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Can't use cyvcf2 against AWS S3 #174

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alanwilter opened this issue Oct 26, 2020 · 28 comments
Open

Can't use cyvcf2 against AWS S3 #174

alanwilter opened this issue Oct 26, 2020 · 28 comments

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@alanwilter
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We started with issue #154 and thought that would have addressed our issues but, alas, setting a index in AWS S3 does not solve the problem.

import os
import boto3
from cyvcf2 import VCF
from dotenv import load_dotenv

load_dotenv(dotenv_path="private.env")

variant_id = '22-38212762-A-G'

chrom, pos, ref, alt, = variant_id.split('-')
pos = int(pos)

s3 = boto3.client('s3', aws_secret_access_key=os.environ['VCF_S3_SECRET'],
                  aws_access_key_id=os.environ['VCF_S3_KEY'],
                  region_name="eu-west-2",
                  config=boto3.session.Config(signature_version='s3v4'))

vcf_s3 = s3.generate_presigned_url('get_object', Params={'Bucket': 'my_bucket', 'Key': 'afile.vcf.gz'}, ExpiresIn=5000)
vcf_index = s3.generate_presigned_url('get_object', Params={'Bucket': 'my_bucket', 'Key': 'afile.vcf.gz.tbi'}, ExpiresIn=5000)

vcfs3 = VCF(vcf_s3)
vcfs3.set_index(vcf_index)

v_s3 = vcfs3("%s:%i-%i" % (chrom, pos-1,pos))
v3 = next(v_s3)

[E::hts_idx_load3] Could not load local index file ''
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-6-7fed85ced56d> in <module>
----> 1 v3 = next(v_s3)

/usr/local/Caskroom/miniconda/base/envs/cyvcf2/lib/python3.7/site-packages/cyvcf2/cyvcf2.pyx in __call__()

AssertionError: error loading tabix index for b'https://my_bucket.s3.amazonaws.com/afile.vcf.gz?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAJB5WHD7JFTU4RSJA%2F20201026%2Feu-west-2%2Fs3%2Faws4_request&X-Amz-Date=20201026T122250Z&X-Amz-Expires=5000&X-Amz-SignedHeaders=host&X-Amz-Signature=77299f7d86ec30378a539f68795f219506558fe3b6b773d209575e9709e994a5'
@brentp
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brentp commented Oct 27, 2020

you might need to build your own htslib, instead of using the one that cyvcf2 builds for you. I'm not sure it has everything to support S3 access (curl + ?).

@alanwilter
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I'm using Conda to manage my packages. I use Pysam and its version 0.16.0.1 fails in a similar way, so I'm using 0.15.4.
Ironically, we were not only trying with CyVCF2 for its speed, but also to get rid of pysam for it's unreliable.
But now I'm starting to understand that the problem is actually elsewhere. I will see what I can do with htslib and curl.

@brentp
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brentp commented Oct 28, 2020

@ccwang002 , do you know the best way to do this? (assuming it's related to the compilation of htslib included with cyvcf2)

@ccwang002
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ccwang002 commented Oct 28, 2020

The bioconda version of cyvcf2 links to the conda-wide htslib, which implements the file access using different protocols (HTTP, AWS S3, and etc). This conda-wide htstlib compiles all the supported protocols (see bioconda's htslib meta.yaml and build.sh, and htslib's INSTALL for general instructions).

Unfortunately, I think the current htsilb build is a bit broken on macOS (I ran into issues like bioconda/bioconda-recipes#15415), and I am not sure if it's the reason that breaks the S3 function. Since the latest version of htstlib is 1.11 and cyvcf2 is on 1.10, I will investigate it a bit more and try to fill a issue/PR to fix the older version build upstream.

Do you have a publicly available VCF on S3 that I can test? This will help me dissect the problems.

I will put down some notes here how to locally build cyvcf2 and htslib in the next comment.

@ccwang002
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Meanwhile, you can try to build cyvcf2 and htslib locally following the README's instruction to install from GitHub source:

git clone --recursive https://github.com/brentp/cyvcf2
cd cyvcf2/htslib
autoheader
autoconf
# See htslib's INSTALL to add any other relevant flags
./configure  --enable-libcurl --with-libdeflate --enable-plugins --enable-gcs --enable-s3
make

cd ..
pip install -r requirements.txt
CYTHONIZE=1 pip install -e .

This approach requires all the external dependencies to be manually installed before the compilation. It might fail if any dependency is not found. Happy to look at the error message together if any.

@ccwang002
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ccwang002 commented Oct 28, 2020

Regarding the conda-based installation, an easy way to test if this issue is related to cyvcf2 is to install bcftools in the same environment, since both of them links to the same htslib:

$ conda create -n cyvcf2 python=3.8 cyvcf2 bcftools=1.10 htslib=1.10
$ conda activate cyvcf2
$ bcftools view -h https://github.com/brentp/cyvcf2/raw/master/cyvcf2/tests/test.vcf.gz | head -n 2
[E::idx_test_and_fetch] Format of index file 'https://github.com/brentp/cyvcf2/raw/master/cyvcf2/tests/test.vcf.gz.tbi' is not supported
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
>>> from cyvcf2 import VCF
>>> v = VCF('https://github.com/brentp/cyvcf2/raw/master/cyvcf2/tests/test.vcf.gz')
v[E::idx_test_and_fetch] Format of index file 'https://github.com/brentp/cyvcf2/raw/master/cyvcf2/tests/test.vcf.gz.tbi' is not supported    
>>> v.raw_header.splitlines()[:2]
['##fileformat=VCFv4.1', '##FILTER=<ID=PASS,Description="All filters passed">']

@brentp
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brentp commented Oct 28, 2020

thank you @ccwang002 !

@alanwilter
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alanwilter commented Oct 28, 2020

I haven't build anything yet, just using CONDA so far, but I created an example using a public VCF file in S3

aws s3 ls s3://3kricegenome/test/test.vcf.gz

Using PySAM with S3

import boto3
import botocore
import pysam
from botocore.client import Config

config = Config(signature_version=botocore.UNSIGNED)

s3 = boto3.client('s3', config=config)

vcf_index = s3.generate_presigned_url('get_object', Params={'Bucket': '3kricegenome', 'Key': 'test/test.vcf.gz.tbi'}, ExpiresIn=5000)
vcf_file = s3.generate_presigned_url('get_object', Params={'Bucket': '3kricegenome', 'Key': 'test/test.vcf.gz'}, ExpiresIn=5000)

variant_file = pysam.VariantFile(vcf_file, index_filename=vcf_index)
vsam = variant_file.fetch('9311_chr01', 1009, 1010)
v = next(vsam)
print(dict(v.info))

{'AN': 2, 'DP': 10, 'MQ': 29.079999923706055, 'MQ0': 0}
# Worked as expected

Using CyVCF2 with local file (downloaded from the S3 bucket)

from cyvcf2 import VCF
variant_file = VCF("test.vcf.gz")
variant_file.set_index(index_path = "test.vcf.gz.tbi")
for v in variant_file('9311_chr01:1010-1020'):
  print(str(v))
  
vv = variant_file('9311_chr01:1010-1020')
v = next(vv)
print(dict(v.INFO))
...
{'AN': 2, 'DP': 10, 'MQ': 29.079999923706055, 'MQ0': 0}
# Worked as expected

Using CyVCF2 with S3

import boto3
import botocore
from cyvcf2 import VCF
from botocore.client import Config

config = Config(signature_version=botocore.UNSIGNED)

s3 = boto3.client('s3', config=config)

vcf_index = s3.generate_presigned_url('get_object', Params={'Bucket': '3kricegenome', 'Key': 'test/test.vcf.gz.tbi'}, ExpiresIn=5000)
vcf_file = s3.generate_presigned_url('get_object', Params={'Bucket': '3kricegenome', 'Key': 'test/test.vcf.gz'}, ExpiresIn=5000)

vcfs3 = VCF(vcf_file)
vcfs3.set_index(vcf_index)

for v in vcfs3('9311_chr01:1010-1020'):
  print(str(v))
# does nothing

v = vcfs3('9311_chr01:1010-1020')
next(v)

---------------------------------------------------------------------------
StopIteration                             Traceback (most recent call last)
<ipython-input-7-460873294da3> in <module>
      1 v = vcfs3('9311_chr01:1010-1020')
----> 2 next(v)

StopIteration:

Note that here the behaviour is different from when I tried with a private S3 (see my first post)

@brentp
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brentp commented Oct 28, 2020

I followed the instructions of @ccwang002 above and was able to run cyvcf2 on your final example and see the variants printed.

There's probably some what to incorporate this into the build process. But probably simplest is to include necessary flags (--enable-s3 ) in the bioconda recipe.

@alanwilter
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alanwilter commented Oct 29, 2020

I did in my docker container (using a slim Debian Buster) and all worked as expected. However, I'm using version 0.10.4 (from Dec 18).

I feel ashamed that I may have be lured all this time by this issue being essentially on macOS. Yet, for development, I will need to get it working on my mac.
I'm closing this issue. Thank you all.

@alanwilter
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alanwilter commented Oct 31, 2020

I'm lost, whatever I've tried, haven't work on my Mac so far.
python and pip are from Conda.
I'm trying @ccwang002 suggestion with few alterations:

#For compilers to find openssl you may need to set:
export LDFLAGS="-L/usr/local/opt/openssl/lib"
export CPPFLAGS="-I/usr/local/opt/openssl/include"

#For pkg-config to find openssl you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/openssl/lib/pkgconfig"

# Buggy Accelerate Backend on Mac https://github.com/numpy/numpy/issues/15947
OPENBLAS="$(brew --prefix openblas)" pip install -U --no-cache-dir --force-reinstall --ignore-installed --no-binary :all: cython numpy coloredlogs click

brew install libdeflate autoconf

git clone --recursive https://github.com/brentp/cyvcf2
cd cyvcf2/htslib
autoheader
autoconf
# See htslib's INSTALL to add any other relevant flags
./configure  --enable-libcurl --with-libdeflate --enable-plugins --enable-gcs --enable-s3
make
#make test

