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pysam-developers / pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
https://pysam.readthedocs.io/en/latest/
MIT License
764 stars 275 forks source link

Install from github: failed to set dynamic section sizes: bad value #1176

Closed Hrovatin closed 1 year ago

Hrovatin commented 1 year ago

I tried to install from github repo, but got the below error (I omitted the earlier install outputs as I assume they wont be relevant for the error below). I am installing on linux within condaenv with Cython==0.29.33 and htslib == 1.9 

le_libcurl.o
ranlib libhts.a
building 'pysam.libchtslib' extension
creating build/temp.linux-x86_64-cpython-310
creating build/temp.linux-x86_64-cpython-310/pysam
gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /net/bmc-la
b5/data/kellis/users/khrovati/miniconda/envs/analysis/include -fPIC -O2 -isystem /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include -I/net/bmc-lab5/data/kellis/users/
khrovati/miniconda/envs/analysis/include -fPIC -fPIC -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/pysam -I/net/bmc-lab5/data/kellis
/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/htslib -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/samt
ools -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/samtools/lz4 -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/l
ib/python3.10/site-packages/pysam/bcftools -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam -I/net/bmc-lab5/data/kellis/users/khrovati/
miniconda/envs/analysis/include/python3.10 -c pysam/htslib_util.c -o build/temp.linux-x86_64-cpython-310/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error
=declaration-after-statement
gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /net/bmc-la
b5/data/kellis/users/khrovati/miniconda/envs/analysis/include -fPIC -O2 -isystem /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include -I/net/bmc-lab5/data/kellis/users/
khrovati/miniconda/envs/analysis/include -fPIC -fPIC -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/pysam -I/net/bmc-lab5/data/kellis
/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/htslib -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/samt
ools -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/samtools/lz4 -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/l
ib/python3.10/site-packages/pysam/bcftools -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam -I/net/bmc-lab5/data/kellis/users/khrovati/
miniconda/envs/analysis/include/python3.10 -c pysam/libchtslib.c -o build/temp.linux-x86_64-cpython-310/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=d
eclaration-after-statement
gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/net/bmc-lab5/data/kellis/users/khrovati/min
iconda/envs/analysis/lib -Wl,-rpath-link,/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -Wl,--a
llow-shlib-undefined -Wl,-rpath,/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -Wl,-rpath-link,/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -L
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm -I/net/bmc-lab5/data/kellis
/users/khrovati/miniconda/envs/analysis/include -fPIC build/temp.linux-x86_64-cpython-310/pysam/htslib_util.o build/temp.linux-x86_64-cpython-310/pysam/libchtslib.o htslib/kfunc.o htslib/k
string.o htslib/bcf_sr_sort.o htslib/bgzf.o htslib/errmod.o htslib/faidx.o htslib/header.o htslib/hfile.o htslib/hts.o htslib/hts_expr.o htslib/hts_os.o htslib/md5.o htslib/multipart.o hts
lib/probaln.o htslib/realn.o htslib/regidx.o htslib/region.o htslib/sam.o htslib/synced_bcf_reader.o htslib/vcf_sweep.o htslib/tbx.o htslib/textutils.o htslib/thread_pool.o htslib/vcf.o ht
slib/vcfutils.o htslib/cram/cram_codecs.o htslib/cram/cram_decode.o htslib/cram/cram_encode.o htslib/cram/cram_external.o htslib/cram/cram_index.o htslib/cram/cram_io.o htslib/cram/cram_st
ats.o htslib/cram/mFILE.o htslib/cram/open_trace_file.o htslib/cram/pooled_alloc.o htslib/cram/string_alloc.o htslib/htscodecs/htscodecs/arith_dynamic.o htslib/htscodecs/htscodecs/fqzcomp_
qual.o htslib/htscodecs/htscodecs/htscodecs.o htslib/htscodecs/htscodecs/pack.o htslib/htscodecs/htscodecs/rANS_static4x16pr.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.o htslib/h
tscodecs/htscodecs/rANS_static32x16pr_avx512.o htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.o htslib/htscodecs/htscodecs/rANS_static32x16pr.o htslib/htscodecs/htscodecs/rANS_static.o
 htslib/htscodecs/htscodecs/rle.o htslib/htscodecs/htscodecs/tokenise_name3.o htslib/htscodecs/htscodecs/utils.o htslib/hfile_libcurl.o -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda
/envs/analysis/lib/python3.10/site-packages/pysam/pysam -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam -Lbuild/lib.linux-x86_64-cpyth
on-310/pysam -lz -lz -lm -lbz2 -llzma -lcurl -o build/lib.linux-x86_64-cpython-310/pysam/libchtslib.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat/ld: htslib/kstring.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared 
object; recompile with -fPIC
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat/ld: failed to set dynamic section sizes: bad value
collect2: error: ld returned 1 exit status
error: command '/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcc' failed with exit code 1
AndreasHeger commented 1 year ago

Thanks, if you compiled multiple times, could you please try again from a clean checkout? The error message suggests to compile with -fPIC, which seems to be set in the build trace, which might indicate you are trying to combine objects from different builds.

