Install Error in Linux

[silvewheat]

Hello,

I install the package using: pip install cyvcf2

The error message as below:

Collecting cyvcf2
  Using cached https://files.pythonhosted.org/packages/dd/2e/2c80e524e5f98837274bad981a0b5621717283462fc0aca91823b76ab759/cyvcf2-0.11.5.tar.gz
Requirement already satisfied: numpy in /Dell/user/caiyd/Software/anaconda/lib/python3.7/site-packages (from cyvcf2) (1.17.2)
Building wheels for collected packages: cyvcf2
  Building wheel for cyvcf2 (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/caiyd/Dell_cyd/Software/anaconda/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uhj_v8np/cyvcf2/setup.py'"'"'; __file__='"'"'/tmp/pip-install-uhj_v8np/cyvcf2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-lje90unx --python-tag cp37
       cwd: /tmp/pip-install-uhj_v8np/cyvcf2/
  Complete output (501 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.7
  creating build/lib.linux-x86_64-3.7/cyvcf2
  copying cyvcf2/__init__.py -> build/lib.linux-x86_64-3.7/cyvcf2
  copying cyvcf2/__main__.py -> build/lib.linux-x86_64-3.7/cyvcf2
  copying cyvcf2/cli.py -> build/lib.linux-x86_64-3.7/cyvcf2
  creating build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/__init__.py -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test_cli.py -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test_hemi.py -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test_reader.py -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  running egg_info
  writing cyvcf2.egg-info/PKG-INFO
  writing dependency_links to cyvcf2.egg-info/dependency_links.txt
  writing entry points to cyvcf2.egg-info/entry_points.txt
  writing requirements to cyvcf2.egg-info/requires.txt
  writing top-level names to cyvcf2.egg-info/top_level.txt
  reading manifest file 'cyvcf2.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
  copying cyvcf2/cyvcf2.c -> build/lib.linux-x86_64-3.7/cyvcf2
  copying cyvcf2/cyvcf2.pxd -> build/lib.linux-x86_64-3.7/cyvcf2
  copying cyvcf2/cyvcf2.pyx -> build/lib.linux-x86_64-3.7/cyvcf2
  copying cyvcf2/helpers.c -> build/lib.linux-x86_64-3.7/cyvcf2
  copying cyvcf2/helpers.h -> build/lib.linux-x86_64-3.7/cyvcf2
  copying cyvcf2/relatedness.h -> build/lib.linux-x86_64-3.7/cyvcf2
  copying cyvcf2/tests/__init__.pyc -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/decomposed.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/empty.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/issue_44.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/no-seq-len.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/no-seq-names.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/seg.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test-diff.csi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test.bug.117.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test_cli.pyc -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test_hemi.pyc -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  copying cyvcf2/tests/test_reader.pyc -> build/lib.linux-x86_64-3.7/cyvcf2/tests
  running build_ext
  skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date)
  building 'cyvcf2.cyvcf2' extension
  creating build/temp.linux-x86_64-3.7
  creating build/temp.linux-x86_64-3.7/cyvcf2
  creating build/temp.linux-x86_64-3.7/htslib
  creating build/temp.linux-x86_64-3.7/htslib/cram
  gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c cyvcf2/cyvcf2.c -o build/temp.linux-x86_64-3.7/cyvcf2/cyvcf2.o
  In file included from /home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
                   from /home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from cyvcf2/cyvcf2.c:599:
  /home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/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]
   #warning "Using deprecated NumPy API, disable it with " \
    ^
  In file included from htslib/htslib/hts.h:35:0,
                   from htslib/htslib/vcf.h:39,
                   from cyvcf2/helpers.h:1,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   enum htsLogLevel hts_get_log_level();
        ^
  In file included from htslib/htslib/vcf.h:42:0,
                   from cyvcf2/helpers.h:1,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/hts_endian.h: In function ‘le_to_i32’:
  htslib/htslib/hts_endian.h:245:32: warning: signed and unsigned type in conditional expression [-Wsign-compare]
       return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1;
                                  ^
  htslib/htslib/hts_endian.h: In function ‘le_to_i64’:
  htslib/htslib/hts_endian.h:257:17: warning: signed and unsigned type in conditional expression [-Wsign-compare]
               ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1);
                   ^
  In file included from cyvcf2/cyvcf2.c:604:0:
  htslib/htslib/hfile.h: In function ‘hwrite’:
  htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (fp->limit - fp->begin < nbytes){
                                     ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’:
  cyvcf2/cyvcf2.c:7934:3: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2);
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:443:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_append(bcf_hdr_t *h, const char *line);
           ^
  cyvcf2/cyvcf2.c:7976:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_sync(bcf_hdr_t *h);
           ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’:
  cyvcf2/cyvcf2.c:8492:3: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0);
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:315:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file);
           ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’:
  cyvcf2/cyvcf2.c:8790:3: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4);
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:443:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_append(bcf_hdr_t *h, const char *line);
           ^
  cyvcf2/cyvcf2.c:8843:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_sync(bcf_hdr_t *h);
           ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_20generator’:
  cyvcf2/cyvcf2.c:9263:3: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [enabled by default]
     __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);
     ^
  In file included from htslib/htslib/vcf.h:39:0,
                   from cyvcf2/helpers.h:1,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/hts.h:675:16: note: expected ‘void *’ but argument is of type ‘const struct bcf_hdr_t *’
       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);
                  ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_26generator2’:
  cyvcf2/cyvcf2.c:10548:5: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __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)
       ^
  cyvcf2/cyvcf2.c:2913:61: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
   static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/
                                                               ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_37__dealloc__’:
  cyvcf2/cyvcf2.c:12204:5: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [enabled by default]
       bcf_hdr_destroy(__pyx_v_self->hdr);
       ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:261:10: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       void bcf_hdr_destroy(bcf_hdr_t *h);
            ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’:
  cyvcf2/cyvcf2.c:12685:3: warning: ‘bcf_hdr_fmt_text’ is deprecated (declared at htslib/htslib/vcf.h:439): use bcf_hdr_format() instead [-Wdeprecated-declarations]
     __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen));
     ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’:
  cyvcf2/cyvcf2.c:12979:18: warning: assignment from incompatible pointer type [enabled by default]
     __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
                    ^
  cyvcf2/cyvcf2.c:13088:7: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [enabled by default]
         __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
         ^
  In file included from htslib/htslib/vcf.h:39:0,
                   from cyvcf2/helpers.h:1,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/hts.h:677:18: note: expected ‘void *’ but argument is of type ‘const struct bcf_hdr_t *’
       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
                    ^
  cyvcf2/cyvcf2.c:13088:22: warning: assignment from incompatible pointer type [enabled by default]
         __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
                        ^
  cyvcf2/cyvcf2.c:13171:22: warning: assignment from incompatible pointer type [enabled by default]
         __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
                        ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’:
  cyvcf2/cyvcf2.c:24200:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) {
                                   ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’:
  cyvcf2/cyvcf2.c:26211:17: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id);
                   ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’:
  cyvcf2/cyvcf2.c:33773:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
                                   ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’:
  cyvcf2/cyvcf2.c:34038:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
                                   ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’:
  cyvcf2/cyvcf2.c:34252:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
                                   ^
  cyvcf2/cyvcf2.c:34310:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0);
                               ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’:
  cyvcf2/cyvcf2.c:36422:13: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_v_h = __pyx_t_6;
               ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’:
  cyvcf2/cyvcf2.c:39465:16: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key);
                  ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’:
  cyvcf2/cyvcf2.c:40448:18: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_v_i->hdr = __pyx_t_4;
                    ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’:
  cyvcf2/cyvcf2.c:41102:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
     (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr));
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_sync(bcf_hdr_t *h);
           ^
  cyvcf2/cyvcf2.c:41130:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
     (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_sync(bcf_hdr_t *h);
           ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2from_string’:
  cyvcf2/cyvcf2.c:41457:3: warning: passing argument 1 of ‘bcf_hdr_parse’ discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_t_2 = ((bcf_hdr_parse(__pyx_v_self->__pyx_base.hdr, __pyx_t_7) != 0) != 0);
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:478:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt);
           ^
  cyvcf2/cyvcf2.c:41493:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
     __pyx_t_2 = ((bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr) != 0) != 0);
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_sync(bcf_hdr_t *h);
           ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_6write_header’:
  cyvcf2/cyvcf2.c:41871:3: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [enabled by default]
     (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr));
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:320:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h);
           ^
  cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_8write_record’:
  cyvcf2/cyvcf2.c:42043:5: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0);
       ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:482:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
           ^
  cyvcf2/cyvcf2.c:42081:5: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
       (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
       ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_hdr_sync(bcf_hdr_t *h);
           ^