cd ..
pip install -r requirements.txt
CYTHONIZE=1 pip install -e .
and I got this long error message:
CYTHONIZE=1 pip install -e .
Obtaining file:///Users/alan/Programmes/cyvcf2
Requirement already satisfied: numpy in /usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages (from cyvcf2==0.20.9) (1.19.3)
Requirement already satisfied: coloredlogs in /usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages (from cyvcf2==0.20.9) (14.0)
Requirement already satisfied: click in /usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages (from cyvcf2==0.20.9) (7.1.2)
Requirement already satisfied: humanfriendly>=7.1 in /usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages (from coloredlogs->cyvcf2==0.20.9) (8.2)
Installing collected packages: cyvcf2
  Running setup.py develop for cyvcf2
    ERROR: Command errored out with exit status 1:
     command: /usr/local/Caskroom/miniconda/base/bin/python3.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/alan/Programmes/cyvcf2/setup.py'"'"'; __file__='"'"'/Users/alan/Programmes/cyvcf2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
         cwd: /Users/alan/Programmes/cyvcf2/
    Complete output (352 lines):
    running develop
    running egg_info
    creating cyvcf2.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
    writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
    reading manifest file 'cyvcf2.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
    running build_ext
    building 'cyvcf2.cyvcf2' extension
    creating build
    creating build/temp.macosx-10.9-x86_64-3.7
    creating build/temp.macosx-10.9-x86_64-3.7/cyvcf2
    creating build/temp.macosx-10.9-x86_64-3.7/htslib
    creating build/temp.macosx-10.9-x86_64-3.7/htslib/cram
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c cyvcf2/cyvcf2.c -o build/temp.macosx-10.9-x86_64-3.7/cyvcf2/cyvcf2.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    In file included from cyvcf2/cyvcf2.c:697:
    In file included from /usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
    In file included from /usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
    In file included from /usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
    /usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
    #warning "Using deprecated NumPy API, disable it with " \
     ^
    cyvcf2/cyvcf2.c:9068:32: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2);
                                   ^~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:561:35: note: passing argument to parameter 'h' here
        int bcf_hdr_append(bcf_hdr_t *h, const char *line);
                                      ^
    cyvcf2/cyvcf2.c:9110:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
                                 ^~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
        int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                    ^
    cyvcf2/cyvcf2.c:9677:37: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_5), 0);
                                        ^~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:342:40: note: passing argument to parameter 'hdr' here
        int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file) HTS_RESULT_USED;
                                           ^
    cyvcf2/cyvcf2.c:9981:32: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4);
                                   ^~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:561:35: note: passing argument to parameter 'h' here
        int bcf_hdr_append(bcf_hdr_t *h, const char *line);
                                      ^
    cyvcf2/cyvcf2.c:10034:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
                                 ^~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
        int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                    ^
    cyvcf2/cyvcf2.c:10581:34: warning: passing 'const bcf_hdr_t *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __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);
                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:1123:102: note: expanded from macro 'bcf_itr_querys'
        #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec)
                                                                                                         ^~~~~
    htslib/htslib/hts.h:1074:93: note: passing argument to parameter 'hdr' here
    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:11927:134: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
        __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, 484, __pyx_L1_error)
                                                                                                                                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    cyvcf2/cyvcf2.c:3070:118: note: passing argument to parameter here
    static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/
                                                                                                                         ^
    cyvcf2/cyvcf2.c:13501:21: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
        bcf_hdr_destroy(__pyx_v_self->hdr);
                        ^~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:271:37: note: passing argument to parameter 'h' here
        void bcf_hdr_destroy(bcf_hdr_t *h);
                                        ^
    cyvcf2/cyvcf2.c:14362:18: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    cyvcf2/cyvcf2.c:14471:24: warning: passing 'const bcf_hdr_t *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
          __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
                           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:1140:111: note: expanded from macro 'bcf_index_seqnames'
        #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr))
                                                                                                                  ^~~~~
    htslib/htslib/hts.h:1097:88: note: passing argument to parameter 'hdr' here
    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:14471:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
          __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
                         ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    cyvcf2/cyvcf2.c:14554:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
          __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
                         ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    cyvcf2/cyvcf2.c:28103:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
        __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id);
                    ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    cyvcf2/cyvcf2.c:39064:13: warning: assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_h = __pyx_t_6;
                ^ ~~~~~~~~~
    cyvcf2/cyvcf2.c:42196:16: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key);
                   ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    cyvcf2/cyvcf2.c:43191:18: warning: assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_i->hdr = __pyx_t_4;
                     ^ ~~~~~~~~~
    cyvcf2/cyvcf2.c:43744:23: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr));
                          ^~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
        int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                    ^
    cyvcf2/cyvcf2.c:43772:23: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
        int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                    ^
    cyvcf2/cyvcf2.c:44355:31: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_t_3 = ((bcf_hdr_parse(__pyx_v_self->__pyx_base.hdr, __pyx_t_2) != 0) != 0);
                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:613:34: note: passing argument to parameter 'hdr' here
        int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt);
                                     ^
    cyvcf2/cyvcf2.c:44391:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_t_3 = ((bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr) != 0) != 0);
                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
        int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                    ^
    cyvcf2/cyvcf2.c:44770:65: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.__pyx_base.hts, __pyx_v_self->__pyx_base.hdr));
                                                                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:353:47: note: passing argument to parameter 'h' here
        int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h) HTS_RESULT_USED;
                                                  ^
    cyvcf2/cyvcf2.c:44948:36: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
        __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0);
                                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:638:37: note: passing argument to parameter 'hdr' here
        int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
                                        ^
    cyvcf2/cyvcf2.c:44986:25: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
        (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
                            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
        int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                    ^
    cyvcf2/cyvcf2.c:45045:87: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2365, __pyx_L1_error)
                                                                                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/htslib/vcf.h:419:43: note: passing argument to parameter 'h' here
        int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v) HTS_RESULT_USED;
                                              ^
    26 warnings generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/faidx.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/faidx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/vcfutils.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/vcfutils.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/hfile_s3_write.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_s3_write.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/regidx.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/regidx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/hts_os.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/hts_os.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/tbx.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/tbx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/probaln.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/probaln.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/kfunc.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/kfunc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/hfile_gcs.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_gcs.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/errmod.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/errmod.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/multipart.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/multipart.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/realn.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/realn.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/region.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/region.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/hfile_net.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_net.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/textutils.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/textutils.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/hts.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/hts.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/vcf_sweep.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/vcf_sweep.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/bcf_sr_sort.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/bcf_sr_sort.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/synced_bcf_reader.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/synced_bcf_reader.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/sam.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/sam.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/bgzf.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/bgzf.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/header.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/header.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/vcf.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/vcf.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/hfile_libcurl.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_libcurl.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/kstring.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/kstring.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/md5.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/md5.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/hfile_s3.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_s3.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/thread_pool.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/thread_pool.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    htslib/thread_pool.c:667:9: warning: code will never be executed [-Wunreachable-code]
            printf("%d waiting, %d running, %d output, %d, arun %d => %d\t", p->njobs,
            ^~~~~~
    htslib/thread_pool.c:666:9: note: silence by adding parentheses to mark code as explicitly dead
        if (0) {
            ^
            /* DISABLES CODE */ ( )
    2 warnings generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/hfile.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/knetfile.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/knetfile.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/rANS_static.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/rANS_static.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/cram_index.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_index.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/open_trace_file.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/open_trace_file.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/cram_external.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_external.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/mFILE.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/mFILE.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/cram_samtools.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_samtools.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/pooled_alloc.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/pooled_alloc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/string_alloc.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/string_alloc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/cram_codecs.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_codecs.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/cram_stats.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_stats.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/cram_encode.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_encode.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    htslib/cram/cram_encode.c:1727:13: warning: code will never be executed [-Wunreachable-code]
                cram_byte_array_len_encoder e;
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    htslib/cram/cram_encode.c:1717:13: note: silence by adding parentheses to mark code as explicitly dead
            if (1) {
                ^
                /* DISABLES CODE */ ( )
    htslib/cram/cram_encode.c:3045:24: warning: unused variable 'brg' [-Wunused-variable]
            sam_hrec_rg_t *brg = sam_hrecs_find_rg(fd->header->hrecs, "UNKNOWN");
                           ^
    htslib/cram/cram_encode.c:2874:40: warning: code will never be executed [-Wunreachable-code]
                                    int ol=l;
                                           ^
    htslib/cram/cram_encode.c:2871:33: note: silence by adding parentheses to mark code as explicitly dead
                                if (0 && CRAM_MAJOR_VERS(fd->version) >= 3) {
                                    ^
                                    /* DISABLES CODE */ ( )
    htslib/cram/cram_encode.c:2835:17: warning: code will never be executed [-Wunreachable-code]
                    int l;
                    ^~~~~~
    5 warnings generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/cram_io.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_io.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c htslib/cram/cram_decode.c -o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_decode.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    1 warning generated.
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/Caskroom/miniconda/base/include -arch x86_64 -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/usr/local/Caskroom/miniconda/base/lib/python3.7/site-packages/numpy/core/include -I/usr/local/Caskroom/miniconda/base/include/python3.7m -c cyvcf2/helpers.c -o build/temp.macosx-10.9-x86_64-3.7/cyvcf2/helpers.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
    cyvcf2/helpers.c:53:20: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
            else if((a == b)) {
                     ~~^~~~
    cyvcf2/helpers.c:53:20: note: remove extraneous parentheses around the comparison to silence this warning
            else if((a == b)) {
                    ~  ^   ~
    cyvcf2/helpers.c:53:20: note: use '=' to turn this equality comparison into an assignment
            else if((a == b)) {
                       ^~
                       =
    cyvcf2/helpers.c:110:21: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
            else if ((a == b)) {
                      ~~^~~~
    cyvcf2/helpers.c:110:21: note: remove extraneous parentheses around the comparison to silence this warning
            else if ((a == b)) {
                     ~  ^   ~
    cyvcf2/helpers.c:110:21: note: use '=' to turn this equality comparison into an assignment
            else if ((a == b)) {
                        ^~
                        =
    3 warnings generated.
    creating build/lib.macosx-10.9-x86_64-3.7
    creating build/lib.macosx-10.9-x86_64-3.7/cyvcf2
    gcc -bundle -undefined dynamic_lookup -L/usr/local/Caskroom/miniconda/base/lib -arch x86_64 -L/usr/local/Caskroom/miniconda/base/lib -arch x86_64 -L/usr/local/opt/openssl/lib -I/usr/local/opt/openssl/include -arch x86_64 build/temp.macosx-10.9-x86_64-3.7/cyvcf2/cyvcf2.o build/temp.macosx-10.9-x86_64-3.7/htslib/faidx.o build/temp.macosx-10.9-x86_64-3.7/htslib/vcfutils.o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_s3_write.o build/temp.macosx-10.9-x86_64-3.7/htslib/regidx.o build/temp.macosx-10.9-x86_64-3.7/htslib/hts_os.o build/temp.macosx-10.9-x86_64-3.7/htslib/tbx.o build/temp.macosx-10.9-x86_64-3.7/htslib/probaln.o build/temp.macosx-10.9-x86_64-3.7/htslib/kfunc.o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_gcs.o build/temp.macosx-10.9-x86_64-3.7/htslib/errmod.o build/temp.macosx-10.9-x86_64-3.7/htslib/multipart.o build/temp.macosx-10.9-x86_64-3.7/htslib/realn.o build/temp.macosx-10.9-x86_64-3.7/htslib/region.o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_net.o build/temp.macosx-10.9-x86_64-3.7/htslib/textutils.o build/temp.macosx-10.9-x86_64-3.7/htslib/hts.o build/temp.macosx-10.9-x86_64-3.7/htslib/vcf_sweep.o build/temp.macosx-10.9-x86_64-3.7/htslib/bcf_sr_sort.o build/temp.macosx-10.9-x86_64-3.7/htslib/synced_bcf_reader.o build/temp.macosx-10.9-x86_64-3.7/htslib/sam.o build/temp.macosx-10.9-x86_64-3.7/htslib/bgzf.o build/temp.macosx-10.9-x86_64-3.7/htslib/header.o build/temp.macosx-10.9-x86_64-3.7/htslib/vcf.o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_libcurl.o build/temp.macosx-10.9-x86_64-3.7/htslib/kstring.o build/temp.macosx-10.9-x86_64-3.7/htslib/md5.o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_s3.o build/temp.macosx-10.9-x86_64-3.7/htslib/thread_pool.o build/temp.macosx-10.9-x86_64-3.7/htslib/hfile.o build/temp.macosx-10.9-x86_64-3.7/htslib/knetfile.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/rANS_static.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_index.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/open_trace_file.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_external.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/mFILE.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_samtools.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/pooled_alloc.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/string_alloc.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_codecs.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_stats.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_encode.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_io.o build/temp.macosx-10.9-x86_64-3.7/htslib/cram/cram_decode.o build/temp.macosx-10.9-x86_64-3.7/cyvcf2/helpers.o -lz -lbz2 -llzma -lcurl -lssl -o build/lib.macosx-10.9-x86_64-3.7/cyvcf2/cyvcf2.cpython-37m-darwin.so
    duplicate symbol '_hfile_plugin_init' in:
        build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_s3_write.o
        build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_gcs.o
    duplicate symbol '_hfile_plugin_init' in:
        build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_s3_write.o
        build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_libcurl.o
    duplicate symbol '_hfile_plugin_init' in:
        build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_s3_write.o
        build/temp.macosx-10.9-x86_64-3.7/htslib/hfile_s3.o
    ld: 3 duplicate symbols for architecture x86_64
    clang: error: linker command failed with exit code 1 (use -v to see invocation)
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/Caskroom/miniconda/base/bin/python3.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/alan/Programmes/cyvcf2/setup.py'"'"'; __file__='"'"'/Users/alan/Programmes/cyvcf2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.

@alanwilter alanwilter reopened this Oct 31, 2020
@alanwilter
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I've tried to sort this myself. I've created this patch:

diff --git a/hfile_gcs.c b/hfile_gcs.c
index e6f72ae..c757d84 100644
--- a/hfile_gcs.c
+++ b/hfile_gcs.c
@@ -116,7 +116,8 @@ static hFILE *gcs_vopen(const char *url, const char *mode_colon, va_list args0)
     return fp;
 }

-int PLUGIN_GLOBAL(hfile_plugin_init,_gcs)(struct hFILE_plugin *self)
+// int PLUGIN_GLOBAL(hfile_plugin_init,_gcs)(struct hFILE_plugin *self)
+int hfile_plugin_init_gcs(struct hFILE_plugin *self)
 {
     static const struct hFILE_scheme_handler handler =
         { gcs_open, hfile_always_remote, "Google Cloud Storage",
diff --git a/hfile_libcurl.c b/hfile_libcurl.c
index 235b4c1..bfacff5 100644
--- a/hfile_libcurl.c
+++ b/hfile_libcurl.c
@@ -1438,7 +1438,8 @@ static hFILE *vhopen_libcurl(const char *url, const char *modes, va_list args)
     return fp;
 }

-int PLUGIN_GLOBAL(hfile_plugin_init,_libcurl)(struct hFILE_plugin *self)
+// int PLUGIN_GLOBAL(hfile_plugin_init,_libcurl)(struct hFILE_plugin *self)
+int hfile_plugin_init_libcurl(struct hFILE_plugin *self)
 {
     static const struct hFILE_scheme_handler handler =
         { hopen_libcurl, hfile_always_remote, "libcurl",
diff --git a/hfile_s3.c b/hfile_s3.c
index 3f094d3..df10d27 100644
--- a/hfile_s3.c
+++ b/hfile_s3.c
@@ -1236,7 +1236,8 @@ static hFILE *s3_vopen(const char *url, const char *mode_colon, va_list args0)
     return fp;
 }

-int PLUGIN_GLOBAL(hfile_plugin_init,_s3)(struct hFILE_plugin *self)
+// int PLUGIN_GLOBAL(hfile_plugin_init,_s3)(struct hFILE_plugin *self)
+int hfile_plugin_init_s3(struct hFILE_plugin *self)
 {
     static const struct hFILE_scheme_handler handler =
         { s3_open, hfile_always_remote, "Amazon S3", 2000 + 50, s3_vopen
diff --git a/hfile_s3_write.c b/hfile_s3_write.c
index 9008622..d1ef808 100644
--- a/hfile_s3_write.c
+++ b/hfile_s3_write.c
@@ -832,8 +832,8 @@ static void s3_write_exit() {
 }


-int PLUGIN_GLOBAL(hfile_plugin_init,_s3_write)(struct hFILE_plugin *self) {
-
+// int PLUGIN_GLOBAL(hfile_plugin_init,_s3_write)(struct hFILE_plugin *self) {
+int hfile_plugin_init_s3_write(struct hFILE_plugin *self) {
     static const struct hFILE_scheme_handler handler =
         { hopen_s3_write, hfile_always_remote, "S3 Multipart Upload",
           2000 + 50, vhopen_s3_write

so I could get around the duplicate symbol issue in htslib (or so I wished).