Also, can you please provide your build command, any environment variables you set and what kind of linux system you are working on?

Hrovatin commented 1 year ago

By clean checkout do you mean downloading the package files again?

For the install I simply called python setup.py install

Operating system: Operating System: CentOS Linux 7 (Core) CPE OS Name: cpe:/o:centos:centos:7 Kernel: Linux 3.10.0-514.2.2.el7.x86_64 Architecture: x86-64

Env vars:

RSTUDIO_WHICH_R=/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/bin/R                                                                                                      
LDFLAGS=-L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm                                                                                         
MANPATH=/opt/ohpc/pub/mpi/mvapich2-gnu/2.2/man:/opt/ohpc/pub/compiler/gcc/5.4.0/share/man:/opt/ohpc/pub/autotools/share/man:/usr/local/share/man:/usr/share/man/overrides:/usr/share/man/en:
/usr/share/man                                                                                                                                                                              
R_HOME_OLD=                                                                                                                                                                                 
XDG_SESSION_ID=358758                                                                                                                                                                       
LDFLAGS_OLD=                                                                                                                                                                                
_ModuleTable003_=bWUiXT0ib2hwYyIsWyJsb2FkT3JkZXIiXT01LHByb3BUPXt9LFsic2hvcnQiXT0ib2hwYyIsWyJzdGF0dXMiXT0iYWN0aXZlIix9LHBydW49e1siRk4iXT0iL29wdC9vaHBjL3B1Yi9tb2R1bGVmaWxlcy9wcnVuLzEuMSIsWyJ
kZWZhdWx0Il09MSxbImZ1bGxOYW1lIl09InBydW4vMS4xIixbImxvYWRPcmRlciJdPTIscHJvcFQ9e30sWyJzaG9ydCJdPSJwcnVuIixbInN0YXR1cyJdPSJhY3RpdmUiLH0sfSxtcGF0aEE9eyIvb3B0L29ocGMvcHViL21vZHVsZWRlcHMvZ251LW1
2YXBpY2gyIiwiL29wdC9vaHBjL3B1Yi9tb2R1bGVkZXBzL2dudSIsIi9vcHQvb2hwYy9wdWIvbW9kdWxlZmlsZXMiLCIvaG9tZS9zb2Z0d2FyZS9tb2R1bGVmaWxlcyIsfSxbInN5c3RlbUJhc2VNUEFU                                   
TERM_PROGRAM=tmux                                                                                                                                                                           
HOSTNAME=luria                                                                                                                                                                              
TERM=tmux-256color                                                                                                                                                                          
SHELL=/bin/bash                                                                                                                                                                             
HISTSIZE=1000                                                                                                                                                                               
SSH_CLIENT=18.30.139.89 49817 22                                                                                                                                                            
LMOD_DEFAULT_MODULEPATH=/opt/ohpc/pub/modulefiles:/home/software/modulefiles                                                                                                                
CONDA_SHLVL=4                                                                                                                                                                               
TERM_PROGRAM_VERSION=3.3                                                                                                                                                                    
CONDA_PROMPT_MODIFIER=(analysis)                                                                                                                                                            
GSETTINGS_SCHEMA_DIR_CONDA_BACKUP=                                                                                                                                                          
LMOD_PKG=/opt/ohpc/admin/lmod/lmod                                                                                                                                                          
OLDPWD=/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages                                                                                        