  cyvcf2/cyvcf2.c:42140:3: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [enabled by default]
     __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)
     ^
  In file included from cyvcf2/helpers.h:1:0,
                   from cyvcf2/cyvcf2.c:602:
  htslib/htslib/vcf.h:370:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
       int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v);
           ^
  cyvcf2/cyvcf2.c: At top level:
  cyvcf2/cyvcf2.c:6618:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function]
   static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) {
                    ^
  gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/bcf_sr_sort.c -o build/temp.linux-x86_64-3.7/htslib/bcf_sr_sort.o
  In file included from htslib/htslib/hts.h:35:0,
                   from htslib/htslib/synced_bcf_reader.h:59,
                   from htslib/bcf_sr_sort.h:37,
                   from htslib/bcf_sr_sort.c:29:
  htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   enum htsLogLevel hts_get_log_level();
        ^
  In file included from htslib/htslib/vcf.h:42:0,
                   from htslib/htslib/synced_bcf_reader.h:60,
                   from htslib/bcf_sr_sort.h:37,
                   from htslib/bcf_sr_sort.c:29:
  htslib/htslib/hts_endian.h: In function ‘le_to_i32’:
  htslib/htslib/hts_endian.h:245:32: warning: signed and unsigned type in conditional expression [-Wsign-compare]
       return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1;
                                  ^
  htslib/htslib/hts_endian.h: In function ‘le_to_i64’:
  htslib/htslib/hts_endian.h:257:17: warning: signed and unsigned type in conditional expression [-Wsign-compare]
               ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1);
                   ^
  htslib/bcf_sr_sort.c: In function ‘kbs_bitwise_or’:
  htslib/bcf_sr_sort.c:69:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i=0; i<dst->n; i++) dst->b[i] |= src->b[i];
                  ^
  htslib/bcf_sr_sort.c: In function ‘bcf_sr_sort_set’:
  htslib/bcf_sr_sort.c:363:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (k=0; k < kh_end(hash); k++)
                   ^
  htslib/bcf_sr_sort.c:366:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (k=0; k < kh_end(hash); k++)
                   ^
  gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/bgzf.c -o build/temp.linux-x86_64-3.7/htslib/bgzf.o
  In file included from htslib/htslib/hts.h:35:0,
                   from htslib/bgzf.c:42:
  htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   enum htsLogLevel hts_get_log_level();
        ^
  In file included from htslib/bgzf.c:44:0:
  htslib/htslib/hfile.h: In function ‘hwrite’:
  htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (fp->limit - fp->begin < nbytes){
                                     ^
  In file included from htslib/bgzf.c:46:0:
  htslib/htslib/hts_endian.h: In function ‘le_to_i32’:
  htslib/htslib/hts_endian.h:245:32: warning: signed and unsigned type in conditional expression [-Wsign-compare]
       return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1;
                                  ^
  htslib/htslib/hts_endian.h: In function ‘le_to_i64’:
  htslib/htslib/hts_endian.h:257:17: warning: signed and unsigned type in conditional expression [-Wsign-compare]
               ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1);
                   ^
  htslib/bgzf.c: In function ‘bgzf_read’:
  htslib/bgzf.c:983:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       while (bytes_read < length) {
                         ^
  htslib/bgzf.c:996:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           copy_length = length - bytes_read < available? length - bytes_read : available;
                                             ^
  htslib/bgzf.c:996:76: warning: signed and unsigned type in conditional expression [-Wsign-compare]
           copy_length = length - bytes_read < available? length - bytes_read : available;
                                                                              ^
  htslib/bgzf.c: In function ‘bgzf_mt_writer’:
  htslib/bgzf.c:1107:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (hwrite(fp->fp, j->comp_data, j->comp_len) != j->comp_len) {
                                                         ^
  htslib/bgzf.c: In function ‘bgzf_block_write’:
  htslib/bgzf.c:1594:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           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;
                                           ^
  htslib/bgzf.c:1602:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (fp->block_offset == ublock_size) {
                                ^
  htslib/bgzf.c: In function ‘bgzf_useek’:
  htslib/bgzf.c:2049:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1;
                        ^
  htslib/bgzf.c:2050:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1;
                             ^
  gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/errmod.c -o build/temp.linux-x86_64-3.7/htslib/errmod.o
  In file included from htslib/htslib/hts.h:35:0,
                   from htslib/errmod.c:29:
  htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   enum htsLogLevel hts_get_log_level();
        ^
  gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/faidx.c -o build/temp.linux-x86_64-3.7/htslib/faidx.o
  In file included from htslib/faidx.c:40:0:
  htslib/htslib/hfile.h: In function ‘hwrite’:
  htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (fp->limit - fp->begin < nbytes){
                                     ^
  In file included from htslib/htslib/hts.h:35:0,
                   from htslib/hts_internal.h:29,
                   from htslib/faidx.c:43:
  htslib/htslib/hts_log.h: At top level:
  htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   enum htsLogLevel hts_get_log_level();
        ^
  In file included from htslib/hts_internal.h:31:0,
                   from htslib/faidx.c:43:
  htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   hts_json_token * hts_json_alloc_token();
   ^
  htslib/faidx.c: In function ‘fai_retrieve’:
  htslib/faidx.c:711:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       while ( l < end - beg && (c=bgzf_getc(fai->bgzf))>=0 )
                 ^
  htslib/faidx.c: In function ‘fai_get_val’:
  htslib/faidx.c:789:45: warning: signed and unsigned type in conditional expression [-Wsign-compare]
           end = i < k? strtol(s + i, &ep, 10) : val->len;
                                               ^
  htslib/faidx.c:801:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (beg >= val->len) beg = val->len;
               ^
  htslib/faidx.c:802:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (end >= val->len) end = val->len;
               ^
  htslib/faidx.c: In function ‘faidx_adjust_position’:
  htslib/faidx.c:882:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       else if(val->len <= *p_beg_i)
                        ^
  htslib/faidx.c:887:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       else if(val->len <= *p_end_i)
                        ^
  gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/hfile.c -o build/temp.linux-x86_64-3.7/htslib/hfile.o
  In file included from htslib/hfile.c:36:0:
  htslib/htslib/hfile.h: In function ‘hwrite’:
  htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (fp->limit - fp->begin < nbytes){
                                     ^
  In file included from htslib/hfile_internal.h:32:0,
                   from htslib/hfile.c:37:
  htslib/textutils_internal.h: At top level:
  htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   hts_json_token * hts_json_alloc_token();
   ^
  htslib/hfile.c: In function ‘hfile_set_blksize’:
  htslib/hfile.c:200:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (bufsiz < curr_used)
                  ^
  htslib/hfile.c: In function ‘hseek’:
  htslib/hfile.c:436:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (offset > 0 || -offset > length) {
                                     ^
  In file included from htslib/htslib/hts.h:35:0,
                   from htslib/hts_internal.h:29,
                   from htslib/hfile.c:737:
  htslib/htslib/hts_log.h: At top level:
  htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   enum htsLogLevel hts_get_log_level();
        ^
  htslib/hfile.c:874:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   static void hfile_exit()
               ^
  htslib/hfile.c:934:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   static void load_hfile_plugins()
               ^
  htslib/hfile.c: In function ‘find_scheme_handler’:
  htslib/hfile.c:1004:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < sizeof scheme; i++)
                     ^
  htslib/hfile.c:1011:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       if (i <= 1 || i >= sizeof scheme) return NULL;
                       ^
  gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/hfile_gcs.c -o build/temp.linux-x86_64-3.7/htslib/hfile_gcs.o
  In file included from htslib/htslib/hts.h:35:0,
                   from htslib/hfile_gcs.c:33:
  htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   enum htsLogLevel hts_get_log_level();
        ^
  In file included from htslib/hfile_internal.h:30:0,
                   from htslib/hfile_gcs.c:35:
  htslib/htslib/hfile.h: In function ‘hwrite’:
  htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (fp->limit - fp->begin < nbytes){
                                     ^
  In file included from htslib/hfile_internal.h:32:0,
                   from htslib/hfile_gcs.c:35:
  htslib/textutils_internal.h: At top level:
  htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   hts_json_token * hts_json_alloc_token();
   ^
  gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/hfile_libcurl.c -o build/temp.linux-x86_64-3.7/htslib/hfile_libcurl.o
  In file included from htslib/hfile_internal.h:30:0,
                   from htslib/hfile_libcurl.c:37:
  htslib/htslib/hfile.h: In function ‘hwrite’:
  htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
           if (fp->limit - fp->begin < nbytes){
                                     ^
  In file included from htslib/hfile_internal.h:32:0,
                   from htslib/hfile_libcurl.c:37:
  htslib/textutils_internal.h: At top level:
  htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   hts_json_token * hts_json_alloc_token();
   ^
  In file included from htslib/htslib/hts.h:35:0,
                   from htslib/hfile_libcurl.c:41:
  htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
   enum htsLogLevel hts_get_log_level();
        ^
  htslib/hfile_libcurl.c:45:23: fatal error: curl/curl.h: No such file or directory
   #include <curl/curl.h>
                         ^
  compilation terminated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for cyvcf2
  Running setup.py clean for cyvcf2
Failed to build cyvcf2
Installing collected packages: cyvcf2
  Running setup.py install for cyvcf2 ... error
    ERROR: Command errored out with exit status 1:
     command: /home/caiyd/Dell_cyd/Software/anaconda/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uhj_v8np/cyvcf2/setup.py'"'"'; __file__='"'"'/tmp/pip-install-uhj_v8np/cyvcf2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-oiw_7fdn/install-record.txt --single-version-externally-managed --compile
         cwd: /tmp/pip-install-uhj_v8np/cyvcf2/
    Complete output (501 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.7
    creating build/lib.linux-x86_64-3.7/cyvcf2
    copying cyvcf2/__init__.py -> build/lib.linux-x86_64-3.7/cyvcf2
    copying cyvcf2/__main__.py -> build/lib.linux-x86_64-3.7/cyvcf2
    copying cyvcf2/cli.py -> build/lib.linux-x86_64-3.7/cyvcf2
    creating build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/__init__.py -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test_cli.py -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test_hemi.py -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test_reader.py -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    running egg_info
    writing cyvcf2.egg-info/PKG-INFO
    writing dependency_links to cyvcf2.egg-info/dependency_links.txt
    writing entry points to cyvcf2.egg-info/entry_points.txt
    writing requirements to cyvcf2.egg-info/requires.txt
