘bcf_hdr_t *’ but argument is of type ‘const bcf_hdr_t *’ 2021-07-15T17:14:49,682 370 | int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v); 2021-07-15T17:14:49,682 | ~~~~~~~~~~~^ 2021-07-15T17:14:50,930 cyvcf2/cyvcf2.c: In function ‘__Pyx_ParseOptionalKeywords’: 2021-07-15T17:14:50,973 cyvcf2/cyvcf2.c:63586:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:50,974 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:50,974 | ^ 2021-07-15T17:14:50,986 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:50,986 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:50,987 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:50,987 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T17:14:50,987 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T17:14:50,987 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,060 cyvcf2/cyvcf2.c:63586:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,060 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,061 | ^ 2021-07-15T17:14:51,061 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,061 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,061 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,062 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T17:14:51,062 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T17:14:51,062 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,099 cyvcf2/cyvcf2.c:63586:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,100 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,100 | ^ 2021-07-15T17:14:51,100 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,101 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,101 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,101 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T17:14:51,101 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T17:14:51,102 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,138 cyvcf2/cyvcf2.c:63586:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,139 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,139 | ^ 2021-07-15T17:14:51,139 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,140 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,140 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,141 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T17:14:51,141 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T17:14:51,141 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,177 cyvcf2/cyvcf2.c:63586:21: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,178 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,178 | ^ 2021-07-15T17:14:51,178 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,178 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,179 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,179 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T17:14:51,179 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T17:14:51,180 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,235 cyvcf2/cyvcf2.c:63586:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,236 63586 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,236 | ^ 2021-07-15T17:14:51,237 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,237 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,237 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,238 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T17:14:51,238 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T17:14:51,238 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,320 cyvcf2/cyvcf2.c:63602:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,321 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,321 | ^ 2021-07-15T17:14:51,321 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,321 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,322 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,322 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T17:14:51,322 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T17:14:51,322 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,379 cyvcf2/cyvcf2.c:63602:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,380 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,380 | ^ 2021-07-15T17:14:51,380 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,381 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,381 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,381 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T17:14:51,381 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T17:14:51,382 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,421 cyvcf2/cyvcf2.c:63602:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,422 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,422 | ^ 2021-07-15T17:14:51,422 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,423 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,423 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,423 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T17:14:51,423 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T17:14:51,424 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,461 cyvcf2/cyvcf2.c:63602:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,461 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,461 | ^ 2021-07-15T17:14:51,461 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,462 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,462 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,462 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T17:14:51,462 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T17:14:51,463 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,518 cyvcf2/cyvcf2.c:63602:25: warning: ‘PyUnicode_AsUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,518 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,519 | ^ 2021-07-15T17:14:51,519 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,520 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,520 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,520 /usr/include/python3.9/cpython/unicodeobject.h:580:45: note: declared here 2021-07-15T17:14:51,520 580 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode( 2021-07-15T17:14:51,521 | ^~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:51,567 cyvcf2/cyvcf2.c:63602:25: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:51,567 63602 | (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : 2021-07-15T17:14:51,568 | ^ 2021-07-15T17:14:51,568 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:51,568 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:51,568 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:51,569 /usr/include/python3.9/cpython/unicodeobject.h:446:26: note: declared here 2021-07-15T17:14:51,569 446 | static inline Py_ssize_t _PyUnicode_get_wstr_length(PyObject *op) { 2021-07-15T17:14:51,569 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:52,124 cyvcf2/cyvcf2.c: In function ‘__Pyx_decode_c_bytes’: 2021-07-15T17:14:52,157 cyvcf2/cyvcf2.c:64591:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:52,158 64591 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-15T17:14:52,158 | ^~~~~~ 2021-07-15T17:14:52,158 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:52,159 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:52,159 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:52,159 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-15T17:14:52,159 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-15T17:14:52,160 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:53,052 cyvcf2/cyvcf2.c: In function ‘__Pyx_decode_c_string’: 2021-07-15T17:14:53,085 cyvcf2/cyvcf2.c:66444:9: warning: ‘PyUnicode_FromUnicode’ is deprecated [-Wdeprecated-declarations] 2021-07-15T17:14:53,086 66444 | return PyUnicode_FromUnicode(NULL, 0); 2021-07-15T17:14:53,086 | ^~~~~~ 2021-07-15T17:14:53,087 In file included from /usr/include/python3.9/unicodeobject.h:1026, 2021-07-15T17:14:53,087 from /usr/include/python3.9/Python.h:97, 2021-07-15T17:14:53,088 from cyvcf2/cyvcf2.c:4: 2021-07-15T17:14:53,088 /usr/include/python3.9/cpython/unicodeobject.h:551:42: note: declared here 2021-07-15T17:14:53,089 551 | Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode( 2021-07-15T17:14:53,089 | ^~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:14:56,341 At top level: 2021-07-15T17:14:56,345 cyvcf2/cyvcf2.c:6618:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function] 2021-07-15T17:14:56,346 6618 | static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) { 2021-07-15T17:14:56,347 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:16:55,477 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 2021-07-15T17:16:55,711 In file included from htslib/htslib/vcf.h:42, 2021-07-15T17:16:55,711 from cyvcf2/helpers.h:1, 2021-07-15T17:16:55,712 from cyvcf2/helpers.c:1: 2021-07-15T17:16:55,712 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:16:55,713 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] 2021-07-15T17:16:55,714 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:16:55,714 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:16:55,715 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:16:55,716 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] 2021-07-15T17:16:55,716 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:16:55,716 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:16:56,053 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 2021-07-15T17:16:56,250 In file included from htslib/htslib/vcf.h:42, 2021-07-15T17:16:56,250 from htslib/htslib/synced_bcf_reader.h:60, 2021-07-15T17:16:56,250 from htslib/bcf_sr_sort.h:37, 2021-07-15T17:16:56,251 from htslib/bcf_sr_sort.c:29: 2021-07-15T17:16:56,251 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:16:56,252 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] 2021-07-15T17:16:56,252 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:16:56,252 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:16:56,252 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:16:56,253 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] 2021-07-15T17:16:56,253 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:16:56,253 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:16:56,322 htslib/bcf_sr_sort.c: In function ‘kbs_bitwise_or’: 2021-07-15T17:16:56,323 htslib/bcf_sr_sort.c:69:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:16:56,323 69 | for (i=0; in; i++) dst->b[i] |= src->b[i]; 2021-07-15T17:16:56,323 | ^ 2021-07-15T17:16:56,334 htslib/bcf_sr_sort.c: In function ‘bcf_sr_sort_set’: 2021-07-15T17:16:56,334 htslib/bcf_sr_sort.c:363:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:16:56,335 363 | for (k=0; k < kh_end(hash); k++) 2021-07-15T17:16:56,335 | ^ 2021-07-15T17:16:56,335 htslib/bcf_sr_sort.c:366:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:16:56,336 366 | for (k=0; k < kh_end(hash); k++) 2021-07-15T17:16:56,336 | ^ 2021-07-15T17:16:59,536 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 2021-07-15T17:17:00,068 In file included from htslib/bgzf.c:44: 2021-07-15T17:17:00,068 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:17:00,069 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:00,070 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:17:00,071 | ^ 2021-07-15T17:17:00,075 In file included from htslib/bgzf.c:46: 