LMOD_VERSION=6.5.11                                                                                                                                                                         
SSH_TTY=/dev/pts/16                                                                                                                                                                         
QT_GRAPHICSSYSTEM_CHECKED=1                                                                                                                                                                 
USER=khrovati                                                                                                                                                                               
QT_QPA_PLATFORM_OLD=                                                                                                                                                                        
LS_COLORS=                                                                                                                                                                                  
LD_LIBRARY_PATH=/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/R/lib/                                                                                                 
CONDA_EXE=/net/bmc-lab5/data/kellis/users/khrovati/miniconda/bin/conda                                                                                                                      
_ModuleTable004_=SCJdPSIvb3B0L29ocGMvcHViL21vZHVsZWZpbGVzOi9ob21lL3NvZnR3YXJlL21vZHVsZWZpbGVzIixbInZlcnNpb24iXT0yLH0=                                                                       
TMOUT=2592000                                                                                                                                                                               
TMUX=/tmp/tmux-240741/default,1763,0                                                                                                                                                        
_CE_CONDA=                                                                                                                                                                                  
LMOD_PREPEND_BLOCK=normal   
CONDA_PREFIX=/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis
R_LIBS=
PWD=/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam
_LMFILES_=/opt/ohpc/pub/modulefiles/autotools:/opt/ohpc/pub/modulefiles/prun/1.1:/opt/ohpc/pub/modulefiles/gnu/5.4.0:/opt/ohpc/pub/moduledeps/gnu/mvapich2/2.2:/opt/ohpc/pub/modulefiles/ohp
c
R_LIBS_OLD=
LD_LIBRARY_PATH_OLD=
LANG=en_GB.UTF-8
MODULEPATH=/opt/ohpc/pub/moduledeps/gnu-mvapich2:/opt/ohpc/pub/moduledeps/gnu:/opt/ohpc/pub/modulefiles:/home/software/modulefiles
_ModuleTable_Sz_=4
WS=/net/bmc-lab5/data/kellis/users/khrovati/
LOADEDMODULES=autotools:prun/1.1:gnu/5.4.0:mvapich2/2.2:ohpc
KDEDIRS=/usr
TMUX_PANE=%0
QT_QPA_PLATFORM=offscreen
LMOD_CMD=/opt/ohpc/admin/lmod/lmod/libexec/lmod 
CFLAGS_OLD=
_CE_M=
KRB5CCNAME=KEYRING:persistent:240741:240741
HISTCONTROL=ignoredups
SHLVL=2
HOME=/home/khrovati
CFLAGS=-I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include 
MPI_DIR=/opt/ohpc/pub/mpi/mvapich2-gnu/2.2
_ModuleTable002_=Rk4iXT0iL29wdC9vaHBjL3B1Yi9tb2R1bGVmaWxlcy9nbnUvNS40LjAiLFsiZGVmYXVsdCJdPTEsWyJmdWxsTmFtZSJdPSJnbnUvNS40LjAiLFsibG9hZE9yZGVyIl09Myxwcm9wVD17fSxbInNob3J0Il09ImdudSIsWyJzdGF
0dXMiXT0iYWN0aXZlIix9LG12YXBpY2gyPXtbIkZOIl09Ii9vcHQvb2hwYy9wdWIvbW9kdWxlZGVwcy9nbnUvbXZhcGljaDIvMi4yIixbImRlZmF1bHQiXT0xLFsiZnVsbE5hbWUiXT0ibXZhcGljaDIvMi4yIixbImxvYWRPcmRlciJdPTQscHJvcFQ
9e30sWyJzaG9ydCJdPSJtdmFwaWNoMiIsWyJzdGF0dXMiXT0iYWN0aXZlIix9LG9ocGM9e1siRk4iXT0iL29wdC9vaHBjL3B1Yi9tb2R1bGVmaWxlcy9vaHBjIixbImRlZmF1bHQiXT0wLFsiZnVsbE5h
HTSLIB_CONFIGURE_OPTIONS=--enable-plugins
BASH_ENV=/opt/ohpc/admin/lmod/lmod/init/bash
LOGNAME=khrovati
CONDA_PYTHON_EXE=/net/bmc-lab5/data/kellis/users/khrovati/miniconda/bin/python
SSH_CONNECTION=18.30.139.89 49817 10.159.3.125 22
MODULESHOME=/opt/ohpc/admin/lmod/lmod
PKG_CONFIG_PATH=/opt/ohpc/pub/mpi/mvapich2-gnu/2.2/lib/pkgconfig
LESSOPEN=||/usr/bin/lesspipe.sh %s
CONDA_DEFAULT_ENV=analysis
R_HOME=/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/R
LMOD_FULL_SETTARG_SUPPORT=no
LMOD_FAMILY_COMPILER=gnu
XDG_RUNTIME_DIR=/run/user/240741
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
LMOD_DIR=/opt/ohpc/admin/lmod/lmod/libexec
INCLUDE=/opt/ohpc/pub/compiler/gcc/5.4.0/include
LMOD_FAMILY_MPI=mvapich2
LMOD_COLORIZE=no
BASH_FUNC_module()=() {  eval $($LMOD_CMD bash "$@");
 [ $? = 0 ] && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
}
BASH_FUNC_ml()=() {  eval $($LMOD_DIR/ml_cmd "$@")
}
_=/usr/bin/printenv
jmarshall commented 1 year ago

You have values set for CFLAGS and LDFLAGS that don't include -fPIC, so I suspect this is a variation on #1146.