It did compiled this time but when testing cyvcf2, I've got an error. See below the whole sequence I'm running:

conda create -n cyvcf2 python=3.9 -y
conda activate cyvcf2

brew install libdeflate autoconf

#For compilers to find openssl you may need to set:
export LDFLAGS="-L/usr/local/opt/openssl/lib"
export CPPFLAGS="-I/usr/local/opt/openssl/include"

#For pkg-config to find openssl you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/openssl/lib/pkgconfig"

# https://github.com/numpy/numpy/issues/15947
OPENBLAS="$(brew --prefix openblas)" pip install --no-binary :all: cython coloredlogs click
# in principal this was to install numpy but it's failing, so numpy is installed via wheel

git clone --recursive https://github.com/brentp/cyvcf2

cd cyvcf2/htslib
git apply ~/Programmes/patch2.diff
autoheader
autoconf
# See htslib's INSTALL to add any other relevant flags
./configure  --enable-libcurl --with-libdeflate --enable-plugins --enable-gcs --enable-s3
make test

All fine up to here

cd ..
pip install -r requirements.txt
# binary numpy 1.19.4 is installed

CYTHONIZE=1 pip install -e .

Obtaining file:///Users/alan/Programmes/cyvcf2
Requirement already satisfied: numpy in /usr/local/Caskroom/miniconda/base/envs/cyvcf2/lib/python3.9/site-packages (from cyvcf2==0.20.9) (1.19.4)
Requirement already satisfied: coloredlogs in /usr/local/Caskroom/miniconda/base/envs/cyvcf2/lib/python3.9/site-packages (from cyvcf2==0.20.9) (14.0)
Requirement already satisfied: click in /usr/local/Caskroom/miniconda/base/envs/cyvcf2/lib/python3.9/site-packages (from cyvcf2==0.20.9) (7.1.2)
Requirement already satisfied: humanfriendly>=7.1 in /usr/local/Caskroom/miniconda/base/envs/cyvcf2/lib/python3.9/site-packages (from coloredlogs->cyvcf2==0.20.9) (8.2)
Installing collected packages: cyvcf2
  Running setup.py develop for cyvcf2
Successfully installed cyvcf2

No error messages! Let's test:

python setup.py test
running test
WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
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'
running build_ext
copying build/lib.macosx-10.9-x86_64-3.9/cyvcf2/cyvcf2.cpython-39-darwin.so -> cyvcf2
/Users/alan/Programmes/cyvcf2/.eggs/nose-1.3.7-py3.9.egg/nose/config.py:264: RuntimeWarning: Option 'with-coverage' in config file 'setup.cfg' ignored: excluded by runtime environment
  warn(msg, RuntimeWarning)
Failure: ImportError (dlopen(/Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so, 2): Symbol not found: _close_plugin
  Referenced from: /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so
  Expected in: flat namespace
 in /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so) ... ERROR

======================================================================
ERROR: Failure: ImportError (dlopen(/Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so, 2): Symbol not found: _close_plugin
  Referenced from: /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so
  Expected in: flat namespace
 in /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/alan/Programmes/cyvcf2/.eggs/nose-1.3.7-py3.9.egg/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/Users/alan/Programmes/cyvcf2/.eggs/nose-1.3.7-py3.9.egg/nose/loader.py", line 417, in loadTestsFromName
    module = self.importer.importFromPath(
  File "/Users/alan/Programmes/cyvcf2/.eggs/nose-1.3.7-py3.9.egg/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/Users/alan/Programmes/cyvcf2/.eggs/nose-1.3.7-py3.9.egg/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/lib/python3.9/imp.py", line 244, in load_module
    return load_package(name, filename)
  File "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/lib/python3.9/imp.py", line 216, in load_package
    return _load(spec)
  File "<frozen importlib._bootstrap>", line 711, in _load
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 790, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/Users/alan/Programmes/cyvcf2/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: dlopen(/Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so, 2): Symbol not found: _close_plugin
  Referenced from: /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so
  Expected in: flat namespace
 in /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so

----------------------------------------------------------------------
Ran 1 test in 0.583s

FAILED (errors=1)
Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=1 errors=1 failures=0>

cyvcf2 was installed at /usr/local/Caskroom/miniconda/base/envs/cyvcf2/bin/cyvcf2
Running it:

Traceback (most recent call last):
  File "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/bin/cyvcf2", line 33, in <module>
    sys.exit(load_entry_point('cyvcf2', 'console_scripts', 'cyvcf2')())
  File "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/bin/cyvcf2", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/lib/python3.9/importlib/metadata.py", line 77, in load
    module = import_module(match.group('module'))
  File "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 972, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 790, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/Users/alan/Programmes/cyvcf2/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: dlopen(/Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so, 2): Symbol not found: _close_plugin
  Referenced from: /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so
  Expected in: flat namespace
 in /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so

Well, I wouldn't be surprised if this is because of my patch above but, alas, I'm desperate to get cyvcf2 to work with (private) S3 on a Mac.

I've tried many things. In one of my attempts, using conda packages, I got it to work with my open S3 example listed above, but when I tried with a private S3, it failed.

Could anyone, specially a mac user/developer, tell me which environment are you using to succeed with cyvcf2? Is it only brew? Are you sure it's working for you with a private S3?

@ccwang002
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ccwang002 commented Nov 4, 2020

Hi @alanwilter, I created a private S3 bucket and put your test file there. I was able to access the private S3 file. I think this is an issue regarding the S3 authentication, less likely related to with how cyvcf2 is built.

In fact, the current cyvcf2 from bioconda works on macOS. This is how I install my conda env: conda create -n cyvcf2 python=3.8 cyvcf2 bcftools=1.10 htslib=1.10. Don't use python 3.9 (not available on bioconda) or htslib 1.11 (not supported by cyvcf2).

I have two identical files on S3:

  • s3://cyvcf2-s3-test/test.vcf.gz[.tbi] (private on us-east-2)
  • s3://3kricegenome/test/test.vcf.gz[.tbi] (public)

The public VCF can be read by htslib (and thus also readable by cyvcf2)

$ htsfile -vv 's3://3kricegenome/test/test.vcf.gz' 
[D::init_add_plugin] Loaded "knetfile"
[D::init_add_plugin] Loaded "mem"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_s3.bundle"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_s3_write.bundle"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_libcurl.bundle"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_gcs.bundle"
s3://3kricegenome/test/test.vcf.gz:	VCF version 4.1 BGZF-compressed variant calling data
>>> from cyvcf2 import VCF
>>> v = VCF('s3://3kricegenome/test/test.vcf.gz')
next(v[E::idx_test_and_fetch] Format of index file 's3://3kricegenome/test/test.vcf.gz.tbi' is not supported
>>> next(v)
Variant(9311_chr01:1001 C/)

And the private VCF works too (on cyvcf2 as well):

$ export AWS_DEFAULT_REGION=us-east-2   # Set the region of the S3 file for htslib
$ htsfile -vv 's3://cyvcf2-s3-test/test.vcf.gz'
[D::init_add_plugin] Loaded "knetfile"
[D::init_add_plugin] Loaded "mem"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_s3.bundle"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_s3_write.bundle"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_libcurl.bundle"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_gcs.bundle"
s3://cyvcf2-s3-test/test.vcf.gz:	VCF version 4.1 BGZF-compressed variant calling data

As shown by htsfile's log message, which show how the VCFs are loaded by htslib and cyvcf2, the htslib S3 plugin is properly built and loaded. If I increase the verbose level by htsfile -vvvvv 's3://cyvcf2-s3-test/test.vcf.gz', you can see the detailed authentication requests:

Full output
[D::init_add_plugin] Loaded "knetfile"
[D::init_add_plugin] Loaded "mem"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_s3.bundle"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_s3_write.bundle"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_libcurl.bundle"
[D::init_add_plugin] Loaded "/Users/liang/miniconda3/envs/cyvcf2/libexec/htslib/hfile_gcs.bundle"
*   Trying 52.219.88.140:443...
* Connected to cyvcf2-s3-test.s3.amazonaws.com (52.219.88.140) port 443 (#0)
* ALPN, offering h2
* ALPN, offering http/1.1
* successfully set certificate verify locations:
*   CAfile: /Users/liang/miniconda3/envs/cyvcf2/ssl/cacert.pem
  CApath: none
* SSL connection using TLSv1.2 / ECDHE-RSA-AES128-GCM-SHA256
* ALPN, server did not agree to a protocol
* Server certificate:
*  subject: C=US; ST=Washington; L=Seattle; O=Amazon.com, Inc.; CN=*.s3.amazonaws.com
*  start date: Nov  9 00:00:00 2019 GMT
*  expire date: Mar 12 12:00:00 2021 GMT
*  subjectAltName: host "cyvcf2-s3-test.s3.amazonaws.com" matched cert's "*.s3.amazonaws.com"
*  issuer: C=US; O=DigiCert Inc; OU=www.digicert.com; CN=DigiCert Baltimore CA-2 G2
*  SSL certificate verify ok.
> GET /test.vcf.gz HTTP/1.1
Host: cyvcf2-s3-test.s3.amazonaws.com
User-Agent: htslib/1.10.2 libcurl/7.71.1
Accept: */*
Authorization: AWS4-HMAC-SHA256 Credential=AKIAY6KGQEGDKJGH3HUS/20201104/us-east-2/s3/aws4_request,SignedHeaders=host;x-amz-content-sha256;x-amz-date,Signature=cfccb0009f0b0ff9bd3e840da82862139ecc3773e8cc5a193b6b7cd2e81d4a53
x-amz-date: 20201104T175315Z
x-amz-content-sha256: e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855

* Mark bundle as not supporting multiuse
< HTTP/1.1 200 OK
< x-amz-id-2: CGLVCMQxKplno37FrpZoeEYkStoUmhJEEHgrmQ3XQ1grKr0bbFP0VzDFrl8FIwtHmHvZ1VtzUvE=
< x-amz-request-id: 889BDCFBB309596D
< Date: Wed, 04 Nov 2020 17:53:16 GMT
< Last-Modified: Wed, 04 Nov 2020 16:28:41 GMT
< ETag: "a8b866a51e7a2f2c45d05fc1f198ba89"
< Accept-Ranges: bytes
< Content-Type: application/x-gzip
< Content-Length: 588269
< Server: AmazonS3
< 
s3://cyvcf2-s3-test/test.vcf.gz:	VCF version 4.1 BGZF-compressed variant calling data
* Closing connection 0

htslib is able to detect my AWS credentials from ~/.aws/credentials.

To sum up,

  • If you cannot see the plugins being loaded (or both htsfile and cyvcf2 don't work) --> check the htslib compilation process
  • If htsfile works but cyvcf2 doesn't --> check the cyvcf2 build process (not an issue if you use bioconda)
  • If public S3 works but private S3 doesn't --> check the AWS config

Hope it helps.

@ccwang002
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I spent my whole morning testing this, and I found a related bug on htslib 1.11 (either from bioconda or compiled from source ), where none of the htslib plugins work on macOS. htslib 1.10 works fine. Will file a bug upstream.

@alanwilter
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alanwilter commented Nov 4, 2020

Thanks @ccwang002.

I've been spending days on it. I'm testing with tabix as well (via brew install htslib). I will check all again. I've tried to create another private S3 with a VCF that I know it works on my local mac so I can try with it from the S3.