2021-07-15T17:17:00,075 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:00,076 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] 2021-07-15T17:17:00,076 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:00,076 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:00,077 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:00,078 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] 2021-07-15T17:17:00,078 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:00,079 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:00,157 htslib/bgzf.c: In function ‘bgzf_read’: 2021-07-15T17:17:00,157 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] 2021-07-15T17:17:00,157 983 | while (bytes_read < length) { 2021-07-15T17:17:00,158 | ^ 2021-07-15T17:17:00,158 htslib/bgzf.c:996:43: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:00,158 996 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-15T17:17:00,159 | ^ 2021-07-15T17:17:00,159 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] 2021-07-15T17:17:00,159 996 | copy_length = length - bytes_read < available? length - bytes_read : available; 2021-07-15T17:17:00,160 | ^~~~~~~~~ 2021-07-15T17:17:00,162 htslib/bgzf.c: In function ‘bgzf_mt_writer’: 2021-07-15T17:17:00,163 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] 2021-07-15T17:17:00,163 1107 | if (hwrite(fp->fp, j->comp_data, j->comp_len) != j->comp_len) { 2021-07-15T17:17:00,163 | ^~ 2021-07-15T17:17:00,201 htslib/bgzf.c: In function ‘bgzf_block_write’: 2021-07-15T17:17:00,202 htslib/bgzf.c:1594:41: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:00,202 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; 2021-07-15T17:17:00,203 | ^ 2021-07-15T17:17:00,204 htslib/bgzf.c:1602:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-15T17:17:00,204 1602 | if (fp->block_offset == ublock_size) { 2021-07-15T17:17:00,204 | ^~ 2021-07-15T17:17:00,262 htslib/bgzf.c: In function ‘bgzf_useek’: 2021-07-15T17:17:00,263 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] 2021-07-15T17:17:00,263 2049 | if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1; 2021-07-15T17:17:00,263 | ^ 2021-07-15T17:17:00,264 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] 2021-07-15T17:17:00,264 2050 | else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1; 2021-07-15T17:17:00,265 | ^~ 2021-07-15T17:17:04,657 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 2021-07-15T17:17:05,041 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:05,041 from htslib/cram/misc.h:66, 2021-07-15T17:17:05,042 from htslib/cram/cram_io.h:46, 2021-07-15T17:17:05,042 from htslib/cram/cram.h:48, 2021-07-15T17:17:05,042 from htslib/cram/cram_codecs.c:45: 2021-07-15T17:17:05,042 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:05,043 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] 2021-07-15T17:17:05,043 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:05,044 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:05,044 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:05,044 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] 2021-07-15T17:17:05,044 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:05,045 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:05,050 In file included from htslib/cram/cram.h:48, 2021-07-15T17:17:05,050 from htslib/cram/cram_codecs.c:45: 2021-07-15T17:17:05,050 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:17:05,051 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] 2021-07-15T17:17:05,051 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:17:05,052 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:05,063 In file included from htslib/cram/cram.h:52, 2021-07-15T17:17:05,063 from htslib/cram/cram_codecs.c:45: 2021-07-15T17:17:05,064 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:17:05,065 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] 2021-07-15T17:17:05,065 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:17:05,066 | ^~ 2021-07-15T17:17:05,066 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:05,067 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:17:05,067 | ^ 2021-07-15T17:17:05,068 htslib/cram/cram_codecs.c: In function ‘get_one_bits_MSB’: 2021-07-15T17:17:05,069 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] 2021-07-15T17:17:05,069 79 | if (block->byte >= block->uncomp_size) 2021-07-15T17:17:05,069 | ^~ 2021-07-15T17:17:05,070 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] 2021-07-15T17:17:05,070 86 | if (block->byte == block->uncomp_size && (b&1)) 2021-07-15T17:17:05,070 | ^~ 2021-07-15T17:17:05,071 htslib/cram/cram_codecs.c: In function ‘get_zero_bits_MSB’: 2021-07-15T17:17:05,071 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] 2021-07-15T17:17:05,071 97 | if (block->byte >= block->uncomp_size) 2021-07-15T17:17:05,072 | ^~ 2021-07-15T17:17:05,072 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] 2021-07-15T17:17:05,072 104 | if (block->byte == block->uncomp_size && !(b&1)) 2021-07-15T17:17:05,073 | ^~ 2021-07-15T17:17:05,081 htslib/cram/cram_codecs.c: In function ‘cram_beta_decode_init’: 2021-07-15T17:17:05,082 htslib/cram/cram_codecs.c:555:47: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:05,082 555 | || c->beta.nbits < 0 || c->beta.nbits > 8 * sizeof(int)) { 2021-07-15T17:17:05,082 | ^ 2021-07-15T17:17:05,094 htslib/cram/cram_codecs.c: In function ‘cram_huffman_decode_init’: 2021-07-15T17:17:05,095 htslib/cram/cram_codecs.c:976:16: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:05,095 976 | if (ncodes >= SIZE_MAX / sizeof(*codes)) { 2021-07-15T17:17:05,095 | ^~ 2021-07-15T17:17:05,098 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] 2021-07-15T17:17:05,098 1044 | if (val > max_val) 2021-07-15T17:17:05,099 | ^ 2021-07-15T17:17:05,124 htslib/cram/cram_codecs.c: In function ‘cram_byte_array_stop_decode_block’: 2021-07-15T17:17:05,125 htslib/cram/cram_codecs.c:1643:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:05,125 1643 | if (cp_end - cp < out->alloc - out->byte) { 2021-07-15T17:17:05,126 | ^ 2021-07-15T17:17:09,913 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/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 2021-07-15T17:17:10,321 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:10,322 from htslib/cram/misc.h:66, 2021-07-15T17:17:10,322 from htslib/cram/cram_io.h:46, 2021-07-15T17:17:10,322 from htslib/cram/cram.h:48, 2021-07-15T17:17:10,323 from htslib/cram/cram_decode.c:49: 2021-07-15T17:17:10,323 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:10,324 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] 2021-07-15T17:17:10,324 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:10,325 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:10,326 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:10,327 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] 2021-07-15T17:17:10,327 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:10,327 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:10,336 In file included from htslib/cram/cram.h:48, 2021-07-15T17:17:10,337 from htslib/cram/cram_decode.c:49: 2021-07-15T17:17:10,337 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:17:10,338 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] 2021-07-15T17:17:10,339 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:17:10,339 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:10,351 In file included from htslib/cram/cram.h:52, 2021-07-15T17:17:10,351 from htslib/cram/cram_decode.c:49: 2021-07-15T17:17:10,352 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:17:10,353 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] 2021-07-15T17:17:10,353 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:17:10,353 | ^~ 2021-07-15T17:17:10,354 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:10,354 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:17:10,355 | ^ 2021-07-15T17:17:10,362 htslib/cram/cram_decode.c: In function ‘cram_decode_TD’: 2021-07-15T17:17:10,363 htslib/cram/cram_decode.c:102:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:10,363 102 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-15T17:17:10,364 | ^ 2021-07-15T17:17:10,365 htslib/cram/cram_decode.c:114:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:10,365 114 | for (nTL = i = 0; i < BLOCK_SIZE(b); i++) { 2021-07-15T17:17:10,366 | ^ 2021-07-15T17:17:10,367 htslib/cram/cram_decode.c: In function ‘cram_decode_compression_header’: 2021-07-15T17:17:10,368 htslib/cram/cram_decode.c:156:33: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:10,369 156 | hdr->num_landmarks >= SIZE_MAX / sizeof(int32_t))) { 2021-07-15T17:17:10,369 | ^~ 2021-07-15T17:17:10,396 htslib/cram/cram_decode.c: In function ‘cram_dependent_data_series’: 2021-07-15T17:17:10,397 htslib/cram/cram_decode.c:800:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:10,397 800 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-15T17:17:10,397 | ^ 2021-07-15T17:17:10,400 htslib/cram/cram_decode.c:894:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:10,401 894 | for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) { 2021-07-15T17:17:10,401 | ^ 2021-07-15T17:17:10,409 htslib/cram/cram_decode.c: In function ‘cram_decode_slice_header’: 2021-07-15T17:17:10,410 htslib/cram/cram_decode.c:1114:30: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:10,410 1114 | hdr->num_content_ids >= SIZE_MAX / sizeof(int32_t)) { 2021-07-15T17:17:10,410 | ^~ 2021-07-15T17:17:10,418 htslib/cram/cram_decode.c: In function ‘cram_decode_seq’: 2021-07-15T17:17:10,420 htslib/cram/cram_decode.c:1286:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:10,420 1286 | if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) { 2021-07-15T17:17:10,420 | ^ 2021-07-15T17:17:10,427 htslib/cram/cram_decode.c:1437:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:10,427 1437 | if (cr->ref_id < 0 || ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-15T17:17:10,428 | ^~ 2021-07-15T17:17:10,433 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] 2021-07-15T17:17:10,434 1483 | if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) { 2021-07-15T17:17:10,434 | ^~ 2021-07-15T17:17:10,437 htslib/cram/cram_decode.c:1494:54: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:10,437 1494 | if (bfd->ref[cr->ref_id].len >= ref_pos) { 2021-07-15T17:17:10,438 | ^~ 2021-07-15T17:17:10,446 htslib/cram/cram_decode.c:1587:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:10,447 1587 | if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-15T17:17:10,447 | ^~ 2021-07-15T17:17:10,454 htslib/cram/cram_decode.c:1660:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:10,455 1660 | if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) { 2021-07-15T17:17:10,455 | ^~ 2021-07-15T17:17:10,464 htslib/cram/cram_decode.c:1767:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:10,464 1767 | if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) { 2021-07-15T17:17:10,465 | ^ 2021-07-15T17:17:10,504 htslib/cram/cram_decode.c: In function ‘cram_decode_slice’: 2021-07-15T17:17:10,506 htslib/cram/cram_decode.c:2403:20: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:10,506 2403 | bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap)) 2021-07-15T17:17:10,507 | ^~ 2021-07-15T17:17:21,162 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 