    writing top-level names to cyvcf2.egg-info/top_level.txt
    reading manifest file 'cyvcf2.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
    copying cyvcf2/cyvcf2.c -> build/lib.linux-x86_64-3.7/cyvcf2
    copying cyvcf2/cyvcf2.pxd -> build/lib.linux-x86_64-3.7/cyvcf2
    copying cyvcf2/cyvcf2.pyx -> build/lib.linux-x86_64-3.7/cyvcf2
    copying cyvcf2/helpers.c -> build/lib.linux-x86_64-3.7/cyvcf2
    copying cyvcf2/helpers.h -> build/lib.linux-x86_64-3.7/cyvcf2
    copying cyvcf2/relatedness.h -> build/lib.linux-x86_64-3.7/cyvcf2
    copying cyvcf2/tests/__init__.pyc -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/bug.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/decomposed.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/empty.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/issue_44.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/no-seq-len.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/no-seq-names.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/o.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/seg.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test-diff.csi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test-format-string.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test-haploidX.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test-hemi.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test.bug.117.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test.snpeff.bcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test.snpeff.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test_cli.pyc -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test_hemi.pyc -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    copying cyvcf2/tests/test_reader.pyc -> build/lib.linux-x86_64-3.7/cyvcf2/tests
    running build_ext
    skipping 'cyvcf2/cyvcf2.c' Cython extension (up-to-date)
    building 'cyvcf2.cyvcf2' extension
    creating build/temp.linux-x86_64-3.7
    creating build/temp.linux-x86_64-3.7/cyvcf2
    creating build/temp.linux-x86_64-3.7/htslib
    creating build/temp.linux-x86_64-3.7/htslib/cram
    gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c cyvcf2/cyvcf2.c -o build/temp.linux-x86_64-3.7/cyvcf2/cyvcf2.o
    In file included from /home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
                     from /home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                     from /home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from cyvcf2/cyvcf2.c:599:
    /home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/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]
     #warning "Using deprecated NumPy API, disable it with " \
      ^
    In file included from htslib/htslib/hts.h:35:0,
                     from htslib/htslib/vcf.h:39,
                     from cyvcf2/helpers.h:1,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     enum htsLogLevel hts_get_log_level();
          ^
    In file included from htslib/htslib/vcf.h:42:0,
                     from cyvcf2/helpers.h:1,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/hts_endian.h: In function ‘le_to_i32’:
    htslib/htslib/hts_endian.h:245:32: warning: signed and unsigned type in conditional expression [-Wsign-compare]
         return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1;
                                    ^
    htslib/htslib/hts_endian.h: In function ‘le_to_i64’:
    htslib/htslib/hts_endian.h:257:17: warning: signed and unsigned type in conditional expression [-Wsign-compare]
                 ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1);
                     ^
    In file included from cyvcf2/cyvcf2.c:604:0:
    htslib/htslib/hfile.h: In function ‘hwrite’:
    htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (fp->limit - fp->begin < nbytes){
                                       ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_4add_to_header’:
    cyvcf2/cyvcf2.c:7934:3: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2);
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:443:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_append(bcf_hdr_t *h, const char *line);
             ^
    cyvcf2/cyvcf2.c:7976:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_sync(bcf_hdr_t *h);
             ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_12set_samples’:
    cyvcf2/cyvcf2.c:8492:3: warning: passing argument 1 of ‘bcf_hdr_set_samples’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_6), 0);
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:315:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file);
             ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_14update’:
    cyvcf2/cyvcf2.c:8790:3: warning: passing argument 1 of ‘bcf_hdr_append’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4);
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:443:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_append(bcf_hdr_t *h, const char *line);
             ^
    cyvcf2/cyvcf2.c:8843:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_sync(bcf_hdr_t *h);
             ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_20generator’:
    cyvcf2/cyvcf2.c:9263:3: warning: passing argument 4 of ‘hts_itr_querys’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __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);
       ^
    In file included from htslib/htslib/vcf.h:39:0,
                     from cyvcf2/helpers.h:1,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/hts.h:675:16: note: expected ‘void *’ but argument is of type ‘const struct bcf_hdr_t *’
         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);
                    ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_gb_6cyvcf2_6cyvcf2_3VCF_26generator2’:
    cyvcf2/cyvcf2.c:10548:5: warning: passing argument 2 of ‘__pyx_f_6cyvcf2_6cyvcf2_newHREC’ discards ‘const’ qualifier from pointer target type [enabled by default]
         __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)
         ^
    cyvcf2/cyvcf2.c:2913:61: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