However this should have been recently worked around on master. Hence:

  1. What exact git commit (e.g. as reported by git describe --tags) are you building?
  2. Please show the complete build log.
Hrovatin commented 1 year ago

I downloaded the git repository again from master: v0.20.0-40-g3888168

This is full output of install:

# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: (sysconfig) CC=gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat
# pysam: (env) CFLAGS=-I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include  -fPIC
# pysam: (env) LDFLAGS=-L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm 
checking for gcc... gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... configure: error: in `/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/htslib':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
checking for gcc... gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... configure: error: in `/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/htslib':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
# pysam: htslib configure options: None
# pysam: htslib_config HTS_CFLAGS_AVX2=-mavx2
# pysam: htslib_config HTS_CFLAGS_AVX512=-mavx512f
# pysam: htslib_config HTS_CFLAGS_SSE4=-mpopcnt -msse4.1 -mssse3
# pysam: htslib_config HTS_HAVE_NEON=
# pysam: htslib_config LIBHTS_OBJS=kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o
# pysam: htslib_config LIBS=-lz -lm -lbz2 -llzma -lcurl
# pysam: htslib_config PLATFORM=Linux
# pysam: config_option: ENABLE_GCS=0
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: ENABLE_S3=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_LIBBZ2=0
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_LIBDEFLATE=0
# pysam: config_option: HAVE_LIBLZMA=0
# pysam: config_option: HAVE_MMAP=0
running install
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running bdist_egg
running egg_info
creating pysam.egg-info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing requirements to pysam.egg-info/requires.txt
writing top-level names to pysam.egg-info/top_level.txt
writing manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
warning: no files found matching 'pysam/libc*.c'
warning: no previously-included files found matching 'htslib/config.mk'
adding license file 'AUTHORS'
writing manifest file 'pysam.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib.linux-x86_64-cpython-310
creating build/lib.linux-x86_64-cpython-310/pysam
copying pysam/Pileup.py -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/__init__.py -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/bcftools.py -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/samtools.py -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/utils.py -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/version.py -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/config.py -> build/lib.linux-x86_64-cpython-310/pysam
creating build/lib.linux-x86_64-cpython-310/pysam/include
copying pysam/include/__init__.py -> build/lib.linux-x86_64-cpython-310/pysam/include
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'pysam.include.htslib.cram' as data is deprecated, please list it in `packages`.
    !!

    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'pysam.include.htslib.cram' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'pysam.include.htslib.cram' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'pysam.include.htslib.cram' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.

!!

  check.warn(importable)
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'pysam.include.htslib.htscodecs.htscodecs' as data is deprecated, please list it in `packages`.
    !!

    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'pysam.include.htslib.htscodecs.htscodecs' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'pysam.include.htslib.htscodecs.htscodecs' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'pysam.include.htslib.htscodecs.htscodecs' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.

!!

  check.warn(importable)
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'pysam.include.htslib.m4' as data is deprecated, please list it in `packages`.
    !!

    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'pysam.include.htslib.m4' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'pysam.include.htslib.m4' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'pysam.include.htslib.m4' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.

!!

  check.warn(importable)
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'pysam.include.htslib.os' as data is deprecated, please list it in `packages`.
    !!

    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'pysam.include.htslib.os' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'pysam.include.htslib.os' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'pysam.include.htslib.os' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.

!!

  check.warn(importable)
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'pysam.include.samtools.lz4' as data is deprecated, please list it in `packages`.
    !!

    ############################
    # Package would be ignored #
    ############################
    Python recognizes 'pysam.include.samtools.lz4' as an importable package,
    but it is not listed in the `packages` configuration of setuptools.

    'pysam.include.samtools.lz4' has been automatically added to the distribution only
    because it may contain data files, but this behavior is likely to change
    in future versions of setuptools (and therefore is considered deprecated).

    Please make sure that 'pysam.include.samtools.lz4' is included as a package by using
    the `packages` configuration field or the proper discovery methods
    (for example by using `find_namespace_packages(...)`/`find_namespace:`
    instead of `find_packages(...)`/`find:`).

    You can read more about "package discovery" and "data files" on setuptools
    documentation page.

!!