2021-07-15T17:17:21,525 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:21,525 from htslib/cram/misc.h:66, 2021-07-15T17:17:21,526 from htslib/cram/cram_io.h:46, 2021-07-15T17:17:21,526 from htslib/cram/cram.h:48, 2021-07-15T17:17:21,527 from htslib/cram/cram_encode.c:43: 2021-07-15T17:17:21,527 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:21,528 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] 2021-07-15T17:17:21,528 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:21,529 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:21,529 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:21,530 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] 2021-07-15T17:17:21,530 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:21,531 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:21,540 In file included from htslib/cram/cram.h:48, 2021-07-15T17:17:21,540 from htslib/cram/cram_encode.c:43: 2021-07-15T17:17:21,541 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:17:21,542 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] 2021-07-15T17:17:21,542 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:17:21,543 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:21,554 In file included from htslib/cram/cram.h:52, 2021-07-15T17:17:21,554 from htslib/cram/cram_encode.c:43: 2021-07-15T17:17:21,555 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:17:21,556 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] 2021-07-15T17:17:21,556 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:17:21,557 | ^~ 2021-07-15T17:17:21,558 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:21,558 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:17:21,558 | ^ 2021-07-15T17:17:21,608 htslib/cram/cram_encode.c: In function ‘cram_encode_slice’: 2021-07-15T17:17:21,609 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] 2021-07-15T17:17:21,610 1044 | for (id = 1; id < s->hdr->num_blocks; id++) { 2021-07-15T17:17:21,610 | ^ 2021-07-15T17:17:21,616 htslib/cram/cram_encode.c: In function ‘lossy_read_names’: 2021-07-15T17:17:21,617 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] 2021-07-15T17:17:21,618 1168 | if (u.counts.e != e) { 2021-07-15T17:17:21,618 | ^~ 2021-07-15T17:17:21,620 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] 2021-07-15T17:17:21,621 1198 | if (kh_val(names, k) == -1) 2021-07-15T17:17:21,621 | ^~ 2021-07-15T17:17:21,679 htslib/cram/cram_encode.c: In function ‘process_one_read’: 2021-07-15T17:17:21,681 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] 2021-07-15T17:17:21,681 2636 | while (cr->cigar + cr->ncigar >= s->cigar_alloc) { 2021-07-15T17:17:21,682 | ^~ 2021-07-15T17:17:21,684 htslib/cram/cram_encode.c:2666:44: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:21,685 2666 | int end = cig_len+apos < c->ref_end 2021-07-15T17:17:21,685 | ^ 2021-07-15T17:17:21,687 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] 2021-07-15T17:17:21,688 2667 | ? cig_len : c->ref_end - apos; 2021-07-15T17:17:21,688 | ^~~~~~~~~~~~~~~~~ 2021-07-15T17:17:21,693 htslib/cram/cram_encode.c:2710:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:21,694 2710 | if (l < cig_len && cr->len) { 2021-07-15T17:17:21,694 | ^ 2021-07-15T17:17:21,697 htslib/cram/cram_encode.c:2718:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:21,697 2718 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-15T17:17:21,697 | ^ 2021-07-15T17:17:21,700 htslib/cram/cram_encode.c:2727:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:21,700 2727 | for (; l < cig_len && seq[spos]; l++, spos++) { 2021-07-15T17:17:21,700 | ^ 2021-07-15T17:17:21,706 htslib/cram/cram_encode.c:2759:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:21,706 2759 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-15T17:17:21,707 | ^ 2021-07-15T17:17:21,711 htslib/cram/cram_encode.c:2776:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:21,711 2776 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-15T17:17:21,712 | ^ 2021-07-15T17:17:21,715 htslib/cram/cram_encode.c:2780:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:21,715 2780 | for (l = 0; l < cig_len; l++, spos++) { 2021-07-15T17:17:21,716 | ^ 2021-07-15T17:17:21,722 htslib/cram/cram_encode.c:2834:17: warning: unused variable ‘brg’ [-Wunused-variable] 2021-07-15T17:17:21,723 2834 | SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); 2021-07-15T17:17:21,723 | ^~~ 2021-07-15T17:17:21,746 htslib/cram/cram_encode.c: In function ‘cram_put_bam_seq’: 2021-07-15T17:17:21,749 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] 2021-07-15T17:17:21,749 3077 | (c->s_num_bases >= fd->bases_per_slice)) { 2021-07-15T17:17:21,750 | ^~ 2021-07-15T17:17:21,754 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] 2021-07-15T17:17:21,754 3100 | c->s_num_bases >= fd->bases_per_slice) { 2021-07-15T17:17:21,755 | ^~ 2021-07-15T17:17:31,052 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 2021-07-15T17:17:31,169 In file included from htslib/cram/cram_external.c:43: 2021-07-15T17:17:31,170 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:17:31,170 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:31,170 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:17:31,171 | ^ 2021-07-15T17:17:31,366 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:31,366 from htslib/cram/misc.h:66, 2021-07-15T17:17:31,366 from htslib/cram/cram_io.h:46, 2021-07-15T17:17:31,367 from htslib/cram/cram.h:48, 2021-07-15T17:17:31,367 from htslib/cram/cram_external.c:44: 2021-07-15T17:17:31,367 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:31,376 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] 2021-07-15T17:17:31,376 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:31,376 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:31,377 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:31,377 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] 2021-07-15T17:17:31,377 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:31,378 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:31,384 In file included from htslib/cram/cram.h:48, 2021-07-15T17:17:31,384 from htslib/cram/cram_external.c:44: 2021-07-15T17:17:31,385 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:17:31,386 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] 2021-07-15T17:17:31,386 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:17:31,387 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:31,414 In file included from htslib/cram/cram.h:52, 2021-07-15T17:17:31,414 from htslib/cram/cram_external.c:44: 2021-07-15T17:17:31,415 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:17:31,415 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] 2021-07-15T17:17:31,415 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:17:31,416 | ^~ 2021-07-15T17:17:31,416 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:31,416 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:17:31,417 | ^ 2021-07-15T17:17:32,171 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 2021-07-15T17:17:32,442 In file included from htslib/cram/cram_index.c:64: 2021-07-15T17:17:32,443 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:17:32,443 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:32,443 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:17:32,444 | ^ 2021-07-15T17:17:32,713 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:32,713 from htslib/cram/misc.h:66, 2021-07-15T17:17:32,713 from htslib/cram/cram_io.h:46, 2021-07-15T17:17:32,714 from htslib/cram/cram.h:48, 2021-07-15T17:17:32,714 from htslib/cram/cram_index.c:66: 2021-07-15T17:17:32,715 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:32,726 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] 2021-07-15T17:17:32,726 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:32,727 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:32,727 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:32,727 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] 2021-07-15T17:17:32,728 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:32,728 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:32,734 In file included from htslib/cram/cram.h:48, 2021-07-15T17:17:32,735 from htslib/cram/cram_index.c:66: 2021-07-15T17:17:32,735 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:17:32,735 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] 2021-07-15T17:17:32,736 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:17:32,736 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:32,769 In file included from htslib/cram/cram.h:52, 2021-07-15T17:17:32,769 from htslib/cram/cram_index.c:66: 2021-07-15T17:17:32,769 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:17:32,770 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] 2021-07-15T17:17:32,770 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:17:32,770 | ^~ 2021-07-15T17:17:32,771 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:32,771 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:17:32,771 | ^ 2021-07-15T17:17:32,797 htslib/cram/cram_index.c: In function ‘cram_index_build’: 2021-07-15T17:17:32,798 htslib/cram/cram_index.c:587:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] 2021-07-15T17:17:32,799 587 | off_t cpos, spos, hpos; 2021-07-15T17:17:32,800 | ^~~~ 2021-07-15T17:17:34,090 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 2021-07-15T17:17:34,709 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:34,709 from htslib/cram/misc.h:66, 2021-07-15T17:17:34,709 from htslib/cram/cram_io.h:46, 2021-07-15T17:17:34,710 from htslib/cram/cram.h:48, 2021-07-15T17:17:34,710 from htslib/cram/cram_io.c:77: 2021-07-15T17:17:34,710 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:34,713 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] 2021-07-15T17:17:34,714 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:34,714 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:34,715 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:34,716 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] 2021-07-15T17:17:34,716 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:34,716 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:34,724 In file included from htslib/cram/cram.h:48, 2021-07-15T17:17:34,725 from htslib/cram/cram_io.c:77: 2021-07-15T17:17:34,725 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:17:34,728 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] 2021-07-15T17:17:34,729 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:17:34,729 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:34,740 In file included from htslib/cram/cram.h:52, 2021-07-15T17:17:34,740 from htslib/cram/cram_io.c:77: 2021-07-15T17:17:34,740 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:17:34,741 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] 2021-07-15T17:17:34,742 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:17:34,742 | ^~ 2021-07-15T17:17:34,743 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:34,743 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:17:34,743 | ^ 2021-07-15T17:17:34,752 In file included from htslib/cram/cram_io.c:94: 2021-07-15T17:17:34,753 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:17:34,753 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:34,753 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:17:34,754 | ^ 2021-07-15T17:17:34,771 htslib/cram/cram_io.c: In function ‘itf8_decode_crc’: 2021-07-15T17:17:34,772 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] 2021-07-15T17:17:34,772 241 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:17:34,772 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:34,834 htslib/cram/cram_io.c: In function ‘expand_cache_path’: 2021-07-15T17:17:34,835 htslib/cram/cram_io.c:1920:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:34,836 1920 | if (cp-dir >= sz) return -1; 2021-07-15T17:17:34,836 | ^~ 2021-07-15T17:17:34,839 In file included from htslib/cram/cram_io.h:46, 2021-07-15T17:17:34,839 from htslib/cram/cram.h:48, 2021-07-15T17:17:34,840 from htslib/cram/cram_io.c:77: 2021-07-15T17:17:34,840 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:34,840 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-15T17:17:34,841 | ^ 2021-07-15T17:17:34,841 htslib/cram/cram_io.c:1938:17: note: in expansion of macro ‘MIN’ 2021-07-15T17:17:34,841 1938 | l = MIN(l, strlen(fn)); 2021-07-15T17:17:34,841 | ^~~ 2021-07-15T17:17:34,843 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] 2021-07-15T17:17:34,843 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-15T17:17:34,843 | ^~~ 2021-07-15T17:17:34,844 htslib/cram/cram_io.c:1938:17: note: in expansion of macro ‘MIN’ 2021-07-15T17:17:34,844 1938 | l = MIN(l, strlen(fn)); 2021-07-15T17:17:34,844 | ^~~ 2021-07-15T17:17:34,846 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] 2021-07-15T17:17:34,846 1940 | if (l >= sz) return -1; 2021-07-15T17:17:34,846 | ^~ 2021-07-15T17:17:34,896 htslib/cram/cram_io.c: In function ‘cram_read_container’: 2021-07-15T17:17:34,898 htslib/cram/cram_io.c:2882:50: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:34,898 2882 | if (c2.num_landmarks < 0 || c2.num_landmarks >= SIZE_MAX / sizeof(int32_t)) 2021-07-15T17:17:34,899 | ^~ 2021-07-15T17:17:35,011 In file included from htslib/cram/cram.h:48, 2021-07-15T17:17:35,012 from htslib/cram/cram_io.c:77: 2021-07-15T17:17:35,012 htslib/cram/cram_io.c: In function ‘cram_write_SAM_hdr’: 2021-07-15T17:17:35,035 htslib/cram/cram_io.h:511:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:35,035 511 | while((b)->alloc <= (l)) { \ 2021-07-15T17:17:35,035 | ^~ 2021-07-15T17:17:35,036 htslib/cram/cram_io.c:3925:13: note: in expansion of macro ‘BLOCK_RESIZE’ 2021-07-15T17:17:35,036 3925 | BLOCK_RESIZE(b, padded_length); 2021-07-15T17:17:35,036 | ^~~~~~~~~~~~ 2021-07-15T17:17:43,085 In file included from /usr/include/string.h:495, 2021-07-15T17:17:43,085 from htslib/cram/cram_io.c:53: 2021-07-15T17:17:43,085 In function ‘strncpy’, 2021-07-15T17:17:43,086 inlined from ‘full_path’ at htslib/cram/cram_io.c:3748:13, 2021-07-15T17:17:43,086 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-15T17:17:43,087 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-15T17:17:43,087 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-15T17:17:43,087 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:43,088 In function ‘strncpy’, 2021-07-15T17:17:43,089 inlined from ‘full_path’ at htslib/cram/cram_io.c:3740:9, 2021-07-15T17:17:43,089 inlined from ‘cram_write_SAM_hdr’ at htslib/cram/cram_io.c:3823:17: 2021-07-15T17:17:43,090 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation] 2021-07-15T17:17:43,090 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-15T17:17:43,090 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:43,687 In function ‘strncpy’, 2021-07-15T17:17:43,688 inlined from ‘cram_dopen’ at htslib/cram/cram_io.c:4126:9: 2021-07-15T17:17:43,688 /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound 20 equals destination size [-Wstringop-truncation] 2021-07-15T17:17:43,689 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); 2021-07-15T17:17:43,689 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:44,827 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 2021-07-15T17:17:45,116 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:45,116 from htslib/cram/misc.h:66, 2021-07-15T17:17:45,117 from htslib/cram/cram_io.h:46, 2021-07-15T17:17:45,117 from htslib/cram/cram.h:48, 2021-07-15T17:17:45,118 from htslib/cram/cram_samtools.c:37: 2021-07-15T17:17:45,118 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:45,119 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] 2021-07-15T17:17:45,119 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:45,119 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:45,120 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:45,120 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] 2021-07-15T17:17:45,120 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:45,121 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:45,125 In file included from htslib/cram/cram.h:48, 2021-07-15T17:17:45,126 from htslib/cram/cram_samtools.c:37: 2021-07-15T17:17:45,126 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:17:45,127 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] 2021-07-15T17:17:45,127 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:17:45,127 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:45,137 In file included from htslib/cram/cram.h:52, 2021-07-15T17:17:45,137 from htslib/cram/cram_samtools.c:37: 2021-07-15T17:17:45,138 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:17:45,138 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] 2021-07-15T17:17:45,139 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:17:45,139 | ^~ 2021-07-15T17:17:45,140 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:45,140 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:17:45,140 | ^ 2021-07-15T17:17:45,143 htslib/cram/cram_samtools.c: In function ‘bam_construct_seq’: 2021-07-15T17:17:45,144 htslib/cram/cram_samtools.c:85:19: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:45,144 85 | if (b->m_data < bam_len) { 2021-07-15T17:17:45,144 | ^ 2021-07-15T17:17:45,444 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 2021-07-15T17:17:45,899 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:45,900 from htslib/cram/misc.h:66, 2021-07-15T17:17:45,900 from htslib/cram/cram_io.h:46, 2021-07-15T17:17:45,901 from htslib/cram/cram.h:48, 2021-07-15T17:17:45,901 from htslib/cram/cram_stats.c:43: 2021-07-15T17:17:45,901 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:45,902 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-15T17:17:45,902 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:45,903 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:45,903 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:45,904 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] 2021-07-15T17:17:45,904 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:45,904 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:45,911 In file included from htslib/cram/cram.h:48, 2021-07-15T17:17:45,911 from htslib/cram/cram_stats.c:43: 2021-07-15T17:17:45,911 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:17:45,912 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] 2021-07-15T17:17:45,913 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:17:45,913 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:45,924 In file included from htslib/cram/cram.h:52, 2021-07-15T17:17:45,924 from htslib/cram/cram_stats.c:43: 2021-07-15T17:17:45,924 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:17:45,925 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] 2021-07-15T17:17:45,925 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:17:45,926 | ^~ 2021-07-15T17:17:45,926 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:45,926 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:17:45,927 | ^ 2021-07-15T17:17:46,634 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 2021-07-15T17:17:46,754 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:46,754 from htslib/cram/misc.h:66, 2021-07-15T17:17:46,754 from htslib/cram/files.c:34: 2021-07-15T17:17:46,755 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:46,756 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] 2021-07-15T17:17:46,756 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:46,757 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:46,757 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:46,757 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] 2021-07-15T17:17:46,758 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:46,758 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:47,097 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 2021-07-15T17:17:47,376 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:47,376 from htslib/cram/mFILE.c:44: 2021-07-15T17:17:47,377 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:47,377 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] 2021-07-15T17:17:47,378 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:47,378 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:47,378 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:47,379 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] 2021-07-15T17:17:47,379 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:47,380 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:47,387 htslib/cram/mFILE.c: In function ‘mfload’: 2021-07-15T17:17:47,387 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] 2021-07-15T17:17:47,388 103 | } while (!feof(fp) && (fn == NULL || used < sb.st_size)); 2021-07-15T17:17:47,388 | ^ 2021-07-15T17:17:47,395 htslib/cram/mFILE.c: In function ‘mftruncate’: 2021-07-15T17:17:47,396 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] 2021-07-15T17:17:47,396 476 | mf->size = offset != -1 ? offset : mf->offset; 2021-07-15T17:17:47,397 | ^~~~~~ 2021-07-15T17:17:48,086 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 2021-07-15T17:17:48,364 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:48,364 from htslib/cram/open_trace_file.c:74: 2021-07-15T17:17:48,364 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:48,365 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] 2021-07-15T17:17:48,365 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:48,366 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:48,366 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:48,366 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] 2021-07-15T17:17:48,367 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:48,367 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:48,381 In file included from htslib/cram/open_trace_file.c:81: 2021-07-15T17:17:48,382 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:17:48,383 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:48,383 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:17:48,383 | ^ 2021-07-15T17:17:48,391 In file included from htslib/cram/open_trace_file.c:80: 2021-07-15T17:17:48,391 htslib/cram/open_trace_file.c: In function ‘expand_path’: 2021-07-15T17:17:48,392 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-15T17:17:48,393 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-15T17:17:48,393 | ^ 2021-07-15T17:17:48,393 htslib/cram/open_trace_file.c:251:29: note: in expansion of macro ‘MIN’ 2021-07-15T17:17:48,394 251 | path_end += MIN(strlen(file), l); 2021-07-15T17:17:48,394 | ^~~ 2021-07-15T17:17:48,395 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] 2021-07-15T17:17:48,395 