So far I've got this awkward behaviour where the format is not identified:

I can't explain this:

$ htsfile -vv /Users/alan/Downloads/annotations/Fujinami2020.vcf.gz
/Users/alan/Downloads/annotations/Fujinami2020.vcf.gz:	VCF version 4.2 BGZF-compressed variant calling data

$ aws s3 cp /Users/alan/Downloads/annotations/Fujinami2020.vcf.gz s3://vcf-test/atest/
upload: Downloads/annotations/Fujinami2020.vcf.gz to s3://vcf-test/atest/Fujinami2020.vcf.gz

$ htsfile -vvvv s3://vcf-test/atest/Fujinami2020.vcf.gz
[D::init_add_plugin] Loaded "knetfile"
[D::init_add_plugin] Loaded "mem"
[D::init_add_plugin] Loaded "crypt4gh-needed"
[D::init_add_plugin] Loaded "libcurl"
[D::init_add_plugin] Loaded "gcs"
[D::init_add_plugin] Loaded "s3"
[D::init_add_plugin] Loaded "s3w"
s3://vcf-test/atest/Fujinami2020.vcf.gz:	unknown text

$ htsfile -vv s3://3kricegenome/test/test.vcf.gz
...
[D::init_add_plugin] Loaded "s3w"
s3://3kricegenome/test/test.vcf.gz:	VCF version 4.1 BGZF-compressed variant calling data

and hence, tabix does not work. I frankly don't know why the file in S3 is not recognised as a VCF while the public and my other private is recognised as VCF.

But later I will test using your steps.

@alanwilter
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I spent my whole morning testing this, and I found a related bug on htslib 1.11 (either from bioconda or compiled from source ), where none of the htslib plugins work on macOS. htslib 1.10 works fine. Will file a bug upstream.

I'm using brew and htslib version is 1.11 and that is working with the plugins.

@alanwilter
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Many thank @ccwang002

I got a workable solution and, no, conda did not work for me. I will stop nagging you guys, but conda is a dead end for me. Going back to the basic brew and python -m venv.

I tried with conda, got these packages installed:

bcftools           bioconda/osx-64::bcftools-1.10.2-h4c7ce49_3
htslib             bioconda/osx-64::htslib-1.10.2-h422799e_1
cyvcf2             bioconda/osx-64::cyvcf2-0.20.9-py38h8a9ad84_0

But when I run this:

htsfile -vv 's3://3kricegenome/test/test.vcf.gz'
[D::init_add_plugin] Loaded "knetfile"
[D::init_add_plugin] Loaded "mem"
[D::init_add_plugin] Loaded "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/libexec/htslib/hfile_s3.bundle"
[D::init_add_plugin] Loaded "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/libexec/htslib/hfile_s3_write.bundle"
[D::init_add_plugin] Loaded "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/libexec/htslib/hfile_libcurl.bundle"
[D::init_add_plugin] Loaded "/usr/local/Caskroom/miniconda/base/envs/cyvcf2/libexec/htslib/hfile_gcs.bundle"
htsfile: can't open "s3://3kricegenome/test/test.vcf.gz": Input/output error

I'm closing this issue but the only solution that seemed to work for me was:

brew install python

python3 -m venv myenv2

source myenv2/bin/activate

pip install --upgrade pip

pip install -U boto3 wheel cython ipython

export HTSLIB_CONFIGURE_OPTIONS=--enable-plugins
export HTSLIB_LIBRARY_DIR=/usr/local/lib
export HTSLIB_INCLUDE_DIR=/usr/local/include
pip install pysam cyvcf2
# pysam 0.16.0.1
# cyvcf2 0.20.9

then either use ~/.aws/credentials or, since I use Docker as well:

export AWS_ACCESS_KEY_ID=....
export AWS_SECRET_ACCESS_KEY=....

and my tests, with ipython, now work:

from pysam import VariantFile
from cyvcf2 import VCF

# Public S3 VCF ex1
vcfs3 = VCF('s3://3kricegenome/test/test.vcf.gz')
vv = vcfs3('9311_chr01:1011-1011')
v1 = next(vv)
print(dict(v1.INFO))
{'AN': 2, 'DP': 12, 'MQ': 26.549999237060547, 'MQ0': 2}
# OK: Mac, Docker

# Private S3 VCF ex1
vcfs3 = VCF('s3://vcf-test/atest/test.vcf.gz')
vv = vcfs3('9311_chr01:1011-1011')
v1 = next(vv)
print(dict(v1.INFO))
{'AN': 2, 'DP': 12, 'MQ': 26.549999237060547, 'MQ0': 2}
# OK: Mac, Docker

However, for pysam, at least on Docker (using amazon linux:latest, pysam=0.15.3, any newer won't work), a similar solution above does not work, I still need to do:

import os
import boto3
import botocore
import pysam

s3 = boto3.client('s3', aws_secret_access_key=os.environ["AWS_SECRET_ACCESS_KEY"],
                  aws_access_key_id=os.environ["AWS_ACCESS_KEY_ID"],
                  region_name="eu-west-2",
                  config=boto3.session.Config(signature_version='s3v4'))
vcf_index = s3.generate_presigned_url('get_object', Params={'Bucket': 'vcf-test', 'Key': 'atest/test.vcf.gz.tbi'}, ExpiresIn=5000)
vcf_file = s3.generate_presigned_url('get_object', Params={'Bucket': 'vcf-test', 'Key': 'atest/test.vcf.gz'}, ExpiresIn=5000)

# Private S3+Boto PYSAM ex1
variant_file = pysam.VariantFile(vcf_file, index_filename=vcf_index)
vsam = variant_file.fetch('9311_chr01', 1010, 1011)
v = next(vsam)
print(dict(v.info))
# OK: Mac, Docker
{'AN': 2, 'DP': 12, 'MQ': 26.549999237060547, 'MQ0': 2}

The bottom line for me is, unfortunately, there's something broken for the pypi and conda packages even for Linux and worse for Mac.

Anyway, now I hope to get to the point where I can compare pysam x cyvcf2 in my project and, hopefully, do the transition.

Thanks again and sorry for taking much of your time just to find out that, actually, cyvcf2 is not the culprit.

@alanwilter alanwilter reopened this Mar 17, 2021
@alanwilter
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alanwilter commented Mar 17, 2021

Sorry guys, now I'm trying to get cyvcf2 to work with Linux Ubuntu 18 or 20 (intel).

This is my test case:

from cyvcf2 import VCF

# Public S3 VCF ex1
vcfs3 = VCF('s3://3kricegenome/test/test.vcf.gz')
vv = vcfs3('9311_chr01:1011-1011')
v1 = next(vv)
print(dict(v1.INFO))

Thats works fine on my macOS Big Sur and prints:
{'AN': 2, 'DP': 12, 'MQ': 26.549999237060547, 'MQ0': 2}

1. Using pip install cyvcf2 (version 0.30.4)

  • this work on my mac, but when trying with Ubuntu I got:
In [3]: vcfs3 = VCF('s3://3kricegenome/test/test.vcf.gz')
[E::hts_open_format] Failed to open file "s3://3kricegenome/test/test.vcf.gz" : Input/output error
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
<ipython-input-3-4ffad091729e> in <module>
----> 1 vcfs3 = VCF('s3://3kricegenome/test/test.vcf.gz')

~/phenopolis_browser/venv/lib/python3.6/site-packages/cyvcf2/cyvcf2.pyx in cyvcf2.cyvcf2.VCF.__init__()

~/phenopolis_browser/venv/lib/python3.6/site-packages/cyvcf2/cyvcf2.pyx in cyvcf2.cyvcf2.HTSFile._open_htsfile()

OSError: Error opening s3://3kricegenome/test/test.vcf.gz

2. Using a fresh (virtual) Ubuntu 20.04 with sudo apt-get install python3-cyvcf2 (version '0.11.6')

  • That worked, but it's a quite old version, isn't it? And it is NOT an option for Ubuntu 18.04, package python3-cyvcf2 is not available.

3. Trying with pip install -U --no-cache-dir --force-reinstall --ignore-installed --no-binary :all: cyvcf2

  • which basically try to rebuild everything from source, but it failed with:
...
Running setup.py install for cyvcf2 ... error
    ERROR: Command errored out with exit status 1:
...
    x86_64-linux-gnu-gcc: error: cyvcf2/cyvcf2.c: No such file or directory
    x86_64-linux-gnu-gcc: fatal error: no input files
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-u_yrgbgu/cyvcf2/setup.py'"'"'; __file__='"'"'/tmp/pip-install-u_yrgbgu/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-cwm5sfp2/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/alan/.local/include/python3.8/cyvcf2 Check the logs for full command output.

4. Again, on fresh Ubuntu, trying to install from sources (version 0.30.6):

sudo apt-get install libbz2-dev liblzma-dev libdeflate-dev libcurl4-openssl-dev
git clone --recursive https://github.com/brentp/cyvcf2
cd cyvcf2/htslib
autoheader
autoconf
./configure  --enable-libcurl --with-libdeflate --enable-plugins --enable-gcs --enable-s3
make
make test
...
#Number of tests:
#    total   .. 153
#    passed  .. 153
#    failed  .. 0
cd ..
pip install -r requirements.txt
# all fine so far
CYTHONIZE=1 pip install -e .

failed!