  check.warn(importable)
copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/csamtools_util.h -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/htslib_util.c -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/htslib_util.h -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcalignedsegment.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcalignedsegment.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcalignmentfile.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcalignmentfile.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcbcf.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcbcf.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcbcftools.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcbcftools.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcbgzf.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcbgzf.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcfaidx.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcfaidx.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libchtslib.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libchtslib.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcsamfile.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcsamfile.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcsamtools.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcsamtools.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libctabix.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libctabix.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libctabix.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libctabixproxies.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libctabixproxies.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcutils.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcutils.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcutils.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcvcf.pyi -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/libcvcf.pyx -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/py.typed -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/pysam_stream.h -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/pysam_util.c -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/pysam_util.h -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/version.h -> build/lib.linux-x86_64-cpython-310/pysam
copying pysam/version.pyi -> build/lib.linux-x86_64-cpython-310/pysam
creating build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/LICENSE -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/README -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/amplicon_stats.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/amplicon_stats.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam2depth.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam2depth.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_addrprg.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_addrprg.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_ampliconclip.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_ampliconclip.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_aux.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_aux.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_cat.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_cat.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_color.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_color.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_consensus.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_fastq.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_fastq.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_flags.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_flags.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_import.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_import.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_index.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_index.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_lpileup.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_lpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_markdup.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_markdup.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_mate.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_mate.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_md.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_md.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_plbuf.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_plbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_plcmd.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_plcmd.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_quickcheck.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_quickcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_reheader.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_rmdup.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_rmdup.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_rmdupse.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_rmdupse.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_samples.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_samples.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_sort.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_sort.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_split.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_split.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_stat.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bam_stat.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bamshuf.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bamshuf.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bamtk.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bamtk.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bedcov.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bedcov.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bedidx.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bedidx.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/consensus_pileup.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/consensus_pileup.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/consensus_pileup.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/coverage.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/coverage.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/cram_size.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/cram_size.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/cut_target.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/cut_target.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/dict.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/dict.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/faidx.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/faidx.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/padding.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/padding.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/phase.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/phase.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/reference.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/reference.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/reset.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/reset.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sam_opts.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sam_opts.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sam_utils.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sam_utils.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sam_utils.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sam_view.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sam_view.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sample.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sample.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/sample.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/samtools.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/samtools.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/splaysort.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/stats.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/stats.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/stats_isize.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/stats_isize.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/tmp_file.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/tmp_file.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
copying samtools/version.sh -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
creating build/lib.linux-x86_64-cpython-310/pysam/include/samtools/lz4
copying samtools/lz4/LICENSE -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools/lz4
copying samtools/lz4/lz4.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools/lz4
copying samtools/lz4/lz4.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools/lz4
copying samtools/lz4/lz4.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools/lz4
copying samtools/config.h -> build/lib.linux-x86_64-cpython-310/pysam/include/samtools
creating build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/HMM.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/HMM.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/LICENSE -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/README -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/abuf.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/abuf.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/abuf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam2bcf.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam2bcf.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam2bcf_iaux.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam2bcf_indel.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam_sample.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam_sample.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bcftools.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bin.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bin.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/call.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/ccall.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/ccall.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/cigar_state.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/cols.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/cols.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/cols.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/consensus.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/convert.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/convert.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/csq.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/csq.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/dbuf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/dist.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/dist.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/dist.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/em.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/em.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/extsort.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/extsort.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/extsort.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/filter.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/filter.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/gvcf.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/gvcf.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/hclust.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/hclust.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/hex.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/kmin.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/kmin.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/main.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/main.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/mcall.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/mcall.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/mpileup.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/mpileup.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/ploidy.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/ploidy.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/prob1.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/prob1.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/read_consensus.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/read_consensus.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/read_consensus.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/regidx.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/regidx.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/reheader.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/reheader.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/smpl_ilist.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/smpl_ilist.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/str_finder.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/str_finder.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/str_finder.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/tabix.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/tabix.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/tsv2vcf.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/tsv2vcf.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/utlist.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/variantkey.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfannotate.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfannotate.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfbuf.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfbuf.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfcall.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfcall.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfcnv.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfcnv.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfconcat.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfconcat.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfconvert.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfconvert.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcffilter.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcffilter.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfgtcheck.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfhead.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfhead.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfindex.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfindex.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfisec.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfisec.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfmerge.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfmerge.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfnorm.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfnorm.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfplugin.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfplugin.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfquery.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfquery.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfroh.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfroh.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfsom.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfsom.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfsort.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfsort.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfstats.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfstats.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfview.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcfview.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcmp.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcmp.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/version.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/version.c.pysam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/version.sh -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