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-15T17:17:48,395 | ^~~ 2021-07-15T17:17:48,396 htslib/cram/open_trace_file.c:251:29: note: in expansion of macro ‘MIN’ 2021-07-15T17:17:48,396 251 | path_end += MIN(strlen(file), l); 2021-07-15T17:17:48,396 | ^~~ 2021-07-15T17:17:48,397 htslib/cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-15T17:17:48,397 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-15T17:17:48,397 | ^ 2021-07-15T17:17:48,398 htslib/cram/open_trace_file.c:252:29: note: in expansion of macro ‘MIN’ 2021-07-15T17:17:48,398 252 | file += MIN(strlen(file), l); 2021-07-15T17:17:48,398 | ^~~ 2021-07-15T17:17:48,399 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] 2021-07-15T17:17:48,399 103 | #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) ) 2021-07-15T17:17:48,399 | ^~~ 2021-07-15T17:17:48,400 htslib/cram/open_trace_file.c:252:29: note: in expansion of macro ‘MIN’ 2021-07-15T17:17:48,400 252 | file += MIN(strlen(file), l); 2021-07-15T17:17:48,400 | ^~~ 2021-07-15T17:17:49,031 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/pooled_alloc.c -o build/temp.linux-armv7l-3.9/htslib/cram/pooled_alloc.o 2021-07-15T17:17:49,186 In file included from htslib/cram/os.h:80, 2021-07-15T17:17:49,187 from htslib/cram/misc.h:66, 2021-07-15T17:17:49,187 from htslib/cram/pooled_alloc.c:38: 2021-07-15T17:17:49,187 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:17:49,189 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] 2021-07-15T17:17:49,189 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:17:49,189 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:49,190 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:17:49,191 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] 2021-07-15T17:17:49,191 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:17:49,192 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:49,336 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 2021-07-15T17:17:49,527 htslib/cram/rANS_static.c: In function ‘rans_compress_O0’: 2021-07-15T17:17:49,527 htslib/cram/rANS_static.c:86:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:49,528 86 | for (i = 0; i < in_size; i++) { 2021-07-15T17:17:49,528 | ^ 2021-07-15T17:17:49,537 htslib/cram/rANS_static.c: In function ‘rans_compress_O1’: 2021-07-15T17:17:49,537 htslib/cram/rANS_static.c:388:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:17:49,538 388 | for (last_i=i=0; ih, type, &new))) 2021-07-15T17:17:51,907 | ^~ 2021-07-15T17:17:51,910 htslib/cram/sam_header.c: In function ‘sam_hdr_vadd’: 2021-07-15T17:17:51,910 htslib/cram/sam_header.c:451:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:51,911 451 | if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new))) 2021-07-15T17:17:51,911 | ^~ 2021-07-15T17:17:51,934 htslib/cram/sam_header.c: In function ‘sam_hdr_rebuild’: 2021-07-15T17:17:51,934 htslib/cram/sam_header.c:821:31: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:51,935 821 | if (kh_key(hdr->h, k) == K("HD")) 2021-07-15T17:17:51,935 | ^~ 2021-07-15T17:17:55,582 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/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 2021-07-15T17:17:55,906 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 2021-07-15T17:17:57,310 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 2021-07-15T17:17:57,610 In file included from htslib/faidx.c:40: 2021-07-15T17:17:57,611 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:17:57,611 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:17:57,612 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:17:57,612 | ^ 2021-07-15T17:17:57,698 htslib/faidx.c: In function ‘fai_retrieve’: 2021-07-15T17:17:57,699 htslib/faidx.c:711:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘long int’ [-Wsign-compare] 2021-07-15T17:17:57,699 711 | while ( l < end - beg && (c=bgzf_getc(fai->bgzf))>=0 ) 2021-07-15T17:17:57,699 | ^ 2021-07-15T17:17:57,704 htslib/faidx.c: In function ‘fai_get_val’: 2021-07-15T17:17:57,705 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] 2021-07-15T17:17:57,705 789 | end = i < k? strtol(s + i, &ep, 10) : val->len; 2021-07-15T17:17:57,706 | ^~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:17:57,707 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] 2021-07-15T17:17:57,708 801 | if (beg >= val->len) beg = val->len; 2021-07-15T17:17:57,708 | ^~ 2021-07-15T17:17:57,709 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] 2021-07-15T17:17:57,709 802 | if (end >= val->len) end = val->len; 2021-07-15T17:17:57,710 | ^~ 2021-07-15T17:17:57,713 htslib/faidx.c: In function ‘faidx_adjust_position’: 2021-07-15T17:17:57,713 htslib/faidx.c:882:22: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:57,714 882 | else if(val->len <= *p_beg_i) 2021-07-15T17:17:57,714 | ^~ 2021-07-15T17:17:57,715 htslib/faidx.c:887:22: warning: comparison of integer expressions of different signedness: ‘uint64_t’ {aka ‘long long unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:17:57,716 887 | else if(val->len <= *p_end_i) 2021-07-15T17:17:57,716 | ^~ 2021-07-15T17:18:00,468 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 2021-07-15T17:18:00,667 In file included from htslib/hfile.c:36: 2021-07-15T17:18:00,667 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:00,668 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:00,669 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:00,669 | ^ 2021-07-15T17:18:00,695 htslib/hfile.c: In function ‘hfile_set_blksize’: 2021-07-15T17:18:00,696 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] 2021-07-15T17:18:00,696 200 | if (bufsiz < curr_used) 2021-07-15T17:18:00,697 | ^ 2021-07-15T17:18:00,704 htslib/hfile.c: In function ‘hseek’: 2021-07-15T17:18:00,705 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] 2021-07-15T17:18:00,706 436 | if (offset > 0 || -offset > length) { 2021-07-15T17:18:00,706 | ^ 2021-07-15T17:18:00,833 htslib/hfile.c: In function ‘find_scheme_handler’: 2021-07-15T17:18:00,834 htslib/hfile.c:1004:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:18:00,835 1004 | for (i = 0; i < sizeof scheme; i++) 2021-07-15T17:18:00,835 | ^ 2021-07-15T17:18:00,837 htslib/hfile.c:1011:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2021-07-15T17:18:00,838 1011 | if (i <= 1 || i >= sizeof scheme) return NULL; 2021-07-15T17:18:00,838 | ^~ 2021-07-15T17:18:02,945 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 2021-07-15T17:18:03,149 In file included from htslib/hfile_internal.h:30, 2021-07-15T17:18:03,149 from htslib/hfile_gcs.c:35: 2021-07-15T17:18:03,150 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:03,151 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:03,151 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:03,152 | ^ 2021-07-15T17:18:03,895 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 2021-07-15T17:18:04,099 In file included from htslib/hfile_internal.h:30, 2021-07-15T17:18:04,099 from htslib/hfile_libcurl.c:37: 2021-07-15T17:18:04,100 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:04,100 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:04,101 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:04,101 | ^ 2021-07-15T17:18:07,513 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 2021-07-15T17:18:07,645 In file included from htslib/hfile_internal.h:30, 2021-07-15T17:18:07,645 from htslib/hfile_net.c:30: 2021-07-15T17:18:07,646 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:07,646 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:07,647 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:07,647 | ^ 2021-07-15T17:18:07,845 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/home/piwheels/.local/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c htslib/hfile_s3.c -o build/temp.linux-armv7l-3.9/htslib/hfile_s3.o 2021-07-15T17:18:08,215 In file included from htslib/hfile_internal.h:30, 2021-07-15T17:18:08,215 from htslib/hfile_s3.c:33: 2021-07-15T17:18:08,216 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:08,216 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:08,217 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:08,217 | ^ 2021-07-15T17:18:10,085 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 2021-07-15T17:18:10,439 In file included from htslib/cram/os.h:80, 2021-07-15T17:18:10,440 from htslib/cram/misc.h:66, 2021-07-15T17:18:10,440 from htslib/cram/cram_io.h:46, 2021-07-15T17:18:10,440 from htslib/cram/cram.h:48, 2021-07-15T17:18:10,441 from htslib/hts.c:41: 2021-07-15T17:18:10,441 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:18:10,442 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] 2021-07-15T17:18:10,443 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:18:10,443 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:10,444 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:18:10,445 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] 2021-07-15T17:18:10,445 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:18:10,446 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:10,462 In file included from htslib/cram/cram.h:48, 2021-07-15T17:18:10,462 from htslib/hts.c:41: 2021-07-15T17:18:10,462 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:18:10,463 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] 2021-07-15T17:18:10,464 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:18:10,464 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:10,476 In file included from htslib/cram/cram.h:52, 2021-07-15T17:18:10,476 from htslib/hts.c:41: 2021-07-15T17:18:10,477 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:18:10,478 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] 2021-07-15T17:18:10,478 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:18:10,479 | ^~ 2021-07-15T17:18:10,480 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:10,480 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:18:10,480 | ^ 2021-07-15T17:18:10,487 In file included from htslib/hts.c:42: 2021-07-15T17:18:10,488 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:10,488 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:10,489 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:10,489 | ^ 2021-07-15T17:18:10,611 htslib/hts.c: In function ‘hts_idx_init’: 2021-07-15T17:18:10,612 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] 2021-07-15T17:18:10,613 1386 | idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu; 2021-07-15T17:18:10,613 | ^~~ 2021-07-15T17:18:10,617 htslib/hts.c: In function ‘update_loff’: 2021-07-15T17:18:10,636 htslib/hts.c:1420:34: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:10,637 1420 | if ( kh_key(bidx, k) < idx->n_bins ) 2021-07-15T17:18:10,637 | ^ 2021-07-15T17:18:10,640 htslib/hts.c: In function ‘compress_binning’: 2021-07-15T17:18:10,641 htslib/hts.c:1447:55: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:10,641 1447 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue; 2021-07-15T17:18:10,642 | ^~ 2021-07-15T17:18:10,646 htslib/hts.c:1472:51: warning: comparison of integer expressions of different signedness: ‘khint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:10,646 1472 | if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue; 2021-07-15T17:18:10,647 | ^~ 2021-07-15T17:18:10,681 htslib/hts.c: In function ‘hts_idx_load_local’: 2021-07-15T17:18:10,682 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] 