     static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/
                                                                 ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_37__dealloc__’:
    cyvcf2/cyvcf2.c:12204:5: warning: passing argument 1 of ‘bcf_hdr_destroy’ discards ‘const’ qualifier from pointer target type [enabled by default]
         bcf_hdr_destroy(__pyx_v_self->hdr);
         ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:261:10: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         void bcf_hdr_destroy(bcf_hdr_t *h);
              ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_10raw_header___get__’:
    cyvcf2/cyvcf2.c:12685:3: warning: ‘bcf_hdr_fmt_text’ is deprecated (declared at htslib/htslib/vcf.h:439): use bcf_hdr_format() instead [-Wdeprecated-declarations]
       __pyx_v_s = bcf_hdr_fmt_text(__pyx_v_self->hdr, 0, (&__pyx_v_hlen));
       ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’:
    cyvcf2/cyvcf2.c:12979:18: warning: assignment from incompatible pointer type [enabled by default]
       __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
                      ^
    cyvcf2/cyvcf2.c:13088:7: warning: passing argument 4 of ‘hts_idx_seqnames’ discards ‘const’ qualifier from pointer target type [enabled by default]
           __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
           ^
    In file included from htslib/htslib/vcf.h:39:0,
                     from cyvcf2/helpers.h:1,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/hts.h:677:18: note: expected ‘void *’ but argument is of type ‘const struct bcf_hdr_t *’
         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
                      ^
    cyvcf2/cyvcf2.c:13088:22: warning: assignment from incompatible pointer type [enabled by default]
           __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
                          ^
    cyvcf2/cyvcf2.c:13171:22: warning: assignment from incompatible pointer type [enabled by default]
           __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
                          ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8gt_bases___get__’:
    cyvcf2/cyvcf2.c:24200:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_5; __pyx_t_2+=1) {
                                     ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FORMAT___get__’:
    cyvcf2/cyvcf2.c:26211:17: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
         __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id);
                     ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_3ALT___get__’:
    cyvcf2/cyvcf2.c:33773:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (__pyx_t_4 = 1; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
                                     ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6is_snp___get__’:
    cyvcf2/cyvcf2.c:34038:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
                                     ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_8is_indel___get__’:
    cyvcf2/cyvcf2.c:34252:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (__pyx_t_9 = 1; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
                                     ^
    cyvcf2/cyvcf2.c:34310:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         __pyx_t_2 = ((__pyx_t_3 != __pyx_t_6) != 0);
                                 ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_7Variant_6FILTER_2__set__’:
    cyvcf2/cyvcf2.c:36422:13: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_v_h = __pyx_t_6;
                 ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_4INFO_12__next__’:
    cyvcf2/cyvcf2.c:39465:16: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key);
                    ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_f_6cyvcf2_6cyvcf2_newVariant’:
    cyvcf2/cyvcf2.c:40448:18: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_v_i->hdr = __pyx_t_4;
                      ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer___init__’:
    cyvcf2/cyvcf2.c:41102:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
       (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr));
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_sync(bcf_hdr_t *h);
             ^
    cyvcf2/cyvcf2.c:41130:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
       (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_sync(bcf_hdr_t *h);
             ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_2from_string’:
    cyvcf2/cyvcf2.c:41457:3: warning: passing argument 1 of ‘bcf_hdr_parse’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_t_2 = ((bcf_hdr_parse(__pyx_v_self->__pyx_base.hdr, __pyx_t_7) != 0) != 0);
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:478:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt);
             ^
    cyvcf2/cyvcf2.c:41493:3: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __pyx_t_2 = ((bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr) != 0) != 0);
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_sync(bcf_hdr_t *h);
             ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_6write_header’:
    cyvcf2/cyvcf2.c:41871:3: warning: passing argument 2 of ‘bcf_hdr_write’ discards ‘const’ qualifier from pointer target type [enabled by default]
       (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.hts, __pyx_v_self->__pyx_base.hdr));
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:320:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h);
             ^
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_6Writer_8write_record’:
    cyvcf2/cyvcf2.c:42043:5: warning: passing argument 1 of ‘bcf_hdr_add_hrec’ discards ‘const’ qualifier from pointer target type [enabled by default]
         __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0);
         ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:482:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
             ^
    cyvcf2/cyvcf2.c:42081:5: warning: passing argument 1 of ‘bcf_hdr_sync’ discards ‘const’ qualifier from pointer target type [enabled by default]