copying bcftools/config.h -> build/lib.linux-x86_64-cpython-310/pysam/include/bcftools
creating build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/LICENSE -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/Makefile -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/README -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/bcf_sr_sort.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/bgzf.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/bgzip.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/builddir_vars.mk.in -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/config.h.in -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/config.mk.in -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/configure -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/configure.ac -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/errmod.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/faidx.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/header.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/header.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hfile.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hfile_gcs.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hfile_libcurl.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hfile_s3.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hfile_s3_write.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hts.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hts_expr.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hts_os.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/hts_time_funcs.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/htscodecs_bundled.mk -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/htscodecs_external.mk -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/htsfile.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/htslib.mk -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/htslib.pc.in -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/htslib_vars.mk -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/kfunc.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/kstring.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/md5.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/multipart.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/plugin.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/probaln.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/realn.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/regidx.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/region.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/sam.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/sam_internal.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/synced_bcf_reader.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/tabix.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/tbx.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/textutils.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/textutils_internal.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/thread_pool.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/vcf.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/vcf_sweep.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/vcfutils.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
copying htslib/version.sh -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
creating build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_codecs.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_codecs.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_decode.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_decode.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_encode.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_encode.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_external.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_index.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_index.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_io.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_io.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_samtools.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_stats.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_stats.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/cram_structs.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/mFILE.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/mFILE.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/misc.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/open_trace_file.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/open_trace_file.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/os.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/pooled_alloc.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/pooled_alloc.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/string_alloc.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
copying htslib/cram/string_alloc.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/cram
creating build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs
creating build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/arith_dynamic.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/arith_dynamic.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/c_range_coder.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/c_simple_model.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/fqzcomp_qual.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/fqzcomp_qual.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/htscodecs.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/htscodecs.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/htscodecs_endian.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/pack.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/pack.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/permute.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/pooled_alloc.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_byte.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static16_int.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static4x16.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_static4x16pr.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rANS_word.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rle.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/rle.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/tokenise_name3.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/tokenise_name3.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/utils.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/utils.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/varint.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/varint2.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
copying htslib/htscodecs/htscodecs/version.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htscodecs/htscodecs
creating build/lib.linux-x86_64-cpython-310/pysam/include/htslib/m4
copying htslib/m4/ax_check_compile_flag.m4 -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/m4
copying htslib/m4/hts_hide_dynamic_syms.m4 -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/m4
copying htslib/m4/hts_prog_cc_warnings.m4 -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/m4
copying htslib/m4/pkg.m4 -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/m4
creating build/lib.linux-x86_64-cpython-310/pysam/include/htslib/os
copying htslib/os/lzma_stub.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/os
copying htslib/os/rand.c -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/os
copying htslib/config.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib
creating build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/hts_expr.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/kroundup.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-cpython-310/pysam/include/htslib/htslib
running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
cythoning pysam/libcutils.pyx to pysam/libcutils.c
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
warning: pysam/libcalignmentfile.pyx:2572:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2577:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2582:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2621:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2626:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2631:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
cythoning pysam/libctabix.pyx to pysam/libctabix.c
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
creating htslib/config_vars.h for 'pysam.libchtslib' extension
building 'libhts.a'
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o header.o header.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.17"' > version.h
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o hts.o hts.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o hts_expr.o hts_expr.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o md5.o md5.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o multipart.o multipart.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o realn.o realn.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o region.o region.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o sam.o sam.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -g -Wall -O2 -fvisibility=hidden -mavx2 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx2.c
gcc -g -Wall -O2 -fvisibility=hidden -mavx512f -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_avx512.c
gcc -g -Wall -O2 -fvisibility=hidden -mpopcnt -msse4.1 -mssse3 -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr_sse4.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static32x16pr.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o htscodecs/htscodecs/utils.o htscodecs/htscodecs/utils.c
gcc -g -Wall -O2 -fvisibility=hidden  -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement  -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static32x16pr_avx2.o htscodecs/htscodecs/rANS_static32x16pr_avx512.o htscodecs/htscodecs/rANS_static32x16pr_sse4.o htscodecs/htscodecs/rANS_static32x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/utils.o hfile_libcurl.o
ranlib libhts.a
building 'pysam.libchtslib' extension
creating build/temp.linux-x86_64-cpython-310
creating build/temp.linux-x86_64-cpython-310/pysam
gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include -fPIC -O2 -isystem /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include -fPIC -fPIC -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/pysam -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/htslib -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/samtools -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/samtools/lz4 -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/bcftools -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include/python3.10 -c pysam/htslib_util.c -o build/temp.linux-x86_64-cpython-310/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include -fPIC -O2 -isystem /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include -fPIC -fPIC -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/pysam -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/htslib -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/samtools -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/samtools/lz4 -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/bcftools -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include/python3.10 -c pysam/libchtslib.c -o build/temp.linux-x86_64-cpython-310/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -shared -Wl,--allow-shlib-undefined -Wl,-rpath,/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -Wl,-rpath-link,/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -Wl,--allow-shlib-undefined -Wl,-rpath,/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -Wl,-rpath-link,/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include -fPIC build/temp.linux-x86_64-cpython-310/pysam/htslib_util.o build/temp.linux-x86_64-cpython-310/pysam/libchtslib.o htslib/kfunc.o htslib/kstring.o htslib/bcf_sr_sort.o htslib/bgzf.o htslib/errmod.o htslib/faidx.o htslib/header.o htslib/hfile.o htslib/hts.o htslib/hts_expr.o htslib/hts_os.o htslib/md5.o htslib/multipart.o htslib/probaln.o htslib/realn.o htslib/regidx.o htslib/region.o htslib/sam.o htslib/synced_bcf_reader.o htslib/vcf_sweep.o htslib/tbx.o htslib/textutils.o htslib/thread_pool.o htslib/vcf.o htslib/vcfutils.o htslib/cram/cram_codecs.o htslib/cram/cram_decode.o htslib/cram/cram_encode.o htslib/cram/cram_external.o htslib/cram/cram_index.o htslib/cram/cram_io.o htslib/cram/cram_stats.o htslib/cram/mFILE.o htslib/cram/open_trace_file.o htslib/cram/pooled_alloc.o htslib/cram/string_alloc.o htslib/htscodecs/htscodecs/arith_dynamic.o htslib/htscodecs/htscodecs/fqzcomp_qual.o htslib/htscodecs/htscodecs/htscodecs.o htslib/htscodecs/htscodecs/pack.o htslib/htscodecs/htscodecs/rANS_static4x16pr.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.o htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.o htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.o htslib/htscodecs/htscodecs/rANS_static32x16pr.o htslib/htscodecs/htscodecs/rANS_static.o htslib/htscodecs/htscodecs/rle.o htslib/htscodecs/htscodecs/tokenise_name3.o htslib/htscodecs/htscodecs/utils.o htslib/hfile_libcurl.o -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/pysam -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam -Lbuild/lib.linux-x86_64-cpython-310/pysam -lz -lz -lm -lbz2 -llzma -lcurl -o build/lib.linux-x86_64-cpython-310/pysam/libchtslib.cpython-310-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat/ld: htslib/kstring.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat/ld: failed to set dynamic section sizes: bad value
collect2: error: ld returned 1 exit status
error: command '/opt/ohpc/pub/compiler/gcc/5.4.0/bin/gcc' failed with exit code 1
jmarshall commented 1 year ago