2021-07-15T17:18:10,683 1832 | if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail; 2021-07-15T17:18:10,683 | ^~ 2021-07-15T17:18:10,689 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] 2021-07-15T17:18:10,689 1859 | if (bgzf_read(fp, idx->meta + 28, n) != n) goto fail; 2021-07-15T17:18:10,690 | ^~ 2021-07-15T17:18:10,715 htslib/hts.c: In function ‘hts_itr_multi_bam’: 2021-07-15T17:18:10,716 htslib/hts.c:2230:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:10,717 2230 | for(j=0; jcount; j++) { 2021-07-15T17:18:10,717 | ^ 2021-07-15T17:18:10,726 htslib/hts.c: In function ‘hts_itr_multi_cram’: 2021-07-15T17:18:10,727 htslib/hts.c:2341:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:10,728 2341 | for (j=0; j < curr_reg->count; j++) { 2021-07-15T17:18:10,728 | ^ 2021-07-15T17:18:10,758 htslib/hts.c: In function ‘hts_itr_multi_next’: 2021-07-15T17:18:10,760 htslib/hts.c:2737:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint64_t’ {aka ‘long long unsigned int’} [-Wsign-compare] 2021-07-15T17:18:10,760 2737 | if (beg > iter->off[iter->i].max) { 2021-07-15T17:18:10,761 | ^ 2021-07-15T17:18:10,763 htslib/hts.c:2741:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:10,763 2741 | if (beg > iter->reg_list[cr].max_end) 2021-07-15T17:18:10,763 | ^ 2021-07-15T17:18:10,766 htslib/hts.c:2744:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:10,766 2744 | for (i = ci; i < iter->reg_list[cr].count; i++) { 2021-07-15T17:18:10,767 | ^ 2021-07-15T17:18:10,769 htslib/hts.c:2745:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:10,769 2745 | if (end > iter->reg_list[cr].intervals[i].beg && iter->reg_list[cr].intervals[i].end > beg) { 2021-07-15T17:18:10,769 | ^ 2021-07-15T17:18:10,772 htslib/hts.c:2745:98: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:10,772 2745 | if (end > iter->reg_list[cr].intervals[i].beg && iter->reg_list[cr].intervals[i].end > beg) { 2021-07-15T17:18:10,773 | ^ 2021-07-15T17:18:10,777 htslib/hts.c: In function ‘test_and_fetch’: 2021-07-15T17:18:10,779 htslib/hts.c:2798:45: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:10,780 2798 | if (fwrite(buf, 1, l, local_fp) != l) { 2021-07-15T17:18:10,780 | ^~ 2021-07-15T17:18:10,791 htslib/hts.c: In function ‘hts_log’: 2021-07-15T17:18:10,793 htslib/hts.c:2967:18: warning: comparison of integer expressions of different signedness: ‘enum htsLogLevel’ and ‘int’ [-Wsign-compare] 2021-07-15T17:18:10,794 2967 | if (severity <= hts_verbose) { 2021-07-15T17:18:10,794 | ^~ 2021-07-15T17:18:21,134 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 2021-07-15T17:18:21,390 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 2021-07-15T17:18:22,438 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 2021-07-15T17:18:23,843 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ihtslib -Icyvcf2 -I/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 2021-07-15T17:18:24,045 htslib/kstring.c: In function ‘kvsprintf’: 2021-07-15T17:18:24,046 htslib/kstring.c:156:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:24,046 156 | if (l + 1 > s->m - s->l) { 2021-07-15T17:18:24,047 | ^ 2021-07-15T17:18:24,975 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 2021-07-15T17:18:25,104 In file included from htslib/md5.c:53: 2021-07-15T17:18:25,104 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:18:25,106 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] 2021-07-15T17:18:25,106 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:18:25,106 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:25,107 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:18:25,108 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] 2021-07-15T17:18:25,108 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:18:25,108 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:25,904 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 2021-07-15T17:18:26,162 In file included from htslib/hfile_internal.h:30, 2021-07-15T17:18:26,162 from htslib/multipart.c:34: 2021-07-15T17:18:26,162 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:26,165 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:26,166 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:26,166 | ^ 2021-07-15T17:18:26,773 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 2021-07-15T17:18:27,003 htslib/probaln.c: In function ‘probaln_glocal’: 2021-07-15T17:18:27,004 htslib/probaln.c:177:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:27,005 177 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-15T17:18:27,006 | ^~ 2021-07-15T17:18:27,009 htslib/probaln.c:201:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:27,009 201 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-15T17:18:27,010 | ^~ 2021-07-15T17:18:27,015 htslib/probaln.c:239:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:27,015 239 | if (u < 3 || u >= i_dim - 3) continue; 2021-07-15T17:18:27,016 | ^~ 2021-07-15T17:18:28,252 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/realn.c -o build/temp.linux-armv7l-3.9/htslib/realn.o 2021-07-15T17:18:28,482 htslib/realn.c: In function ‘sam_cap_mapq’: 2021-07-15T17:18:28,483 htslib/realn.c:47:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:28,483 47 | for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) { 2021-07-15T17:18:28,484 | ^ 2021-07-15T17:18:28,488 htslib/realn.c: In function ‘realn_check_tag’: 2021-07-15T17:18:28,489 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] 2021-07-15T17:18:28,489 96 | if (b->core.l_qseq != strlen((const char *) tg + 1)) { 2021-07-15T17:18:28,490 | ^~ 2021-07-15T17:18:28,494 htslib/realn.c: In function ‘sam_prob_realn’: 2021-07-15T17:18:28,495 htslib/realn.c:158:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:28,495 158 | for (k = 0; k < c->n_cigar; ++k) { 2021-07-15T17:18:28,496 | ^ 2021-07-15T17:18:28,499 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] 2021-07-15T17:18:28,499 188 | if (extend_baq && lref < c->l_qseq) 2021-07-15T17:18:28,500 | ^ 2021-07-15T17:18:28,502 htslib/realn.c:221:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:28,503 221 | for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { 2021-07-15T17:18:28,503 | ^ 2021-07-15T17:18:28,506 htslib/realn.c:247:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:28,506 247 | for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { 2021-07-15T17:18:28,507 | ^ 2021-07-15T17:18:29,405 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/regidx.c -o build/temp.linux-armv7l-3.9/htslib/regidx.o 2021-07-15T17:18:29,616 htslib/regidx.c: In function ‘regidx_insert’: 2021-07-15T17:18:29,616 htslib/regidx.c:156:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:29,617 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-15T17:18:29,617 | ^ 2021-07-15T17:18:29,618 htslib/regidx.c:156:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:29,618 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-15T17:18:29,619 | ^~ 2021-07-15T17:18:29,620 htslib/regidx.c:156:89: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:29,620 156 | if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 2021-07-15T17:18:29,621 | ^ 2021-07-15T17:18:30,874 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 2021-07-15T17:18:31,314 In file included from htslib/cram/os.h:80, 2021-07-15T17:18:31,315 from htslib/cram/misc.h:66, 2021-07-15T17:18:31,315 from htslib/cram/cram_io.h:46, 2021-07-15T17:18:31,315 from htslib/cram/cram.h:48, 2021-07-15T17:18:31,316 from htslib/sam.c:37: 2021-07-15T17:18:31,316 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:18:31,317 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] 2021-07-15T17:18:31,317 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:18:31,318 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:31,318 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:18:31,318 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] 2021-07-15T17:18:31,319 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:18:31,319 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:31,330 In file included from htslib/cram/cram.h:48, 2021-07-15T17:18:31,331 from htslib/sam.c:37: 2021-07-15T17:18:31,331 htslib/cram/cram_io.h: In function ‘safe_itf8_get’: 2021-07-15T17:18:31,333 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] 2021-07-15T17:18:31,333 296 | *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1; 2021-07-15T17:18:31,334 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:31,351 In file included from htslib/cram/cram.h:52, 2021-07-15T17:18:31,352 from htslib/sam.c:37: 2021-07-15T17:18:31,352 htslib/cram/cram_codecs.h: In function ‘cram_not_enough_bits’: 2021-07-15T17:18:31,354 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] 2021-07-15T17:18:31,354 169 | (blk->byte >= blk->uncomp_size && nbits > 0) || 2021-07-15T17:18:31,354 | ^~ 2021-07-15T17:18:31,355 htslib/cram/cram_codecs.h:171:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:31,356 171 | (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) { 2021-07-15T17:18:31,356 | ^ 2021-07-15T17:18:31,375 In file included from htslib/sam.c:39: 2021-07-15T17:18:31,375 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:31,376 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,376 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:31,377 | ^ 2021-07-15T17:18:31,386 htslib/sam.c: In function ‘bam_hdr_read’: 2021-07-15T17:18:31,387 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] 2021-07-15T17:18:31,388 155 | if (bytes != h->l_text) goto read_err; 2021-07-15T17:18:31,388 | ^~ 2021-07-15T17:18:31,396 htslib/sam.c: In function ‘possibly_expand_bam_data’: 2021-07-15T17:18:31,397 htslib/sam.c:323:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:31,397 323 | if (new_len > INT32_MAX || new_len < b->l_data) { 2021-07-15T17:18:31,398 | ^ 2021-07-15T17:18:31,403 htslib/sam.c: In function ‘bam_tag2cigar’: 2021-07-15T17:18:31,404 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] 2021-07-15T17:18:31,405 408 | if (bam_cigar_op(cigar0[0]) != BAM_CSOFT_CLIP || bam_cigar_oplen(cigar0[0]) != c->l_qseq) return 0; 2021-07-15T17:18:31,405 | ^~ 2021-07-15T17:18:31,420 htslib/sam.c: In function ‘bam_write1’: 2021-07-15T17:18:31,421 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] 2021-07-15T17:18:31,421 564 | return ok? 4 + block_len : -1; 2021-07-15T17:18:31,422 | ^~ 2021-07-15T17:18:31,451 htslib/sam.c: In function ‘sam_hdr_write’: 2021-07-15T17:18:31,452 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] 2021-07-15T17:18:31,453 1108 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-15T17:18:31,453 | ^~ 2021-07-15T17:18:31,457 htslib/sam.c: In function ‘sam_hdr_change_HD’: 2021-07-15T17:18:31,459 htslib/sam.c:1143:36: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:31,460 1143 | && strlen(val) == end - beg - 4) 2021-07-15T17:18:31,460 | ^~ 2021-07-15T17:18:31,497 htslib/sam.c: In function ‘sam_parse1’: 2021-07-15T17:18:31,498 htslib/sam.c:1262:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,498 1262 | for (i = 0; i < c->n_cigar; ++i, ++q) { 2021-07-15T17:18:31,499 | ^ 2021-07-15T17:18:31,520 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] 2021-07-15T17:18:31,521 1392 | _parse_err(bytes / size != n 2021-07-15T17:18:31,521 | ^~ 2021-07-15T17:18:31,521 htslib/sam.c:1202:40: note: in definition of macro ‘_parse_err’ 2021-07-15T17:18:31,522 