Full output
Obtaining file:///home/alan/cyvcf2
Requirement already satisfied: click in /home/alan/.local/lib/python3.8/site-packages (from cyvcf2==0.30.6) (7.1.2)
Requirement already satisfied: coloredlogs in /home/alan/.local/lib/python3.8/site-packages (from cyvcf2==0.30.6) (15.0)
Requirement already satisfied: numpy in /home/alan/.local/lib/python3.8/site-packages (from cyvcf2==0.30.6) (1.20.1)
Requirement already satisfied: humanfriendly>=9.1 in /home/alan/.local/lib/python3.8/site-packages (from coloredlogs->cyvcf2==0.30.6) (9.1)
Installing collected packages: cyvcf2
  Running setup.py develop for cyvcf2
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/alan/cyvcf2/setup.py'"'"'; __file__='"'"'/home/alan/cyvcf2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps --user --prefix=
         cwd: /home/alan/cyvcf2/
    Complete output (91 lines):
    running develop
    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'
    running build_ext
    building 'cyvcf2.cyvcf2' extension
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c cyvcf2/cyvcf2.c -o build/temp.linux-x86_64-3.8/cyvcf2/cyvcf2.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    In file included from /home/alan/.local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944,
                     from /home/alan/.local/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                     from /home/alan/.local/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                     from cyvcf2/cyvcf2.c:701:
    /home/alan/.local/lib/python3.8/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]
       17 | #warning "Using deprecated NumPy API, disable it with " \
          |  ^~~~~~~
    cyvcf2/cyvcf2.c: In function ‘__pyx_pf_6cyvcf2_6cyvcf2_3VCF_8seqnames___get__’:
    cyvcf2/cyvcf2.c:14461:18: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
    14461 |   __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
          |                  ^
    cyvcf2/cyvcf2.c:14570:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
    14570 |       __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
          |                      ^
    cyvcf2/cyvcf2.c:14653:22: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
    14653 |       __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
          |                      ^
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/probaln.c -o build/temp.linux-x86_64-3.8/htslib/probaln.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/errmod.c -o build/temp.linux-x86_64-3.8/htslib/errmod.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/sam.c -o build/temp.linux-x86_64-3.8/htslib/sam.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/knetfile.c -o build/temp.linux-x86_64-3.8/htslib/knetfile.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/region.c -o build/temp.linux-x86_64-3.8/htslib/region.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/regidx.c -o build/temp.linux-x86_64-3.8/htslib/regidx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/textutils.c -o build/temp.linux-x86_64-3.8/htslib/textutils.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/hts.c -o build/temp.linux-x86_64-3.8/htslib/hts.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/kstring.c -o build/temp.linux-x86_64-3.8/htslib/kstring.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/hfile_s3.c -o build/temp.linux-x86_64-3.8/htslib/hfile_s3.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/hfile_gcs.c -o build/temp.linux-x86_64-3.8/htslib/hfile_gcs.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-3.8/htslib/synced_bcf_reader.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/vcfutils.c -o build/temp.linux-x86_64-3.8/htslib/vcfutils.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/hfile_net.c -o build/temp.linux-x86_64-3.8/htslib/hfile_net.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/header.c -o build/temp.linux-x86_64-3.8/htslib/header.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/realn.c -o build/temp.linux-x86_64-3.8/htslib/realn.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/vcf.c -o build/temp.linux-x86_64-3.8/htslib/vcf.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/tbx.c -o build/temp.linux-x86_64-3.8/htslib/tbx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/hfile_libcurl.c -o build/temp.linux-x86_64-3.8/htslib/hfile_libcurl.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/bcf_sr_sort.c -o build/temp.linux-x86_64-3.8/htslib/bcf_sr_sort.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/multipart.c -o build/temp.linux-x86_64-3.8/htslib/multipart.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/bgzf.c -o build/temp.linux-x86_64-3.8/htslib/bgzf.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/faidx.c -o build/temp.linux-x86_64-3.8/htslib/faidx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/kfunc.c -o build/temp.linux-x86_64-3.8/htslib/kfunc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-3.8/htslib/vcf_sweep.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/hfile.c -o build/temp.linux-x86_64-3.8/htslib/hfile.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/thread_pool.c -o build/temp.linux-x86_64-3.8/htslib/thread_pool.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/hts_os.c -o build/temp.linux-x86_64-3.8/htslib/hts_os.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/md5.c -o build/temp.linux-x86_64-3.8/htslib/md5.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/hfile_s3_write.c -o build/temp.linux-x86_64-3.8/htslib/hfile_s3_write.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_stats.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_decode.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-3.8/htslib/cram/open_trace_file.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_index.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    htslib/cram/cram_index.c: In function ‘cram_index_build’:
    htslib/cram/cram_index.c:690:17: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable]
      690 |     off_t cpos, hpos;
          |                 ^~~~
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/rANS_static.c -o build/temp.linux-x86_64-3.8/htslib/cram/rANS_static.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/cram_external.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_external.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-3.8/htslib/cram/mFILE.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-3.8/htslib/cram/pooled_alloc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_io.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-3.8/htslib/cram/string_alloc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_codecs.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_samtools.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-3.8/htslib/cram/cram_encode.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    htslib/cram/cram_encode.c: In function ‘process_one_read’:
    htslib/cram/cram_encode.c:3045:24: warning: unused variable ‘brg’ [-Wunused-variable]
     3045 |         sam_hrec_rg_t *brg = sam_hrecs_find_rg(fd->header->hrecs, "UNKNOWN");
          |                        ^~~
    x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icyvcf2 -Ihtslib -I/home/alan/.local/lib/python3.8/site-packages/numpy/core/include -I/usr/include/python3.8 -c cyvcf2/helpers.c -o build/temp.linux-x86_64-3.8/cyvcf2/helpers.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/cyvcf2/cyvcf2.o build/temp.linux-x86_64-3.8/htslib/probaln.o build/temp.linux-x86_64-3.8/htslib/errmod.o build/temp.linux-x86_64-3.8/htslib/sam.o build/temp.linux-x86_64-3.8/htslib/knetfile.o build/temp.linux-x86_64-3.8/htslib/region.o build/temp.linux-x86_64-3.8/htslib/regidx.o build/temp.linux-x86_64-3.8/htslib/textutils.o build/temp.linux-x86_64-3.8/htslib/hts.o build/temp.linux-x86_64-3.8/htslib/kstring.o build/temp.linux-x86_64-3.8/htslib/hfile_s3.o build/temp.linux-x86_64-3.8/htslib/hfile_gcs.o build/temp.linux-x86_64-3.8/htslib/synced_bcf_reader.o build/temp.linux-x86_64-3.8/htslib/vcfutils.o build/temp.linux-x86_64-3.8/htslib/hfile_net.o build/temp.linux-x86_64-3.8/htslib/header.o build/temp.linux-x86_64-3.8/htslib/realn.o build/temp.linux-x86_64-3.8/htslib/vcf.o build/temp.linux-x86_64-3.8/htslib/tbx.o build/temp.linux-x86_64-3.8/htslib/hfile_libcurl.o build/temp.linux-x86_64-3.8/htslib/bcf_sr_sort.o build/temp.linux-x86_64-3.8/htslib/multipart.o build/temp.linux-x86_64-3.8/htslib/bgzf.o build/temp.linux-x86_64-3.8/htslib/faidx.o build/temp.linux-x86_64-3.8/htslib/kfunc.o build/temp.linux-x86_64-3.8/htslib/vcf_sweep.o build/temp.linux-x86_64-3.8/htslib/hfile.o build/temp.linux-x86_64-3.8/htslib/thread_pool.o build/temp.linux-x86_64-3.8/htslib/hts_os.o build/temp.linux-x86_64-3.8/htslib/md5.o build/temp.linux-x86_64-3.8/htslib/hfile_s3_write.o build/temp.linux-x86_64-3.8/htslib/cram/cram_stats.o build/temp.linux-x86_64-3.8/htslib/cram/cram_decode.o build/temp.linux-x86_64-3.8/htslib/cram/open_trace_file.o build/temp.linux-x86_64-3.8/htslib/cram/cram_index.o build/temp.linux-x86_64-3.8/htslib/cram/rANS_static.o build/temp.linux-x86_64-3.8/htslib/cram/cram_external.o build/temp.linux-x86_64-3.8/htslib/cram/mFILE.o build/temp.linux-x86_64-3.8/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-3.8/htslib/cram/cram_io.o build/temp.linux-x86_64-3.8/htslib/cram/string_alloc.o build/temp.linux-x86_64-3.8/htslib/cram/cram_codecs.o build/temp.linux-x86_64-3.8/htslib/cram/cram_samtools.o build/temp.linux-x86_64-3.8/htslib/cram/cram_encode.o build/temp.linux-x86_64-3.8/cyvcf2/helpers.o -lz -lbz2 -llzma -lcurl -lssl -lcrypt -o build/lib.linux-x86_64-3.8/cyvcf2/cyvcf2.cpython-38-x86_64-linux-gnu.so
    /usr/bin/ld: build/temp.linux-x86_64-3.8/htslib/hfile_gcs.o: in function `hfile_plugin_init':
    /home/alan/cyvcf2/htslib/hfile_gcs.c:120: multiple definition of `hfile_plugin_init'; build/temp.linux-x86_64-3.8/htslib/hfile_s3.o:/home/alan/cyvcf2/htslib/hfile_s3.c:1240: first defined here
    /usr/bin/ld: build/temp.linux-x86_64-3.8/htslib/hfile_libcurl.o: in function `hfile_plugin_init':
    /home/alan/cyvcf2/htslib/hfile_libcurl.c:1442: multiple definition of `hfile_plugin_init'; build/temp.linux-x86_64-3.8/htslib/hfile_s3.o:/home/alan/cyvcf2/htslib/hfile_s3.c:1240: first defined here
    /usr/bin/ld: build/temp.linux-x86_64-3.8/htslib/hfile_s3_write.o: in function `hfile_plugin_init':
    /home/alan/cyvcf2/htslib/hfile_s3_write.c:835: multiple definition of `hfile_plugin_init'; build/temp.linux-x86_64-3.8/htslib/hfile_s3.o:/home/alan/cyvcf2/htslib/hfile_s3.c:1240: first defined here
    collect2: error: ld returned 1 exit status
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/alan/cyvcf2/setup.py'"'"'; __file__='"'"'/home/alan/cyvcf2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps --user --prefix= Check the logs for full command output.

@ccwang002
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I don't think cyvcf2 has changed a lot between v0.11.6 and v0.30.4 except that the former version uses an older htslib (1.9 vs 1.10). If you cannot use conda and you don't mind an older htslib, v0.11.6 is probably the best alternative option at the moment.

  • Your approach 1 is a bug and will need further investigation.
  • The approach 3 failed because of cyvcf2/cyvcf2.c: No such file or directory - linux alpine python 3.7 #196 and we haven't fully fixed the CI to generate the proper source tarball to include the Cythonized output.
  • The approach 4 should work and will need further investigation. Could you try it again on a clean machine without the make test step, and replace the last step with CYTHONIZE=1 python setup.py install?

@alanwilter
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I would be more than happy to have v0.11.6 from a deb package but I need it for Ubuntu 18.04 and this is not available AFAIK, python3-cyvcf2 is only in Ubuntu 20.

Re approach (4), I tried this (keep in mind that for Ubuntu 18, an eventual solution will be different since I don't have libdeflate for Ubuntu 18):

mkdir tmp_test
cd tmp_test

cat << EOF >| Dockerfile_ubuntu
FROM ubuntu:20.04

# set work directory
WORKDIR /app

# set environment variables, to avoid pyc files and flushing buffer
ENV PYTHONDONTWRITEBYTECODE 1
ENV PYTHONUNBUFFERED 1

RUN apt-get update \
    && apt-get install -y python3-pip libbz2-dev liblzma-dev libdeflate-dev \
    libssl-dev libcurl4-openssl-dev git autoconf \
    && pip3 --no-cache-dir install --upgrade pip
RUN git clone --recursive https://github.com/brentp/cyvcf2 \
    && cd cyvcf2/htslib \
    && autoheader \
    && autoconf \
    && ./configure  --enable-libcurl --with-libdeflate --enable-plugins --enable-gcs --enable-s3 \
    && make \
    && cd .. \
    && pip install -r requirements.txt
RUN cd /app/cyvcf2 \
    && CYTHONIZE=1 python3 setup.py install
EOF

docker build -f Dockerfile_ubuntu -t ubuntu20_test .

Got the same error as seen in the approach (4) discussed.

I have re-read this whole ticket and I noticed that I never managed to build cyvcf2 from sources and all the failures have in common something related to hfile_plugin_init: either multiple definition of or duplicate symbol, even tried to "hack" it, but C/C++ is beyond me.

@ccwang002
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I got it working by changing the configuration of htslib (changing only one line of your Dockerfile):

./configure  --enable-libcurl --with-libdeflate --enable-lzma --enable-bz2 --enable-gcs --enable-s3

The culprit here is htslib's --enable-plugins option. Please try again without this option and see if this approach now works for you.

@alanwilter
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Thanks @ccwang002! That nailed the problem, I can at least got one solution finally working. I'll close and I hope you guys may address the pip issues.

@alanwilter
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alanwilter commented May 24, 2021

Here I'm again, now trying to install on macOS Big Sur 11.3.1, cyvcf2 version 0.30.8 from github, following instructions for Mac with Brew, but using autoconf from source, since brew autoconf didn't work with Big Sur:

curl -O http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz
tar zxvf autoconf-2.69.tar.gz
cd autoconf-2.69
./configure && make && sudo make install
I got all installed but when I try to run...

and

./configure  --enable-libcurl --with-libdeflate --enable-lzma --enable-bz2 --enable-gcs --enable-s3
python3 -c "import cyvcf2; print(cyvcf2.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/alan/Programmes/cyvcf2/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: dlopen(/Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so, 2): Symbol not found: _libdeflate_alloc_compressor
  Referenced from: /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so
  Expected in: flat namespace
 in /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so

Any idea?

@alanwilter alanwilter reopened this May 24, 2021
@alanwilter
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alanwilter commented May 28, 2021

Long post!

Mac details:

System Version: macOS 11.4 (20F71) Big Sur, Intel
Kernel Version: Darwin 20.5.0

Homebrew 3.1.9-58-g7ae9cc3
Homebrew/homebrew-core (git revision 35ed9f432a; last commit 2021-05-28)
Homebrew/homebrew-cask (git revision f36feab232; last commit 2021-05-28)

HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j4
CMAKE_PREFIX_PATH: /usr/local
CMAKE_INCLUDE_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Homebrew/Library/Homebrew/os/mac/pkgconfig/11
HOMEBREW_GIT: git
HOMEBREW_SDKROOT: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
ACLOCAL_PATH: /usr/local/share/aclocal
PATH: /usr/local/Homebrew/Library/Homebrew/shims/mac/super:/usr/bin:/bin:/usr/sbin:/sbin

I've tried what I could figure out and no success. Here's the details:

1. Trying the basic standard cyvcf2 install from source, circumventing the issues with [email protected]:

#For compilers to find openssl you may need to set:
export LDFLAGS="-L/usr/local/opt/openssl/lib"
export CPPFLAGS="-I/usr/local/opt/openssl/include"

#For pkg-config to find openssl you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/openssl/lib/pkgconfig"

brew install autoconf # 2.71 --> error
# error: configure: error: cannot find required auxiliary files: config.guess config.sub

brew install [email protected]
export PATH="/usr/local/opt/[email protected]/bin:$PATH"

git clone --recursive https://github.com/brentp/cyvcf2
cd cyvcf2/htslib
git describe --always
# htslib 1.10.2, commit id fd0f895

autoheader
autoconf

# tried both
./configure --enable-libcurl
./configure --enable-libcurl --with-libdeflate --enable-lzma --enable-bz2 --enable-gcs --enable-s3

make

cd ..
pip install -r requirements.txt
CYTHONIZE=1 pip install -e .

python -c "import cyvcf2; print(cyvcf2.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/alan/Programmes/cyvcf2/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: dlopen(/Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so, 2): Symbol not found: _libdeflate_alloc_compressor
  Referenced from: /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so
  Expected in: flat namespace
 in /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so

Error is _libdeflate_alloc_compressor, so I've tried some variations like building cython from source or using
./configure --enable-libcurl --with-libdeflate --enable-lzma --enable-bz2 --enable-gcs --enable-s3
I've got the same error.