         (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
         ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:479:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_hdr_sync(bcf_hdr_t *h);
             ^
    cyvcf2/cyvcf2.c:42140:3: warning: passing argument 2 of ‘bcf_write’ discards ‘const’ qualifier from pointer target type [enabled by default]
       __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)
       ^
    In file included from cyvcf2/helpers.h:1:0,
                     from cyvcf2/cyvcf2.c:602:
    htslib/htslib/vcf.h:370:9: note: expected ‘struct bcf_hdr_t *’ but argument is of type ‘const struct bcf_hdr_t *’
         int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v);
             ^
    cyvcf2/cyvcf2.c: At top level:
    cyvcf2/cyvcf2.c:6618:18: warning: ‘__pyx_f_6cyvcf2_6cyvcf2_xstr’ defined but not used [-Wunused-function]
     static PyObject *__pyx_f_6cyvcf2_6cyvcf2_xstr(PyObject *__pyx_v_s) {
                      ^
    gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/bcf_sr_sort.c -o build/temp.linux-x86_64-3.7/htslib/bcf_sr_sort.o
    In file included from htslib/htslib/hts.h:35:0,
                     from htslib/htslib/synced_bcf_reader.h:59,
                     from htslib/bcf_sr_sort.h:37,
                     from htslib/bcf_sr_sort.c:29:
    htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     enum htsLogLevel hts_get_log_level();
          ^
    In file included from htslib/htslib/vcf.h:42:0,
                     from htslib/htslib/synced_bcf_reader.h:60,
                     from htslib/bcf_sr_sort.h:37,
                     from htslib/bcf_sr_sort.c:29:
    htslib/htslib/hts_endian.h: In function ‘le_to_i32’:
    htslib/htslib/hts_endian.h:245:32: warning: signed and unsigned type in conditional expression [-Wsign-compare]
         return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1;
                                    ^
    htslib/htslib/hts_endian.h: In function ‘le_to_i64’:
    htslib/htslib/hts_endian.h:257:17: warning: signed and unsigned type in conditional expression [-Wsign-compare]
                 ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1);
                     ^
    htslib/bcf_sr_sort.c: In function ‘kbs_bitwise_or’:
    htslib/bcf_sr_sort.c:69:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (i=0; i<dst->n; i++) dst->b[i] |= src->b[i];
                    ^
    htslib/bcf_sr_sort.c: In function ‘bcf_sr_sort_set’:
    htslib/bcf_sr_sort.c:363:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (k=0; k < kh_end(hash); k++)
                     ^
    htslib/bcf_sr_sort.c:366:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (k=0; k < kh_end(hash); k++)
                     ^
    gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/bgzf.c -o build/temp.linux-x86_64-3.7/htslib/bgzf.o
    In file included from htslib/htslib/hts.h:35:0,
                     from htslib/bgzf.c:42:
    htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     enum htsLogLevel hts_get_log_level();
          ^
    In file included from htslib/bgzf.c:44:0:
    htslib/htslib/hfile.h: In function ‘hwrite’:
    htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (fp->limit - fp->begin < nbytes){
                                       ^
    In file included from htslib/bgzf.c:46:0:
    htslib/htslib/hts_endian.h: In function ‘le_to_i32’:
    htslib/htslib/hts_endian.h:245:32: warning: signed and unsigned type in conditional expression [-Wsign-compare]
         return v < 0x80000000U ? v : -((int32_t) (0xffffffffU - v)) - 1;
                                    ^
    htslib/htslib/hts_endian.h: In function ‘le_to_i64’:
    htslib/htslib/hts_endian.h:257:17: warning: signed and unsigned type in conditional expression [-Wsign-compare]
                 ? v : -((int64_t) (0xffffffffffffffffULL - v)) - 1);
                     ^
    htslib/bgzf.c: In function ‘bgzf_read’:
    htslib/bgzf.c:983:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while (bytes_read < length) {
                           ^
    htslib/bgzf.c:996:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             copy_length = length - bytes_read < available? length - bytes_read : available;
                                               ^
    htslib/bgzf.c:996:76: warning: signed and unsigned type in conditional expression [-Wsign-compare]
             copy_length = length - bytes_read < available? length - bytes_read : available;
                                                                                ^
    htslib/bgzf.c: In function ‘bgzf_mt_writer’:
    htslib/bgzf.c:1107:55: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (hwrite(fp->fp, j->comp_data, j->comp_len) != j->comp_len) {
                                                           ^
    htslib/bgzf.c: In function ‘bgzf_block_write’:
    htslib/bgzf.c:1594:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             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;
                                             ^
    htslib/bgzf.c:1602:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (fp->block_offset == ublock_size) {
                                  ^
    htslib/bgzf.c: In function ‘bgzf_useek’:
    htslib/bgzf.c:2049:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1;
                          ^
    htslib/bgzf.c:2050:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1;
                               ^
    gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/errmod.c -o build/temp.linux-x86_64-3.7/htslib/errmod.o
    In file included from htslib/htslib/hts.h:35:0,
                     from htslib/errmod.c:29:
    htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     enum htsLogLevel hts_get_log_level();
          ^
    gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/faidx.c -o build/temp.linux-x86_64-3.7/htslib/faidx.o
    In file included from htslib/faidx.c:40:0:
    htslib/htslib/hfile.h: In function ‘hwrite’:
    htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (fp->limit - fp->begin < nbytes){
                                       ^
    In file included from htslib/htslib/hts.h:35:0,