1202 | #define _parse_err(cond, msg) do { if (cond) { hts_log_error(msg); goto err_ret; } } while (0) 2021-07-15T17:18:31,522 | ^~~~ 2021-07-15T17:18:31,527 htslib/sam.c: In function ‘sam_format1’: 2021-07-15T17:18:31,529 htslib/sam.c:1495:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘const unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,529 1495 | for (i = 0; i < c->n_cigar; ++i) { 2021-07-15T17:18:31,530 | ^ 2021-07-15T17:18:31,539 htslib/sam.c:1586:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,539 1586 | if ((end - s) / sub_type_size < n) 2021-07-15T17:18:31,540 | ^ 2021-07-15T17:18:31,542 htslib/sam.c:1589:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,542 1589 | for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if" 2021-07-15T17:18:31,543 | ^ 2021-07-15T17:18:31,545 htslib/sam.c: In function ‘sam_write1’: 2021-07-15T17:18:31,547 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] 2021-07-15T17:18:31,548 1633 | if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1; 2021-07-15T17:18:31,548 | ^~ 2021-07-15T17:18:31,566 htslib/sam.c: In function ‘bam_aux_append’: 2021-07-15T17:18:31,568 htslib/sam.c:1695:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:31,569 1695 | if (new_len > INT32_MAX || new_len < b->l_data) goto nomem; 2021-07-15T17:18:31,569 | ^ 2021-07-15T17:18:31,574 htslib/sam.c: In function ‘skip_aux’: 2021-07-15T17:18:31,575 htslib/sam.c:1737:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,576 1737 | if (size == 0 || end - s < size * n) return NULL; 2021-07-15T17:18:31,576 | ^ 2021-07-15T17:18:31,630 htslib/sam.c: In function ‘resolve_cigar2’: 2021-07-15T17:18:31,632 htslib/sam.c:2287:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,632 2287 | for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) { 2021-07-15T17:18:31,633 | ^ 2021-07-15T17:18:31,637 htslib/sam.c:2309:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,638 2309 | for (k = s->k + 1; k < c->n_cigar; ++k) { 2021-07-15T17:18:31,638 | ^ 2021-07-15T17:18:31,641 htslib/sam.c:2323:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,641 2323 | if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation 2021-07-15T17:18:31,642 | ^ 2021-07-15T17:18:31,644 htslib/sam.c:2328:50: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,644 2328 | else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding 2021-07-15T17:18:31,645 | ^ 2021-07-15T17:18:31,647 htslib/sam.c:2330:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:31,647 2330 | for (k = s->k + 2; k < c->n_cigar; ++k) { 2021-07-15T17:18:31,648 | ^ 2021-07-15T17:18:44,351 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 2021-07-15T17:18:44,672 In file included from htslib/htslib/vcf.h:42, 2021-07-15T17:18:44,672 from htslib/htslib/synced_bcf_reader.h:60, 2021-07-15T17:18:44,672 from htslib/synced_bcf_reader.c:34: 2021-07-15T17:18:44,672 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:18:44,674 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] 2021-07-15T17:18:44,674 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:18:44,675 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:44,676 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:18:44,677 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] 2021-07-15T17:18:44,677 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:18:44,678 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:44,758 htslib/synced_bcf_reader.c: In function ‘_regions_add’: 2021-07-15T17:18:44,759 htslib/synced_bcf_reader.c:801:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:44,759 801 | if ( start < creg->regs[i].start ) max = i - 1; 2021-07-15T17:18:44,760 | ^ 2021-07-15T17:18:44,761 htslib/synced_bcf_reader.c:802:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:44,761 802 | else if ( start > creg->regs[i].start ) min = i + 1; 2021-07-15T17:18:44,761 | ^ 2021-07-15T17:18:44,762 htslib/synced_bcf_reader.c:805:40: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:44,763 805 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-15T17:18:44,763 | ^~ 2021-07-15T17:18:44,764 htslib/synced_bcf_reader.c:805:68: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:44,765 805 | if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end ) 2021-07-15T17:18:44,765 | ^~ 2021-07-15T17:18:47,993 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 2021-07-15T17:18:48,226 In file included from htslib/tbx.c:35: 2021-07-15T17:18:48,226 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:18:48,228 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] 2021-07-15T17:18:48,228 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:18:48,228 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:48,229 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:18:48,230 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] 2021-07-15T17:18:48,230 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:18:48,230 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:48,261 htslib/tbx.c: In function ‘tbx_index_load2’: 2021-07-15T17:18:48,276 htslib/tbx.c:321:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:48,276 321 | for (; p - nm < l_nm; p += strlen(p) + 1) { 2021-07-15T17:18:48,276 | ^ 2021-07-15T17:18:49,184 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 2021-07-15T17:18:49,323 In file included from htslib/textutils.c:30: 2021-07-15T17:18:49,323 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:49,324 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:49,324 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:49,324 | ^ 2021-07-15T17:18:50,480 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 2021-07-15T17:18:51,963 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/vcf.c -o build/temp.linux-armv7l-3.9/htslib/vcf.o 2021-07-15T17:18:52,246 In file included from htslib/htslib/vcf.h:42, 2021-07-15T17:18:52,246 from htslib/vcf.c:38: 2021-07-15T17:18:52,247 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:18:52,256 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] 2021-07-15T17:18:52,256 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:18:52,257 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:52,257 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:18:52,257 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] 2021-07-15T17:18:52,258 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:18:52,258 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:52,360 In file included from htslib/vcf.c:41: 2021-07-15T17:18:52,361 htslib/htslib/hfile.h: In function ‘hwrite’: 2021-07-15T17:18:52,361 htslib/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:52,362 245 | if (fp->limit - fp->begin < nbytes){ 2021-07-15T17:18:52,362 | ^ 2021-07-15T17:18:52,405 htslib/vcf.c: In function ‘bcf_hdr_sync’: 2021-07-15T17:18:52,406 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] 2021-07-15T17:18:52,406 149 | if ( h->n[i] < kh_size(d) ) 2021-07-15T17:18:52,407 | ^ 2021-07-15T17:18:52,428 htslib/vcf.c: In function ‘bcf_hdr_register_hrec’: 2021-07-15T17:18:52,429 htslib/vcf.c:499:18: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:52,429 499 | if (type == -1) { 2021-07-15T17:18:52,430 | ^~ 2021-07-15T17:18:52,431 htslib/vcf.c:504:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:52,431 504 | if (var == -1) { 2021-07-15T17:18:52,432 | ^~ 2021-07-15T17:18:52,452 htslib/vcf.c: In function ‘bcf_hdr_read’: 2021-07-15T17:18:52,453 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] 2021-07-15T17:18:52,454 917 | if (bgzf_read(fp, htxt, hlen) != hlen) goto fail; 2021-07-15T17:18:52,454 | ^~ 2021-07-15T17:18:52,458 htslib/vcf.c: In function ‘bcf_hdr_write’: 2021-07-15T17:18:52,459 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] 2021-07-15T17:18:52,459 948 | if ( bgzf_write(fp, htxt.s, htxt.l) != htxt.l ) return -1; 2021-07-15T17:18:52,459 | ^~ 2021-07-15T17:18:52,464 htslib/vcf.c: In function ‘bcf_read1_core’: 2021-07-15T17:18:52,465 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] 2021-07-15T17:18:52,466 1033 | if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -2; 2021-07-15T17:18:52,466 | ^~ 2021-07-15T17:18:52,468 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] 2021-07-15T17:18:52,468 1034 | if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -2; 2021-07-15T17:18:52,469 | ^~ 2021-07-15T17:18:52,471 htslib/vcf.c: In function ‘bcf_dec_typed_int1_safe’: 2021-07-15T17:18:52,472 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] 2021-07-15T17:18:52,473 1058 | *val = v < 0x8000 ? v : -((int32_t) (0xffff - v)) - 1; 2021-07-15T17:18:52,473 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:52,475 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] 2021-07-15T17:18:52,476 1063 | *val = v < 0x80000000UL ? v : -((int32_t) (0xffffffffUL - v)) - 1; 2021-07-15T17:18:52,476 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:52,480 htslib/vcf.c: In function ‘bcf_record_check’: 2021-07-15T17:18:52,481 htslib/vcf.c:1125:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:52,482 1125 | if (end - ptr < bytes) goto bad_shared; 2021-07-15T17:18:52,482 | ^ 2021-07-15T17:18:52,484 htslib/vcf.c:1138:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:52,485 1138 | if (end - ptr < bytes) goto bad_shared; 2021-07-15T17:18:52,486 | ^ 2021-07-15T17:18:52,488 htslib/vcf.c:1151:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:52,489 1151 | if (end - ptr < bytes) goto bad_shared; 2021-07-15T17:18:52,489 | ^ 2021-07-15T17:18:52,491 htslib/vcf.c:1152:23: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2021-07-15T17:18:52,491 1152 | for (i = 0; i < num; i++) { 2021-07-15T17:18:52,492 | ^ 2021-07-15T17:18:52,495 htslib/vcf.c:1179:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:52,495 1179 | if (end - ptr < bytes) goto bad_shared; 2021-07-15T17:18:52,496 | ^ 2021-07-15T17:18:52,499 htslib/vcf.c:1202:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:52,499 1202 | if (end - ptr < bytes) goto bad_indiv; 2021-07-15T17:18:52,500 | ^ 2021-07-15T17:18:52,519 htslib/vcf.c: In function ‘bcf_write’: 2021-07-15T17:18:52,520 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] 2021-07-15T17:18:52,521 1533 | if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1; 2021-07-15T17:18:52,521 | ^~ 2021-07-15T17:18:52,523 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] 2021-07-15T17:18:52,523 1534 | if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1; 2021-07-15T17:18:52,524 | ^~ 2021-07-15T17:18:52,582 htslib/vcf.c: In function ‘vcf_parse_format’: 2021-07-15T17:18:52,583 htslib/vcf.c:1970:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-15T17:18:52,584 1970 | if (fmt[j].max_l < l) fmt[j].max_l = l; 2021-07-15T17:18:52,584 | ^ 2021-07-15T17:18:52,599 htslib/vcf.c:2000:33: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘unsigned int’ due to unsignedness of other operand [-Wsign-compare] 2021-07-15T17:18:52,600 2000 | f->size = f->is_gt? f->max_g << 2 : f->max_l; 2021-07-15T17:18:52,600 | ^~~~~~~~~~~~~ 2021-07-15T17:18:52,707 htslib/vcf.c: In function ‘vcf_write_line’: 2021-07-15T17:18:52,709 htslib/vcf.c:2611:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:52,709 2611 | return ret==line->l ? 0 : -1; 2021-07-15T17:18:52,709 | ^~ 2021-07-15T17:18:52,711 htslib/vcf.c: In function ‘vcf_write’: 2021-07-15T17:18:52,712 htslib/vcf.c:2624:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:52,712 2624 | return ret==fp->line.l ? 