Using CYTHONIZE=1 python setup.py install for full details

Compiling cyvcf2/cyvcf2.pyx because it changed.
[1/1] Cythonizing cyvcf2/cyvcf2.pyx
running install
running bdist_egg
running egg_info
creating cyvcf2.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
writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
reading manifest file 'cyvcf2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-11-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.macosx-11-x86_64-3.9
creating build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/__init__.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/cli.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/__main__.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2
creating build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_reader.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_writer.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/__init__.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_hemi.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_cli.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/cyvcf2.c -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/cyvcf2.pxd -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/cyvcf2.pyx -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/helpers.c -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/helpers.h -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/relatedness.h -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/tests/bug.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/decomposed.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/empty.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/issue_198.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/issue_44.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/no-seq-len.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/no-seq-names.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/o.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/seg.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-diff.csi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-format-string.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-haploidX.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-hemi.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-invalid-header.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.bug.117.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.mnp.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.bcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
running build_ext
building 'cyvcf2.cyvcf2' extension
creating build/temp.macosx-11-x86_64-3.9
creating build/temp.macosx-11-x86_64-3.9/cyvcf2
creating build/temp.macosx-11-x86_64-3.9/htslib
creating build/temp.macosx-11-x86_64-3.9/htslib/cram
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c cyvcf2/cyvcf2.c -o build/temp.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
In file included from cyvcf2/cyvcf2.c:702:
In file included from /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
cyvcf2/cyvcf2.c:9128:32: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2);
                               ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:561:35: note: passing argument to parameter 'h' here
    int bcf_hdr_append(bcf_hdr_t *h, const char *line);
                                  ^
cyvcf2/cyvcf2.c:9170:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
                             ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:9737:37: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_5), 0);
                                    ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:342:40: note: passing argument to parameter 'hdr' here
    int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file) HTS_RESULT_USED;
                                       ^
cyvcf2/cyvcf2.c:10041:32: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4);
                               ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:561:35: note: passing argument to parameter 'h' here
    int bcf_hdr_append(bcf_hdr_t *h, const char *line);
                                  ^
cyvcf2/cyvcf2.c:10094:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
                             ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:10641:34: warning: passing 'const bcf_hdr_t *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __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);
                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:1123:102: note: expanded from macro 'bcf_itr_querys'
    #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec)
                                                                                                     ^~~~~
htslib/htslib/hts.h:1074:93: note: passing argument to parameter 'hdr' here
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:11987:134: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    __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, 486, __pyx_L1_error)
                                                                                                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:3093:118: note: passing argument to parameter here
static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/
                                                                                                                     ^
cyvcf2/cyvcf2.c:13561:21: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    bcf_hdr_destroy(__pyx_v_self->hdr);
                    ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:271:37: note: passing argument to parameter 'h' here
    void bcf_hdr_destroy(bcf_hdr_t *h);
                                    ^
cyvcf2/cyvcf2.c:14462:18: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
                 ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:14571:24: warning: passing 'const bcf_hdr_t *' to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:1140:111: note: expanded from macro 'bcf_index_seqnames'
    #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr))
                                                                                                              ^~~~~
htslib/htslib/hts.h:1097:88: note: passing argument to parameter 'hdr' here
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:14571:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:14654:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:28194:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id);
                ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:39518:13: warning: assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_h = __pyx_t_6;
            ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:42650:16: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key);
               ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:43645:18: warning: assigning to 'bcf_hdr_t *' from 'const bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_i->hdr = __pyx_t_4;
                 ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:44198:23: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr));
                      ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:44226:23: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:44809:31: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_t_3 = ((bcf_hdr_parse(__pyx_v_self->__pyx_base.hdr, __pyx_t_2) != 0) != 0);
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:613:34: note: passing argument to parameter 'hdr' here
    int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt);
                                 ^
cyvcf2/cyvcf2.c:44845:30: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_t_3 = ((bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr) != 0) != 0);
                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:45224:65: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.__pyx_base.hts, __pyx_v_self->__pyx_base.hdr));
                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:353:47: note: passing argument to parameter 'h' here
    int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h) HTS_RESULT_USED;
                                              ^
cyvcf2/cyvcf2.c:45402:36: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0);
                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:638:37: note: passing argument to parameter 'hdr' here
    int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
                                    ^
cyvcf2/cyvcf2.c:45440:25: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:624:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:45499:87: warning: passing 'const bcf_hdr_t *' to parameter of type 'bcf_hdr_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2389, __pyx_L1_error)
                                                                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:419:43: note: passing argument to parameter 'h' here
    int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v) HTS_RESULT_USED;
                                          ^
26 warnings generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c cyvcf2/helpers.c -o build/temp.macosx-11-x86_64-3.9/cyvcf2/helpers.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
cyvcf2/helpers.c:52:20: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        else if((a == b)) {
                 ~~^~~~
cyvcf2/helpers.c:52:20: note: remove extraneous parentheses around the comparison to silence this warning
        else if((a == b)) {
                ~  ^   ~
cyvcf2/helpers.c:52:20: note: use '=' to turn this equality comparison into an assignment
        else if((a == b)) {
                   ^~
                   =
cyvcf2/helpers.c:108:21: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        else if ((a == b)) {
                  ~~^~~~
cyvcf2/helpers.c:108:21: note: remove extraneous parentheses around the comparison to silence this warning
        else if ((a == b)) {
                 ~  ^   ~
cyvcf2/helpers.c:108:21: note: use '=' to turn this equality comparison into an assignment
        else if ((a == b)) {
                    ^~
                    =
3 warnings generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/bcf_sr_sort.c -o build/temp.macosx-11-x86_64-3.9/htslib/bcf_sr_sort.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/bgzf.c -o build/temp.macosx-11-x86_64-3.9/htslib/bgzf.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_codecs.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_codecs.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_decode.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_decode.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_encode.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_encode.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
htslib/cram/cram_encode.c:1727:13: warning: code will never be executed [-Wunreachable-code]
            cram_byte_array_len_encoder e;
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_encode.c:1717:13: note: silence by adding parentheses to mark code as explicitly dead
        if (1) {
            ^
            /* DISABLES CODE */ ( )
htslib/cram/cram_encode.c:3045:24: warning: unused variable 'brg' [-Wunused-variable]
        sam_hrec_rg_t *brg = sam_hrecs_find_rg(fd->header->hrecs, "UNKNOWN");
                       ^
htslib/cram/cram_encode.c:2874:40: warning: code will never be executed [-Wunreachable-code]
                                int ol=l;
                                       ^
htslib/cram/cram_encode.c:2871:33: note: silence by adding parentheses to mark code as explicitly dead
                            if (0 && CRAM_MAJOR_VERS(fd->version) >= 3) {
                                ^
                                /* DISABLES CODE */ ( )
htslib/cram/cram_encode.c:2835:17: warning: code will never be executed [-Wunreachable-code]
                int l;
                ^~~~~~
5 warnings generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_external.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_external.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_index.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_index.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_io.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_io.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_samtools.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_samtools.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_stats.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_stats.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/mFILE.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/mFILE.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/open_trace_file.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/open_trace_file.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/pooled_alloc.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/pooled_alloc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/rANS_static.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/rANS_static.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/string_alloc.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/string_alloc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/errmod.c -o build/temp.macosx-11-x86_64-3.9/htslib/errmod.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/faidx.c -o build/temp.macosx-11-x86_64-3.9/htslib/faidx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/header.c -o build/temp.macosx-11-x86_64-3.9/htslib/header.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile_gcs.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile_gcs.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile_libcurl.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile_libcurl.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile_net.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile_net.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile_s3.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile_s3.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile_s3_write.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile_s3_write.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hts.c -o build/temp.macosx-11-x86_64-3.9/htslib/hts.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hts_os.c -o build/temp.macosx-11-x86_64-3.9/htslib/hts_os.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/kfunc.c -o build/temp.macosx-11-x86_64-3.9/htslib/kfunc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/knetfile.c -o build/temp.macosx-11-x86_64-3.9/htslib/knetfile.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/kstring.c -o build/temp.macosx-11-x86_64-3.9/htslib/kstring.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/md5.c -o build/temp.macosx-11-x86_64-3.9/htslib/md5.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/multipart.c -o build/temp.macosx-11-x86_64-3.9/htslib/multipart.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/probaln.c -o build/temp.macosx-11-x86_64-3.9/htslib/probaln.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/realn.c -o build/temp.macosx-11-x86_64-3.9/htslib/realn.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/regidx.c -o build/temp.macosx-11-x86_64-3.9/htslib/regidx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/region.c -o build/temp.macosx-11-x86_64-3.9/htslib/region.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/sam.c -o build/temp.macosx-11-x86_64-3.9/htslib/sam.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/synced_bcf_reader.c -o build/temp.macosx-11-x86_64-3.9/htslib/synced_bcf_reader.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/tbx.c -o build/temp.macosx-11-x86_64-3.9/htslib/tbx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/textutils.c -o build/temp.macosx-11-x86_64-3.9/htslib/textutils.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/thread_pool.c -o build/temp.macosx-11-x86_64-3.9/htslib/thread_pool.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
htslib/thread_pool.c:667:9: warning: code will never be executed [-Wunreachable-code]
        printf("%d waiting, %d running, %d output, %d, arun %d => %d\t", p->njobs,
        ^~~~~~
htslib/thread_pool.c:666:9: note: silence by adding parentheses to mark code as explicitly dead
    if (0) {
        ^
        /* DISABLES CODE */ ( )
2 warnings generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/vcf.c -o build/temp.macosx-11-x86_64-3.9/htslib/vcf.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/vcf_sweep.c -o build/temp.macosx-11-x86_64-3.9/htslib/vcf_sweep.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/vcfutils.c -o build/temp.macosx-11-x86_64-3.9/htslib/vcfutils.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -L/usr/local/opt/openssl/lib -I/usr/local/opt/openssl/include build/temp.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.o build/temp.macosx-11-x86_64-3.9/cyvcf2/helpers.o build/temp.macosx-11-x86_64-3.9/htslib/bcf_sr_sort.o build/temp.macosx-11-x86_64-3.9/htslib/bgzf.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_codecs.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_decode.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_encode.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_external.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_index.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_io.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_samtools.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_stats.o build/temp.macosx-11-x86_64-3.9/htslib/cram/mFILE.o build/temp.macosx-11-x86_64-3.9/htslib/cram/open_trace_file.o build/temp.macosx-11-x86_64-3.9/htslib/cram/pooled_alloc.o build/temp.macosx-11-x86_64-3.9/htslib/cram/rANS_static.o build/temp.macosx-11-x86_64-3.9/htslib/cram/string_alloc.o build/temp.macosx-11-x86_64-3.9/htslib/errmod.o build/temp.macosx-11-x86_64-3.9/htslib/faidx.o build/temp.macosx-11-x86_64-3.9/htslib/header.o build/temp.macosx-11-x86_64-3.9/htslib/hfile.o build/temp.macosx-11-x86_64-3.9/htslib/hfile_gcs.o build/temp.macosx-11-x86_64-3.9/htslib/hfile_libcurl.o build/temp.macosx-11-x86_64-3.9/htslib/hfile_net.o build/temp.macosx-11-x86_64-3.9/htslib/hfile_s3.o build/temp.macosx-11-x86_64-3.9/htslib/hfile_s3_write.o build/temp.macosx-11-x86_64-3.9/htslib/hts.o build/temp.macosx-11-x86_64-3.9/htslib/hts_os.o build/temp.macosx-11-x86_64-3.9/htslib/kfunc.o build/temp.macosx-11-x86_64-3.9/htslib/knetfile.o build/temp.macosx-11-x86_64-3.9/htslib/kstring.o build/temp.macosx-11-x86_64-3.9/htslib/md5.o build/temp.macosx-11-x86_64-3.9/htslib/multipart.o build/temp.macosx-11-x86_64-3.9/htslib/probaln.o build/temp.macosx-11-x86_64-3.9/htslib/realn.o build/temp.macosx-11-x86_64-3.9/htslib/regidx.o build/temp.macosx-11-x86_64-3.9/htslib/region.o build/temp.macosx-11-x86_64-3.9/htslib/sam.o build/temp.macosx-11-x86_64-3.9/htslib/synced_bcf_reader.o build/temp.macosx-11-x86_64-3.9/htslib/tbx.o build/temp.macosx-11-x86_64-3.9/htslib/textutils.o build/temp.macosx-11-x86_64-3.9/htslib/thread_pool.o build/temp.macosx-11-x86_64-3.9/htslib/vcf.o build/temp.macosx-11-x86_64-3.9/htslib/vcf_sweep.o build/temp.macosx-11-x86_64-3.9/htslib/vcfutils.o -L/usr/local/lib -L/usr/local/opt/[email protected]/lib -L/usr/local/opt/sqlite/lib -lz -lbz2 -llzma -lcurl -lssl -o build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.cpython-39-darwin.so
creating build/bdist.macosx-11-x86_64
creating build/bdist.macosx-11-x86_64/egg
creating build/bdist.macosx-11-x86_64/egg/cyvcf2
creating build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.bug.117.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_reader.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/issue_198.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_writer.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-invalid-header.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-alt-repr.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/__init__.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/no-seq-names.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/seg.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-diff.csi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/issue_44.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/empty.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/decomposed.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.mnp.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_cli.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/no-seq-len.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_gt_alt_freqs.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/__init__.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.cpython-39-darwin.so -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/helpers.c -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/relatedness.h -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.c -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cli.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/helpers.h -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/__main__.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/test_reader.py to test_reader.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/test_writer.py to test_writer.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/test_hemi.py to test_hemi.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/test_cli.py to test_cli.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/cli.py to cli.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/__main__.py to __main__.cpython-39.pyc
creating stub loader for cyvcf2/cyvcf2.cpython-39-darwin.so
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/cyvcf2.py to cyvcf2.cpython-39.pyc
creating build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/PKG-INFO -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/SOURCES.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/dependency_links.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/entry_points.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/not-zip-safe -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/requires.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/top_level.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
writing build/bdist.macosx-11-x86_64/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg' and adding 'build/bdist.macosx-11-x86_64/egg' to it
removing 'build/bdist.macosx-11-x86_64/egg' (and everything under it)
Processing cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg
removing '/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg' (and everything under it)
creating /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg
Extracting cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg to /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
cyvcf2 0.30.8 is already the active version in easy-install.pth
Installing cyvcf2 script to /Users/alan/.virtualenvs/pybase/bin