                     from htslib/hts_internal.h:29,
                     from htslib/faidx.c:43:
    htslib/htslib/hts_log.h: At top level:
    htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     enum htsLogLevel hts_get_log_level();
          ^
    In file included from htslib/hts_internal.h:31:0,
                     from htslib/faidx.c:43:
    htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     hts_json_token * hts_json_alloc_token();
     ^
    htslib/faidx.c: In function ‘fai_retrieve’:
    htslib/faidx.c:711:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         while ( l < end - beg && (c=bgzf_getc(fai->bgzf))>=0 )
                   ^
    htslib/faidx.c: In function ‘fai_get_val’:
    htslib/faidx.c:789:45: warning: signed and unsigned type in conditional expression [-Wsign-compare]
             end = i < k? strtol(s + i, &ep, 10) : val->len;
                                                 ^
    htslib/faidx.c:801:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (beg >= val->len) beg = val->len;
                 ^
    htslib/faidx.c:802:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (end >= val->len) end = val->len;
                 ^
    htslib/faidx.c: In function ‘faidx_adjust_position’:
    htslib/faidx.c:882:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         else if(val->len <= *p_beg_i)
                          ^
    htslib/faidx.c:887:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         else if(val->len <= *p_end_i)
                          ^
    gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/hfile.c -o build/temp.linux-x86_64-3.7/htslib/hfile.o
    In file included from htslib/hfile.c:36:0:
    htslib/htslib/hfile.h: In function ‘hwrite’:
    htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (fp->limit - fp->begin < nbytes){
                                       ^
    In file included from htslib/hfile_internal.h:32:0,
                     from htslib/hfile.c:37:
    htslib/textutils_internal.h: At top level:
    htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     hts_json_token * hts_json_alloc_token();
     ^
    htslib/hfile.c: In function ‘hfile_set_blksize’:
    htslib/hfile.c:200:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (bufsiz < curr_used)
                    ^
    htslib/hfile.c: In function ‘hseek’:
    htslib/hfile.c:436:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (offset > 0 || -offset > length) {
                                       ^
    In file included from htslib/htslib/hts.h:35:0,
                     from htslib/hts_internal.h:29,
                     from htslib/hfile.c:737:
    htslib/htslib/hts_log.h: At top level:
    htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     enum htsLogLevel hts_get_log_level();
          ^
    htslib/hfile.c:874:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     static void hfile_exit()
                 ^
    htslib/hfile.c:934:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     static void load_hfile_plugins()
                 ^
    htslib/hfile.c: In function ‘find_scheme_handler’:
    htslib/hfile.c:1004:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (i = 0; i < sizeof scheme; i++)
                       ^
    htslib/hfile.c:1011:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         if (i <= 1 || i >= sizeof scheme) return NULL;
                         ^
    gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/hfile_gcs.c -o build/temp.linux-x86_64-3.7/htslib/hfile_gcs.o
    In file included from htslib/htslib/hts.h:35:0,
                     from htslib/hfile_gcs.c:33:
    htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     enum htsLogLevel hts_get_log_level();
          ^
    In file included from htslib/hfile_internal.h:30:0,
                     from htslib/hfile_gcs.c:35:
    htslib/htslib/hfile.h: In function ‘hwrite’:
    htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (fp->limit - fp->begin < nbytes){
                                       ^
    In file included from htslib/hfile_internal.h:32:0,
                     from htslib/hfile_gcs.c:35:
    htslib/textutils_internal.h: At top level:
    htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     hts_json_token * hts_json_alloc_token();
     ^
    gcc -pthread -B /home/caiyd/Dell_cyd/Software/anaconda/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -I/home/caiyd/Dell_cyd/Software/anaconda/lib/python3.7/site-packages/numpy/core/include -I/home/caiyd/Dell_cyd/Software/anaconda/include/python3.7m -c htslib/hfile_libcurl.c -o build/temp.linux-x86_64-3.7/htslib/hfile_libcurl.o
    In file included from htslib/hfile_internal.h:30:0,
                     from htslib/hfile_libcurl.c:37:
    htslib/htslib/hfile.h: In function ‘hwrite’:
    htslib/htslib/hfile.h:245:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             if (fp->limit - fp->begin < nbytes){
                                       ^
    In file included from htslib/hfile_internal.h:32:0,
                     from htslib/hfile_libcurl.c:37:
    htslib/textutils_internal.h: At top level:
    htslib/textutils_internal.h:68:1: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     hts_json_token * hts_json_alloc_token();
     ^
    In file included from htslib/htslib/hts.h:35:0,
                     from htslib/hfile_libcurl.c:41:
    htslib/htslib/hts_log.h:52:6: warning: function declaration isn’t a prototype [-Wstrict-prototypes]
     enum htsLogLevel hts_get_log_level();
          ^
    htslib/hfile_libcurl.c:45:23: fatal error: curl/curl.h: No such file or directory
     #include <curl/curl.h>
                           ^
    compilation terminated.
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/caiyd/Dell_cyd/Software/anaconda/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-uhj_v8np/cyvcf2/setup.py'"'"'; __file__='"'"'/tmp/pip-install-uhj_v8np/cyvcf2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-oiw_7fdn/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.

[brentp]

hi, you'll need to have at least libcurl, libz, liblzma on your system. Looks like it's not finding libcurl in this case.