0 : -1; 2021-07-15T17:18:52,713 | ^~ 2021-07-15T17:18:52,784 htslib/vcf.c: In function ‘bcf_hdr_set_samples’: 2021-07-15T17:18:52,787 htslib/vcf.c:3136:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare] 2021-07-15T17:18:52,787 3136 | for (k = kh_begin(d); k != kh_end(d); ++k) 2021-07-15T17:18:52,787 | ^~ 2021-07-15T17:18:52,849 htslib/vcf.c: In function ‘_bcf1_sync_alleles’: 2021-07-15T17:18:52,852 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] 2021-07-15T17:18:52,852 3586 | line->rlen = end_info ? end_info->v1.i - line->pos : strlen(line->d.allele[0]); 2021-07-15T17:18:52,853 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:18:52,868 htslib/vcf.c: In function ‘bcf_get_info_values’: 2021-07-15T17:18:52,870 htslib/vcf.c:3716:49: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-15T17:18:52,871 3716 | if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2; // expected different type 2021-07-15T17:18:52,871 | ^~ 2021-07-15T17:18:52,891 htslib/vcf.c: In function ‘bcf_get_format_values’: 2021-07-15T17:18:52,894 htslib/vcf.c:3819:53: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2021-07-15T17:18:52,894 3819 | else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2; // expected different type 2021-07-15T17:18:52,895 | ^~ 2021-07-15T17:19:09,609 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 2021-07-15T17:19:09,810 In file included from htslib/htslib/vcf.h:42, 2021-07-15T17:19:09,810 from htslib/htslib/vcf_sweep.h:30, 2021-07-15T17:19:09,810 from htslib/vcf_sweep.c:27: 2021-07-15T17:19:09,811 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:19:09,812 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] 2021-07-15T17:19:09,812 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:19:09,813 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:19:09,814 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:19:09,815 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] 2021-07-15T17:19:09,815 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:19:09,816 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:19:09,892 htslib/vcf_sweep.c: In function ‘bcf_sweep_fwd’: 2021-07-15T17:19:09,893 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] 2021-07-15T17:19:09,894 164 | if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size ) 2021-07-15T17:19:09,894 | ^ 2021-07-15T17:19:10,215 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 2021-07-15T17:19:10,477 In file included from htslib/htslib/vcf.h:42, 2021-07-15T17:19:10,477 from htslib/htslib/vcfutils.h:29, 2021-07-15T17:19:10,478 from htslib/vcfutils.c:27: 2021-07-15T17:19:10,478 htslib/htslib/hts_endian.h: In function ‘le_to_i32’: 2021-07-15T17:19:10,480 htslib/htslib/hts_endian.h:245:34: warning: operand of ‘?:’ changes signedness from ‘int’ to ‘uint32_t’ {aka ‘unsigned int’} due to unsignedness of other operand [-Wsign-compare] 2021-07-15T17:19:10,480 245 | return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1; 2021-07-15T17:19:10,480 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:19:10,481 htslib/htslib/hts_endian.h: In function ‘le_to_i64’: 2021-07-15T17:19:10,482 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] 2021-07-15T17:19:10,482 257 | ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1); 2021-07-15T17:19:10,483 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2021-07-15T17:19:15,236 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 2021-07-15T17:19:16,372 installing to build/bdist.linux-armv7l/wheel 2021-07-15T17:19:16,372 running install 2021-07-15T17:19:16,373 running install_lib 2021-07-15T17:19:16,459 creating build/bdist.linux-armv7l 2021-07-15T17:19:16,460 creating build/bdist.linux-armv7l/wheel 2021-07-15T17:19:16,464 creating build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,466 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,623 copying build/lib.linux-armv7l-3.9/cyvcf2/relatedness.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,627 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,693 creating build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,695 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.bug.117.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,698 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,701 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,720 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,724 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-alt-repr.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,728 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/decomposed.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,731 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,735 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,738 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/no-seq-names.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,741 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,746 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/seg.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,749 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,754 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/issue_44.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,757 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,763 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-diff.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,766 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/no-seq-len.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,770 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,774 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,780 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,784 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,792 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,796 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_alt_freqs.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,800 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,804 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,807 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/empty.vcf -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,810 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_reader.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,816 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,820 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,823 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,827 copying build/lib.linux-armv7l-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/bdist.linux-armv7l/wheel/cyvcf2/tests 2021-07-15T17:19:16,831 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,835 copying build/lib.linux-armv7l-3.9/cyvcf2/cli.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,839 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.c -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,843 copying build/lib.linux-armv7l-3.9/cyvcf2/helpers.h -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,846 copying build/lib.linux-armv7l-3.9/cyvcf2/__main__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,850 copying build/lib.linux-armv7l-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,856 copying build/lib.linux-armv7l-3.9/cyvcf2/__init__.py -> build/bdist.linux-armv7l/wheel/cyvcf2 2021-07-15T17:19:16,860 running install_egg_info 2021-07-15T17:19:16,876 Copying cyvcf2.egg-info to build/bdist.linux-armv7l/wheel/cyvcf2-0.11.6-py3.9.egg-info 2021-07-15T17:19:16,910 running install_scripts 2021-07-15T17:19:17,039 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2021-07-15T17:19:17,048 creating build/bdist.linux-armv7l/wheel/cyvcf2-0.11.6.dist-info/WHEEL 2021-07-15T17:19:17,053 creating '/tmp/pip-wheel-6g18e6kc/cyvcf2-0.11.6-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2021-07-15T17:19:17,057 adding 'cyvcf2/__init__.py' 2021-07-15T17:19:17,059 adding 'cyvcf2/__main__.py' 2021-07-15T17:19:17,062 adding 'cyvcf2/cli.py' 2021-07-15T17:19:17,400 adding 'cyvcf2/cyvcf2.c' 2021-07-15T17:19:19,683 adding 'cyvcf2/cyvcf2.cpython-39-arm-linux-gnueabihf.so' 2021-07-15T17:19:19,743 adding 'cyvcf2/cyvcf2.pxd' 2021-07-15T17:19:19,756 adding 'cyvcf2/cyvcf2.pyx' 2021-07-15T17:19:19,759 adding 'cyvcf2/helpers.c' 2021-07-15T17:19:19,762 adding 'cyvcf2/helpers.h' 2021-07-15T17:19:19,765 adding 'cyvcf2/relatedness.h' 2021-07-15T17:19:19,769 adding 'cyvcf2/tests/__init__.py' 2021-07-15T17:19:19,772 adding 'cyvcf2/tests/bug.vcf.gz' 2021-07-15T17:19:19,775 adding 'cyvcf2/tests/decomposed.vcf' 2021-07-15T17:19:19,778 adding 'cyvcf2/tests/empty.vcf' 2021-07-15T17:19:19,781 adding 'cyvcf2/tests/issue_44.vcf' 2021-07-15T17:19:19,784 adding 'cyvcf2/tests/no-seq-len.vcf' 2021-07-15T17:19:19,787 adding 'cyvcf2/tests/no-seq-names.vcf' 2021-07-15T17:19:19,795 adding 'cyvcf2/tests/o.vcf.gz' 2021-07-15T17:19:19,798 adding 'cyvcf2/tests/seg.vcf.gz' 2021-07-15T17:19:19,801 adding 'cyvcf2/tests/test-alt-repr.vcf' 2021-07-15T17:19:19,803 adding 'cyvcf2/tests/test-diff.csi' 2021-07-15T17:19:19,806 adding 'cyvcf2/tests/test-format-string.vcf' 2021-07-15T17:19:19,887 adding 'cyvcf2/tests/test-haploidX.vcf' 2021-07-15T17:19:19,908 adding 'cyvcf2/tests/test-hemi.vcf' 2021-07-15T17:19:19,910 adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz' 2021-07-15T17:19:19,913 adding 'cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi' 2021-07-15T17:19:19,916 adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz' 2021-07-15T17:19:19,936 adding 'cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi' 2021-07-15T17:19:19,938 adding 'cyvcf2/tests/test.bug.117.vcf' 2021-07-15T17:19:19,941 adding 'cyvcf2/tests/test.comp_het.3.vcf' 2021-07-15T17:19:19,943 adding 'cyvcf2/tests/test.snpeff.bcf' 2021-07-15T17:19:19,945 adding 'cyvcf2/tests/test.snpeff.bcf.csi' 2021-07-15T17:19:19,958 adding 'cyvcf2/tests/test.snpeff.vcf' 2021-07-15T17:19:20,016 adding 'cyvcf2/tests/test.vcf.gz' 2021-07-15T17:19:20,019 adding 'cyvcf2/tests/test.vcf.gz.tbi' 2021-07-15T17:19:20,027 adding 'cyvcf2/tests/test_cli.py' 2021-07-15T17:19:20,030 adding 'cyvcf2/tests/test_gt_alt_freqs.vcf' 2021-07-15T17:19:20,033 adding 'cyvcf2/tests/test_gt_bases.vcf.gz' 2021-07-15T17:19:20,046 adding 'cyvcf2/tests/test_hemi.py' 2021-07-15T17:19:20,051 adding 'cyvcf2/tests/test_reader.py' 2021-07-15T17:19:20,055 adding 'cyvcf2-0.11.6.dist-info/LICENSE' 2021-07-15T17:19:20,067 adding 'cyvcf2-0.11.6.dist-info/METADATA' 2021-07-15T17:19:20,069 adding 'cyvcf2-0.11.6.dist-info/WHEEL' 2021-07-15T17:19:20,070 adding 'cyvcf2-0.11.6.dist-info/entry_points.txt' 2021-07-15T17:19:20,072 adding 'cyvcf2-0.11.6.dist-info/top_level.txt' 2021-07-15T17:19:20,074 adding 'cyvcf2-0.11.6.dist-info/RECORD' 2021-07-15T17:19:20,141 removing build/bdist.linux-armv7l/wheel 2021-07-15T17:19:20,359 Building wheel for cyvcf2 (setup.py): finished with status 'done' 2021-07-15T17:19:20,409 Created wheel for cyvcf2: filename=cyvcf2-0.11.6-cp39-cp39-linux_armv7l.whl size=3367314 sha256=aea21253bd125ed9466fe8eb4e55f4d2b17e02c4872a162a054e2a581c2d1fba 2021-07-15T17:19:20,410 Stored in directory: /tmp/pip-ephem-wheel-cache-ya3v_46z/wheels/b2/7b/b2/3a409c7c7068d6c901aeaee9b52f89c6eb5dd98a7719c5ef01 2021-07-15T17:19:20,428 Successfully built cyvcf2 2021-07-15T17:19:20,579 Removed build tracker: '/tmp/pip-req-tracker-fkijbdg_'