Installed /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg
Processing dependencies for cyvcf2==0.30.8
Searching for click==7.1.2
Best match: click 7.1.2
Adding click 7.1.2 to easy-install.pth file

Using /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
Searching for coloredlogs==15.0
Best match: coloredlogs 15.0
Adding coloredlogs 15.0 to easy-install.pth file
Installing coloredlogs script to /Users/alan/.virtualenvs/pybase/bin

Using /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
Searching for numpy==1.20.1
Best match: numpy 1.20.1
Adding numpy 1.20.1 to easy-install.pth file
Installing f2py script to /Users/alan/.virtualenvs/pybase/bin
Installing f2py3 script to /Users/alan/.virtualenvs/pybase/bin
Installing f2py3.9 script to /Users/alan/.virtualenvs/pybase/bin

Using /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
Searching for humanfriendly==9.1
Best match: humanfriendly 9.1
Adding humanfriendly 9.1 to easy-install.pth file
Installing humanfriendly script to /Users/alan/.virtualenvs/pybase/bin

Using /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
Finished processing dependencies for cyvcf2==0.30.8

2. Trying htslib master and develop branches:

#For compilers to find openssl you may need to set:
export LDFLAGS="-L/usr/local/opt/openssl/lib"
export CPPFLAGS="-I/usr/local/opt/openssl/include"

#For pkg-config to find openssl you may need to set:
export PKG_CONFIG_PATH="/usr/local/opt/openssl/lib/pkgconfig"

brew install autoconf # 2.71 --> error
# error: configure: error: cannot find required auxiliary files: config.guess config.sub

brew install [email protected]
export PATH="/usr/local/opt/[email protected]/bin:$PATH"

git clone --recursive https://github.com/brentp/cyvcf2
cd cyvcf2/htslib

git checkout master # did the same with develop
git submodule update --init --recursive
git describe --always
# master: 1.12 # autoconf 2.71 still does not work with
# develop: 1.12-40-g57842bb # 40 commits ahead master, autoconf 2.71 still does not work with

autoheader
autoconf

# tried both
./configure --enable-libcurl
./configure --enable-libcurl --with-libdeflate --enable-lzma --enable-bz2 --enable-gcs --enable-s3

make

cd ..
pip install -r requirements.txt

CYTHONIZE=1 pip install -e .
CYTHONIZE=1 python setup.py install # shows complete output

python -c "import cyvcf2; print(cyvcf2.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/alan/Programmes/cyvcf2/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: dlopen(/Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so, 2): Symbol not found: _arith_compress_to
  Referenced from: /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so
  Expected in: flat namespace
 in /Users/alan/Programmes/cyvcf2/cyvcf2/cyvcf2.cpython-39-darwin.so

Have you noticed the different error _arith_compress_to? All variations I tried gave the same error. I understand that the problem likely lies on htslib but I do need cyvcf2 and I don't have the knowledge or skills to fix it. I didn't try my recipes on a Linux since cyvcf2 0.30.4 from pypi seems to be working fine but I need it for my Mac since 0.30.4 is throwing sporadic malloc errors.