The first problem now is this:

checking whether we are cross compiling... configure: error: in `/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/htslib':
configure: error: cannot run C compiled programs.

If you show us htslib/config.log we can try to figure out why this is. Was this build started from a clean directory that you downloaded the git repository into? If not, please try again starting from an empty directory and see if that configure error persists.

Hrovatin commented 1 year ago

I removed the htslib (which was installed prior to pysam) and started install from clean pysam directory, but the error at the end remained the same. This is the pysam/htslib/config.log

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by HTSlib configure 1.17, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure --disable-libcurl

## --------- ##
## Platform. ##
## --------- ##

hostname = luria
uname -m = x86_64
uname -r = 3.10.0-514.2.2.el7.x86_64
uname -s = Linux
uname -v = #1 SMP Tue Dec 6 23:06:41 UTC 2016

/usr/bin/uname -p = x86_64
/bin/uname -X     = unknown

/bin/arch              = x86_64
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /opt/ohpc/pub/mpi/mvapich2-gnu/2.2/bin
PATH: /opt/ohpc/pub/compiler/gcc/5.4.0/bin
PATH: /opt/ohpc/pub/prun/1.1
PATH: /opt/ohpc/pub/autotools/bin
PATH: /opt/ohpc/pub/bin
PATH: /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/bin
PATH: /net/bmc-lab5/data/kellis/users/khrovati/miniconda/condabin
PATH: /home/software/google-cloud-sdk/google-cloud-sdk-193.0.0/google-cloud-sdk/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /usr/local/sbin
PATH: /usr/sbin
PATH: /home/khrovati/.local/bin
PATH: /home/khrovati/bin
PATH: /home/khrovati/.local/bin
PATH: /home/khrovati/bin

## ----------- ##
## Core tests. ##
## ----------- ##

configure:2281: checking for gcc
configure:2308: result: gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat
configure:2537: checking for C compiler version
configure:2546: gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat --version >&5
gcc (GCC) 5.4.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2557: $? = 0
configure:2546: gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/opt/ohpc/pub/compiler/gcc/5.4.0/libexec/gcc/x86_64-unknown-linux-gnu/5.4.0/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../configure --disable-multilib --enable-languages=c,c++,fortran --prefix=/opt/ohpc/pub/compiler/gcc/5.4.0
Thread model: posix
gcc version 5.4.0 (GCC) 
configure:2557: $? = 0
configure:2546: gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2557: $? = 1
configure:2546: gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -qversion >&5
gcc: error: unrecognized command line option '-qversion'
gcc: fatal error: no input files
compilation terminated.
configure:2557: $? = 1
configure:2577: checking whether the C compiler works
configure:2599: gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include  -fPIC  -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm  conftest.c  >&5
configure:2603: $? = 0
configure:2651: result: yes
configure:2654: checking for C compiler default output file name
configure:2656: result: a.out
configure:2662: checking for suffix of executables
configure:2669: gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -o conftest -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include  -fPIC  -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm  conftest.c  >&5
configure:2673: $? = 0
configure:2695: result: 
configure:2717: checking whether we are cross compiling
configure:2725: gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -o conftest -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include  -fPIC  -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm  conftest.c  >&5
configure:2729: $? = 0
configure:2736: ./conftest
./conftest: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory
configure:2740: $? = 127
configure:2747: error: in `/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/htslib':
configure:2749: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_env_CC_set=set
ac_cv_env_CC_value='gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat'
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include  -fPIC'
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value='-L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm '
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_PKG_CONFIG_LIBDIR_set=
ac_cv_env_PKG_CONFIG_LIBDIR_value=
ac_cv_env_PKG_CONFIG_PATH_set=set
ac_cv_env_PKG_CONFIG_PATH_value=/opt/ohpc/pub/mpi/mvapich2-gnu/2.2/lib/pkgconfig
ac_cv_env_PKG_CONFIG_set=
ac_cv_env_PKG_CONFIG_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_prog_ac_ct_CC='gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat'