Using CYTHONIZE=1 python setup.py install for full details

Compiling cyvcf2/cyvcf2.pyx because it changed.
[1/1] Cythonizing cyvcf2/cyvcf2.pyx
running install
running bdist_egg
running egg_info
creating cyvcf2.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
writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
reading manifest file 'cyvcf2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'cyvcf2.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-11-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.macosx-11-x86_64-3.9
creating build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/__init__.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/cli.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/__main__.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2
creating build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_reader.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_writer.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/__init__.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_hemi.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_cli.py -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/cyvcf2.c -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/cyvcf2.pxd -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/cyvcf2.pyx -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/helpers.c -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/helpers.h -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/relatedness.h -> build/lib.macosx-11-x86_64-3.9/cyvcf2
copying cyvcf2/tests/bug.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/decomposed.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/empty.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/issue_198.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/issue_44.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/no-seq-len.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/no-seq-names.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/o.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/seg.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-alt-repr.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-diff.csi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-format-string.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-haploidX.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-hemi.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-invalid-header.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.bug.117.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.comp_het.3.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.mnp.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.bcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.bcf.csi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.snpeff.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test.vcf.gz.tbi -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_gt_alt_freqs.vcf -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
copying cyvcf2/tests/test_gt_bases.vcf.gz -> build/lib.macosx-11-x86_64-3.9/cyvcf2/tests
running build_ext
building 'cyvcf2.cyvcf2' extension
creating build/temp.macosx-11-x86_64-3.9
creating build/temp.macosx-11-x86_64-3.9/cyvcf2
creating build/temp.macosx-11-x86_64-3.9/htslib
creating build/temp.macosx-11-x86_64-3.9/htslib/cram
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c cyvcf2/cyvcf2.c -o build/temp.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
In file included from cyvcf2/cyvcf2.c:699:
In file included from /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944:
/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
cyvcf2/cyvcf2.c:9125:32: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_2);
                               ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:575:35: note: passing argument to parameter 'h' here
    int bcf_hdr_append(bcf_hdr_t *h, const char *line);
                                  ^
cyvcf2/cyvcf2.c:9167:30: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
                             ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:639:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:9734:37: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_set_samples(__pyx_v_self->hdr, ((char const *)__pyx_t_5), 0);
                                    ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:344:40: note: passing argument to parameter 'hdr' here
    int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file) HTS_RESULT_USED;
                                       ^
cyvcf2/cyvcf2.c:10038:32: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_append(__pyx_v_self->hdr, __pyx_t_4);
                               ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:575:35: note: passing argument to parameter 'h' here
    int bcf_hdr_append(bcf_hdr_t *h, const char *line);
                                  ^
cyvcf2/cyvcf2.c:10091:30: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_ret = bcf_hdr_sync(__pyx_v_self->hdr);
                             ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:639:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:10638:34: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __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);
                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:1181:102: note: expanded from macro 'bcf_itr_querys'
    #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec)
                                                                                                     ^~~~~
htslib/htslib/hts.h:1196:93: note: passing argument to parameter 'hdr' here
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:11984:134: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    __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, 486, __pyx_L1_error)
                                                                                                                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:3090:118: note: passing argument to parameter here
static CYTHON_INLINE struct __pyx_obj_6cyvcf2_6cyvcf2_HREC *__pyx_f_6cyvcf2_6cyvcf2_newHREC(bcf_hrec_t *, bcf_hdr_t *); /*proto*/
                                                                                                                     ^
cyvcf2/cyvcf2.c:13558:21: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    bcf_hdr_destroy(__pyx_v_self->hdr);
                    ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:273:37: note: passing argument to parameter 'h' here
    void bcf_hdr_destroy(bcf_hdr_t *h);
                                    ^
cyvcf2/cyvcf2.c:14459:18: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_cnames = bcf_hdr_seqnames(__pyx_v_self->hdr, (&__pyx_v_n));
                 ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:14568:24: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:1198:111: note: expanded from macro 'bcf_index_seqnames'
    #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr))
                                                                                                              ^~~~~
htslib/htslib/hts.h:1219:88: note: passing argument to parameter 'hdr' here
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:14568:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_cnames = bcf_index_seqnames(__pyx_v_self->hidx, __pyx_v_self->hdr, (&__pyx_v_n));
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:14651:22: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers]
      __pyx_v_cnames = tbx_seqnames(__pyx_v_self->idx, (&__pyx_v_n));
                     ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:28191:17: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    __pyx_v_key = bcf_hdr_int2id(__pyx_v_self->vcf->hdr, BCF_DT_ID, __pyx_v_fmt.id);
                ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:39515:13: warning: assigning to 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') from 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_h = __pyx_t_6;
            ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:42647:16: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_name = bcf_hdr_int2id(__pyx_v_self->hdr, BCF_DT_ID, __pyx_v_info->key);
               ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cyvcf2/cyvcf2.c:43642:18: warning: assigning to 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') from 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_v_i->hdr = __pyx_t_4;
                 ^ ~~~~~~~~~
cyvcf2/cyvcf2.c:44195:23: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  (void)(bcf_hdr_sync(__pyx_v_tmpl->hdr));
                      ^~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:639:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:44223:23: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:639:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:44806:31: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_t_3 = ((bcf_hdr_parse(__pyx_v_self->__pyx_base.hdr, __pyx_t_2) != 0) != 0);
                              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:628:34: note: passing argument to parameter 'hdr' here
    int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt);
                                 ^
cyvcf2/cyvcf2.c:44842:30: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_t_3 = ((bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr) != 0) != 0);
                             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:639:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:45221:65: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.__pyx_base.hts, __pyx_v_self->__pyx_base.hdr));
                                                                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:355:47: note: passing argument to parameter 'h' here
    int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h) HTS_RESULT_USED;
                                              ^
cyvcf2/cyvcf2.c:45399:36: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    __pyx_t_1 = ((bcf_hdr_add_hrec(__pyx_v_self->__pyx_base.hdr, __pyx_v_h) < 0) != 0);
                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:670:37: note: passing argument to parameter 'hdr' here
    int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
                                    ^
cyvcf2/cyvcf2.c:45437:25: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
    (void)(bcf_hdr_sync(__pyx_v_self->__pyx_base.hdr));
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:639:33: note: passing argument to parameter 'h' here
    int bcf_hdr_sync(bcf_hdr_t *h) HTS_RESULT_USED;
                                ^
cyvcf2/cyvcf2.c:45496:87: warning: passing 'const bcf_hdr_t *' (aka 'const struct bcf_hdr_t *') to parameter of type 'bcf_hdr_t *' (aka 'struct bcf_hdr_t *') discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_t_2 = __Pyx_PyInt_From_int(bcf_write(__pyx_v_self->__pyx_base.__pyx_base.hts, __pyx_v_self->__pyx_base.hdr, __pyx_v_var->b)); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 2389, __pyx_L1_error)
                                                                                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/htslib/vcf.h:431:43: note: passing argument to parameter 'h' here
    int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v) HTS_RESULT_USED;
                                          ^
26 warnings generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c cyvcf2/helpers.c -o build/temp.macosx-11-x86_64-3.9/cyvcf2/helpers.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
cyvcf2/helpers.c:52:20: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        else if((a == b)) {
                 ~~^~~~
cyvcf2/helpers.c:52:20: note: remove extraneous parentheses around the comparison to silence this warning
        else if((a == b)) {
                ~  ^   ~
cyvcf2/helpers.c:52:20: note: use '=' to turn this equality comparison into an assignment
        else if((a == b)) {
                   ^~
                   =
cyvcf2/helpers.c:108:21: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        else if ((a == b)) {
                  ~~^~~~
cyvcf2/helpers.c:108:21: note: remove extraneous parentheses around the comparison to silence this warning
        else if ((a == b)) {
                 ~  ^   ~
cyvcf2/helpers.c:108:21: note: use '=' to turn this equality comparison into an assignment
        else if ((a == b)) {
                    ^~
                    =
3 warnings generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/bcf_sr_sort.c -o build/temp.macosx-11-x86_64-3.9/htslib/bcf_sr_sort.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/bgzf.c -o build/temp.macosx-11-x86_64-3.9/htslib/bgzf.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_codecs.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_codecs.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_decode.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_decode.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_encode.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_encode.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
htslib/cram/cram_encode.c:1840:13: warning: code will never be executed [-Wunreachable-code]
            cram_byte_array_len_encoder e;
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
htslib/cram/cram_encode.c:1830:13: note: silence by adding parentheses to mark code as explicitly dead
        if (1) {
            ^
            /* DISABLES CODE */ ( )
htslib/cram/cram_encode.c:3057:24: warning: unused variable 'brg' [-Wunused-variable]
        sam_hrec_rg_t *brg = sam_hrecs_find_rg(fd->header->hrecs, "UNKNOWN");
                       ^
htslib/cram/cram_encode.c:2871:42: warning: code will never be executed [-Wunreachable-code]
                                int nl = l;
                                         ^
htslib/cram/cram_encode.c:2848:33: note: silence by adding parentheses to mark code as explicitly dead
                            if (0 && CRAM_MAJOR_VERS(fd->version) >= 3) {
                                ^
                                /* DISABLES CODE */ ( )
htslib/cram/cram_encode.c:2812:17: warning: code will never be executed [-Wunreachable-code]
                int l;
                ^~~~~~
5 warnings generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_external.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_external.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_index.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_index.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_io.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_io.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/cram_stats.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_stats.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/mFILE.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/mFILE.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/open_trace_file.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/open_trace_file.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/pooled_alloc.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/pooled_alloc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/cram/string_alloc.c -o build/temp.macosx-11-x86_64-3.9/htslib/cram/string_alloc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/errmod.c -o build/temp.macosx-11-x86_64-3.9/htslib/errmod.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/faidx.c -o build/temp.macosx-11-x86_64-3.9/htslib/faidx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/header.c -o build/temp.macosx-11-x86_64-3.9/htslib/header.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile_gcs.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile_gcs.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile_libcurl.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile_libcurl.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile_s3.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile_s3.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hfile_s3_write.c -o build/temp.macosx-11-x86_64-3.9/htslib/hfile_s3_write.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hts.c -o build/temp.macosx-11-x86_64-3.9/htslib/hts.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hts_expr.c -o build/temp.macosx-11-x86_64-3.9/htslib/hts_expr.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/hts_os.c -o build/temp.macosx-11-x86_64-3.9/htslib/hts_os.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/kfunc.c -o build/temp.macosx-11-x86_64-3.9/htslib/kfunc.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/kstring.c -o build/temp.macosx-11-x86_64-3.9/htslib/kstring.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/md5.c -o build/temp.macosx-11-x86_64-3.9/htslib/md5.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/multipart.c -o build/temp.macosx-11-x86_64-3.9/htslib/multipart.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/probaln.c -o build/temp.macosx-11-x86_64-3.9/htslib/probaln.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/realn.c -o build/temp.macosx-11-x86_64-3.9/htslib/realn.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/regidx.c -o build/temp.macosx-11-x86_64-3.9/htslib/regidx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/region.c -o build/temp.macosx-11-x86_64-3.9/htslib/region.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/sam.c -o build/temp.macosx-11-x86_64-3.9/htslib/sam.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/synced_bcf_reader.c -o build/temp.macosx-11-x86_64-3.9/htslib/synced_bcf_reader.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/tbx.c -o build/temp.macosx-11-x86_64-3.9/htslib/tbx.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/textutils.c -o build/temp.macosx-11-x86_64-3.9/htslib/textutils.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/thread_pool.c -o build/temp.macosx-11-x86_64-3.9/htslib/thread_pool.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
htslib/thread_pool.c:699:9: warning: code will never be executed [-Wunreachable-code]
        printf("%d waiting, %d running, %d output, %d, arun %d => %d\t", p->njobs,
        ^~~~~~
htslib/thread_pool.c:698:9: note: silence by adding parentheses to mark code as explicitly dead
    if (0) {
        ^
        /* DISABLES CODE */ ( )
2 warnings generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/vcf.c -o build/temp.macosx-11-x86_64-3.9/htslib/vcf.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/vcf_sweep.c -o build/temp.macosx-11-x86_64-3.9/htslib/vcf_sweep.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/opt/openssl/include -Icyvcf2 -Ihtslib -I/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/[email protected]/include -I/usr/local/opt/sqlite/include -I/Users/alan/.virtualenvs/pybase/include -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c htslib/vcfutils.c -o build/temp.macosx-11-x86_64-3.9/htslib/vcfutils.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
warning: unknown warning option '-Wno-discarded-qualifiers'; did you mean '-Wno-ignored-qualifiers'? [-Wunknown-warning-option]
1 warning generated.
clang -bundle -undefined dynamic_lookup -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -L/usr/local/opt/openssl/lib -I/usr/local/opt/openssl/include build/temp.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.o build/temp.macosx-11-x86_64-3.9/cyvcf2/helpers.o build/temp.macosx-11-x86_64-3.9/htslib/bcf_sr_sort.o build/temp.macosx-11-x86_64-3.9/htslib/bgzf.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_codecs.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_decode.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_encode.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_external.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_index.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_io.o build/temp.macosx-11-x86_64-3.9/htslib/cram/cram_stats.o build/temp.macosx-11-x86_64-3.9/htslib/cram/mFILE.o build/temp.macosx-11-x86_64-3.9/htslib/cram/open_trace_file.o build/temp.macosx-11-x86_64-3.9/htslib/cram/pooled_alloc.o build/temp.macosx-11-x86_64-3.9/htslib/cram/string_alloc.o build/temp.macosx-11-x86_64-3.9/htslib/errmod.o build/temp.macosx-11-x86_64-3.9/htslib/faidx.o build/temp.macosx-11-x86_64-3.9/htslib/header.o build/temp.macosx-11-x86_64-3.9/htslib/hfile.o build/temp.macosx-11-x86_64-3.9/htslib/hfile_gcs.o build/temp.macosx-11-x86_64-3.9/htslib/hfile_libcurl.o build/temp.macosx-11-x86_64-3.9/htslib/hfile_s3.o build/temp.macosx-11-x86_64-3.9/htslib/hfile_s3_write.o build/temp.macosx-11-x86_64-3.9/htslib/hts.o build/temp.macosx-11-x86_64-3.9/htslib/hts_expr.o build/temp.macosx-11-x86_64-3.9/htslib/hts_os.o build/temp.macosx-11-x86_64-3.9/htslib/kfunc.o build/temp.macosx-11-x86_64-3.9/htslib/kstring.o build/temp.macosx-11-x86_64-3.9/htslib/md5.o build/temp.macosx-11-x86_64-3.9/htslib/multipart.o build/temp.macosx-11-x86_64-3.9/htslib/probaln.o build/temp.macosx-11-x86_64-3.9/htslib/realn.o build/temp.macosx-11-x86_64-3.9/htslib/regidx.o build/temp.macosx-11-x86_64-3.9/htslib/region.o build/temp.macosx-11-x86_64-3.9/htslib/sam.o build/temp.macosx-11-x86_64-3.9/htslib/synced_bcf_reader.o build/temp.macosx-11-x86_64-3.9/htslib/tbx.o build/temp.macosx-11-x86_64-3.9/htslib/textutils.o build/temp.macosx-11-x86_64-3.9/htslib/thread_pool.o build/temp.macosx-11-x86_64-3.9/htslib/vcf.o build/temp.macosx-11-x86_64-3.9/htslib/vcf_sweep.o build/temp.macosx-11-x86_64-3.9/htslib/vcfutils.o -L/usr/local/lib -L/usr/local/opt/[email protected]/lib -L/usr/local/opt/sqlite/lib -lz -lbz2 -llzma -lcurl -lssl -o build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.cpython-39-darwin.so
creating build/bdist.macosx-11-x86_64
creating build/bdist.macosx-11-x86_64/egg
creating build/bdist.macosx-11-x86_64/egg/cyvcf2
creating build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.bug.117.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_reader.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/issue_198.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz.tbi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_writer.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.vcf.gz.tbi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-invalid-header.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-alt-repr.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.snpeff.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/__init__.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/no-seq-names.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/seg.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-diff.csi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/bug.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-haploidX.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/issue_44.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/empty.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_gt_bases.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-hemi.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/decomposed.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.mnp.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_hemi.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_cli.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-multiallelic-homozygous-alt.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.snpeff.bcf.csi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.comp_het.3.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/no-seq-len.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/o.vcf.gz -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-strict-gt-option-flag.vcf.gz.tbi -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test_gt_alt_freqs.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test.snpeff.bcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/tests/test-format-string.vcf -> build/bdist.macosx-11-x86_64/egg/cyvcf2/tests
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/__init__.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.cpython-39-darwin.so -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/helpers.c -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.pxd -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.pyx -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/relatedness.h -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cyvcf2.c -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/cli.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/helpers.h -> build/bdist.macosx-11-x86_64/egg/cyvcf2
copying build/lib.macosx-11-x86_64-3.9/cyvcf2/__main__.py -> build/bdist.macosx-11-x86_64/egg/cyvcf2
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/test_reader.py to test_reader.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/test_writer.py to test_writer.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/test_hemi.py to test_hemi.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/tests/test_cli.py to test_cli.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/__init__.py to __init__.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/cli.py to cli.cpython-39.pyc
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/__main__.py to __main__.cpython-39.pyc
creating stub loader for cyvcf2/cyvcf2.cpython-39-darwin.so
byte-compiling build/bdist.macosx-11-x86_64/egg/cyvcf2/cyvcf2.py to cyvcf2.cpython-39.pyc
creating build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/PKG-INFO -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/SOURCES.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/dependency_links.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/entry_points.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/not-zip-safe -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/requires.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
copying cyvcf2.egg-info/top_level.txt -> build/bdist.macosx-11-x86_64/egg/EGG-INFO
writing build/bdist.macosx-11-x86_64/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg' and adding 'build/bdist.macosx-11-x86_64/egg' to it
removing 'build/bdist.macosx-11-x86_64/egg' (and everything under it)
Processing cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg
removing '/Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg' (and everything under it)
creating /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg
Extracting cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg to /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
cyvcf2 0.30.8 is already the active version in easy-install.pth
Installing cyvcf2 script to /Users/alan/.virtualenvs/pybase/bin

Installed /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages/cyvcf2-0.30.8-py3.9-macosx-11-x86_64.egg
Processing dependencies for cyvcf2==0.30.8
Searching for click==7.1.2
Best match: click 7.1.2
Adding click 7.1.2 to easy-install.pth file

Using /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
Searching for coloredlogs==15.0
Best match: coloredlogs 15.0
Adding coloredlogs 15.0 to easy-install.pth file
Installing coloredlogs script to /Users/alan/.virtualenvs/pybase/bin

Using /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
Searching for numpy==1.20.1
Best match: numpy 1.20.1
Adding numpy 1.20.1 to easy-install.pth file
Installing f2py script to /Users/alan/.virtualenvs/pybase/bin
Installing f2py3 script to /Users/alan/.virtualenvs/pybase/bin
Installing f2py3.9 script to /Users/alan/.virtualenvs/pybase/bin

Using /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
Searching for humanfriendly==9.1
Best match: humanfriendly 9.1
Adding humanfriendly 9.1 to easy-install.pth file
Installing humanfriendly script to /Users/alan/.virtualenvs/pybase/bin

Using /Users/alan/.virtualenvs/pybase/lib/python3.9/site-packages
Finished processing dependencies for cyvcf2==0.30.8

@brentp
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brentp commented May 28, 2021

did you try: ./configure --enable-libcurl --without-libdeflate?

libdeflate is optoinal and that's what was giving the first error

@alanwilter
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Thanks a lot @brentp, it did work.

@brentp
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brentp commented May 28, 2021

oh excellent!

@alanwilter
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Sorry guys but something in 0.30.14 is broken, it does not work with S3 anymore.

Try this to reproduce the error:

docker run --rm -i -t amazonlinux:latest bash

# inside docker
yum update -y
yum install -y --setopt install_weak_deps=false python3
pip3 install --upgrade pip
pip3 install cyvcf2=0.30.12

export AWS_SECRET_ACCESS_KEY=_use_yours_
export AWS_ACCESS_KEY_ID=_use_yours_

python3 -c "import cyvcf2; print(cyvcf2.__version__)"
# 0.30.12

# test_case
python3 <<EOF
from cyvcf2 import VCF
# Public S3 VCF
vcfs3 = VCF('s3://3kricegenome/test/test.vcf.gz')
vv = vcfs3('9311_chr01:1011-1011')
v1 = next(vv)
print(dict(v1.INFO))
EOF
# {'AN': 2, 'DP': 12, 'MQ': 26.549999237060547, 'MQ0': 2}

# Upgrade to latest cyvcf2:
pip3 install cyvcf2==0.30.14

python3 -c "import cyvcf2; print(cyvcf2.__version__)"
# 0.30.14

# run test_case again and it will fail
Traceback (most recent call last):
  File "<stdin>", line 5, in <module>
StopIteration

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