## ----------------- ##
## Output variables. ##
## ----------------- ##

CC='gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat'
CFLAGS='-I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include  -fPIC'
CFLAGS_ARM=''
CFLAGS_X86=''
CPP=''
CPPFLAGS=''
CRYPTO_LIBS=''
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
EXEEXT=''
GREP=''
HTSDIRslash_if_relsrcdir=''
LDFLAGS='-L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm '
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
OBJEXT=''
PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net'
PACKAGE_NAME='HTSlib'
PACKAGE_STRING='HTSlib 1.17'
PACKAGE_TARNAME='htslib'
PACKAGE_URL='http://www.htslib.org/'
PACKAGE_VERSION='1.17'
PATH_SEPARATOR=':'
PKG_CONFIG=''
PKG_CONFIG_LIBDIR=''
PKG_CONFIG_PATH='/opt/ohpc/pub/mpi/mvapich2-gnu/2.2/lib/pkgconfig'
PLATFORM=''
PLUGIN_EXT=''
RANLIB=''
SHELL='/bin/sh'
VERSION_SCRIPT_LDFLAGS=''
ac_ct_CC='gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat'
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
enable_plugins=''
exec_prefix='NONE'
gcs=''
host_alias=''
htmldir='${docdir}'
hts_cflags_avx2=''
hts_cflags_avx512=''
hts_cflags_sse4=''
hts_have_neon=''
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libcurl=''
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pc_requires=''
pdfdir='${docdir}'
plugindir=''
pluginpath=''
prefix='NONE'
private_LIBS=''
program_transform_name='s,x,x,'
psdir='${docdir}'
runstatedir='${localstatedir}/run'
s3=''
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
static_LDFLAGS=''
static_LIBS=''
sysconfdir='${prefix}/etc'
target_alias=''
with_external_htscodecs=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "HTSlib"
#define PACKAGE_TARNAME "htslib"
#define PACKAGE_VERSION "1.17"
#define PACKAGE_STRING "HTSlib 1.17"
#define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net"
#define PACKAGE_URL "http://www.htslib.org/"

configure: exit 1
jmarshall commented 1 year ago

Configure is failing always, which does not abort the pysam build here — which I suppose is a minor bug in pysam's setup.py.

However the underlying problem is with your environment:

configure:2725: gcc -pthread -B /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/compiler_compat -o conftest -I/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/include  -fPIC  -L/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib -lgsl -lgslcblas -lm  conftest.c  >&5
configure:2729: $? = 0
configure:2736: ./conftest
./conftest: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory
configure:2740: $? = 127
configure:2747: error: in `/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/python3.10/site-packages/pysam/htslib':
configure:2749: error: cannot run C compiled programs.

You have CFLAGS and LDFLAGS environment variables set, with -I and -L paths that look like they have been set up by conda. LDFLAGS is set to always link with libgsl, which might be something set up by you or by conda, but this is failing at runtime because libgsl is not available — possibly because you do not have a libgsl-containing conda environment activated.

So you need to understand why these environment variables are set on your system the way they are, and fix them. If you are not inside conda, you should just unset them. You should almost certainly remove all the -l… options from LDFLAGS. In any case, the current problem here is not in pysam.

Hrovatin commented 1 year ago

The issue was resolved by running export LD_LIBRARY_PATH="/net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/" before the install (although this seems like the same as was set above in -L By default the LD_LIBRARY_PATH in this env is /net/bmc-lab5/data/kellis/users/khrovati/miniconda/envs/analysis/lib/R/lib/ No idea why this was not reported above in -L (since it seemed in the above command that -L was set correctly, but apparently it wasnt since doing the export again helped).