------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 FLAVOR=py39 UNAME_r=6.5 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/construction/biology/py-pysam XDG_CONFIG_HOME=/construction/biology/py-pysam XDG_CACHE_HOME=/construction/biology/py-pysam/.cache HOME=/construction/biology/py-pysam TMPDIR="/tmp" PATH=/construction/biology/py-pysam/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-pysam/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- HTSLIB_MODE=external HTSLIB_LIBRARY_DIR=/usr/local/lib HTSLIB_INCLUDE_DIR=/usr/local/include XDG_DATA_HOME=/construction/biology/py-pysam XDG_CONFIG_HOME=/construction/biology/py-pysam XDG_CACHE_HOME=/construction/biology/py-pysam/.cache HOME=/construction/biology/py-pysam TMPDIR="/tmp" PATH=/construction/biology/py-pysam/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin PKG_CONFIG_LIBDIR=/construction/biology/py-pysam/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/py-pysam/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=6.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/pysam" EXAMPLESDIR="share/examples/pysam" DATADIR="share/pysam" WWWDIR="www/pysam" ETCDIR="etc/pysam" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pysam DOCSDIR=/usr/local/share/doc/pysam EXAMPLESDIR=/usr/local/share/examples/pysam WWWDIR=/usr/local/www/pysam ETCDIR=/usr/local/etc/pysam SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes DFLY_STING_XFAIL=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_COMPRESSION_FORMAT=.tgz DEVELOPER=1 WITH_CCACHE_BUILD=yes CCACHE_DIR=/ccache UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600503 OSVERSION=9999999 OSREL=6.5 _OSRELEASE=6.5-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=13 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.pkg Installing /packages/All/gettext-runtime-0.21.1.pkg Installing /packages/All/gmake-4.3_2.pkg Installing /packages/All/libffi-3.4.4.pkg Installing /packages/All/expat-2.5.0.pkg Installing /packages/All/mpdecimal-2.5.1.pkg Installing /packages/All/ncurses-6.4.pkg ===== Message from ncurses-6.4: -- To get the terminfo database please install the terminfo-db package: pkg install terminfo-db Installing /packages/All/readline-8.2.1.pkg Installing /packages/All/openssl-1.1.1u,1.pkg Installing /packages/All/python39-3.9.17.pkg ===== Message from python39-3.9.17: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 Installing /packages/All/py39-setuptools-63.1.0_1.pkg Installing /packages/All/py39-cython-0.29.35.pkg Installing /packages/All/ccache-3.7.12_4.pkg Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for gcc create symlink for gcc (world) create symlink for g++ create symlink for g++ (world) ===== Message from ccache-3.7.12_4: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. Installing /packages/All/libdeflate-1.18.pkg Installing /packages/All/libnghttp2-1.53.0.pkg Installing /packages/All/libssh2-1.11.0,3.pkg Installing /packages/All/libunistring-1.1.pkg Installing /packages/All/libidn2-2.3.4.pkg Installing /packages/All/libpsl-0.21.2_3.pkg Installing /packages/All/ca_root_nss-3.89.1.pkg ===== Message from ca_root_nss-3.89.1: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/curl-8.1.2.pkg Installing /packages/All/htslib-1.17.pkg SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> py39-pysam-0.21.0 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> py39-pysam-0.21.0 depends on file: /usr/local/sbin/pkg - found => pysam-0.21.0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://files.pythonhosted.org/packages/source/p/pysam/pysam-0.21.0.tar.gz pysam-0.21.0.tar.gz 0% of 3957 kB 0 Bps pysam-0.21.0.tar.gz 3957 kB 44 MBps 00s ===> Fetching all distfiles required by py39-pysam-0.21.0 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> py39-pysam-0.21.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-pysam-0.21.0 for building => SHA256 Checksum OK for pysam-0.21.0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> py39-pysam-0.21.0 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by py39-pysam-0.21.0 for building ===> Extracting for py39-pysam-0.21.0 => SHA256 Checksum OK for pysam-0.21.0.tar.gz. Extracted Memory Use: 26.90M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for py39-pysam-0.21.0 ===> Applying ports patches for py39-pysam-0.21.0 from /xports/biology/py-pysam/files SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> py39-pysam-0.21.0 depends on package: gmake>=4.3 - found ===> py39-pysam-0.21.0 depends on executable: cython-3.9 - found ===> py39-pysam-0.21.0 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pysam-0.21.0 depends on file: /usr/local/bin/python3.9 - found ===> py39-pysam-0.21.0 depends on file: /usr/local/bin/ccache - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> py39-pysam-0.21.0 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> py39-pysam-0.21.0 depends on package: gmake>=4.3 - found ===> py39-pysam-0.21.0 depends on executable: cython-3.9 - found ===> py39-pysam-0.21.0 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pysam-0.21.0 depends on file: /usr/local/bin/python3.9 - found ===> py39-pysam-0.21.0 depends on file: /usr/local/bin/ccache - found ===> py39-pysam-0.21.0 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Configuring for py39-pysam-0.21.0 # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running config SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for py39-pysam-0.21.0 # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running build running build_py creating build creating build/lib.dragonfly-6.5-x86_64-cpython-39 creating build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/Pileup.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/bcftools.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/samtools.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/utils.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/version.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/config.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam creating build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include copying pysam/include/__init__.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include running 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 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' no previously-included directories found matching 'tests/' warning: no previously-included files found matching 'htslib/*config*.h' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/local/lib/python3.9/site-packages/setuptools/command/build_py.py:153: 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.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/csamtools_util.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/htslib_util.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/htslib_util.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcalignedsegment.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcalignedsegment.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcalignedsegment.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcalignedsegment.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcalignmentfile.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcalignmentfile.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcalignmentfile.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcalignmentfile.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbcf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbcf.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbcf.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbcf.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbcftools.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbcftools.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbcftools.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbcftools.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbgzf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbgzf.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcbgzf.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcfaidx.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcfaidx.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcfaidx.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcfaidx.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libchtslib.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libchtslib.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libchtslib.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libchtslib.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcsamfile.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcsamfile.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcsamfile.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcsamfile.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcsamtools.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcsamtools.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcsamtools.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcsamtools.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libctabix.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libctabix.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libctabix.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libctabix.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libctabixproxies.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libctabixproxies.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libctabixproxies.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libctabixproxies.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcutils.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcutils.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcutils.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcutils.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcvcf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcvcf.pxd -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcvcf.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/libcvcf.pyx -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/py.typed -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/pysam_stream.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/pysam_util.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/pysam_util.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/version.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam copying pysam/version.pyi -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam creating build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/LICENSE -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/README -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/amplicon_stats.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/amplicon_stats.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam2depth.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam2depth.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_addrprg.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_addrprg.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_ampliconclip.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_ampliconclip.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_ampliconclip.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_aux.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_aux.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_cat.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_cat.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_color.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_color.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_consensus.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_consensus.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_fastq.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_fastq.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_flags.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_flags.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_import.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_import.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_index.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_index.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_lpileup.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_lpileup.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_lpileup.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_markdup.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_markdup.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_mate.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_mate.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_md.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_md.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_plbuf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_plbuf.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_plbuf.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_plcmd.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_plcmd.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_quickcheck.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_quickcheck.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_reheader.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_reheader.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_rmdup.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_rmdup.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_rmdupse.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_rmdupse.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_samples.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_samples.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_sort.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_sort.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_split.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_split.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_stat.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bam_stat.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bamshuf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bamshuf.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bamtk.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bamtk.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bedcov.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bedcov.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bedidx.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bedidx.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/bedidx.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/consensus_pileup.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/consensus_pileup.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/consensus_pileup.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/coverage.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/coverage.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/cram_size.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/cram_size.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/cut_target.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/cut_target.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/dict.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/dict.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/faidx.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/faidx.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/padding.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/padding.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/phase.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/phase.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/reference.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/reference.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/reset.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/reset.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sam_opts.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sam_opts.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sam_opts.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sam_utils.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sam_utils.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sam_utils.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sam_view.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sam_view.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sample.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sample.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/sample.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/samtools.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/samtools.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/samtools.pysam.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/splaysort.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/stats.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/stats.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/stats_isize.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/stats_isize.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/stats_isize.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/tmp_file.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/tmp_file.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/tmp_file.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools copying samtools/version.sh -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools creating build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/lz4 copying samtools/lz4/LICENSE -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/lz4 copying samtools/lz4/lz4.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/lz4 copying samtools/lz4/lz4.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/lz4 copying samtools/config.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools creating build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/HMM.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/HMM.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/HMM.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/LICENSE -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/README -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/abuf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/abuf.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/abuf.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam2bcf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam2bcf.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam2bcf.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam2bcf_iaux.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam2bcf_indel.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam2bcf_indel.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam_sample.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam_sample.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bam_sample.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bcftools.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bcftools.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bcftools.pysam.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bin.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bin.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/bin.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/call.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/ccall.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/ccall.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/cigar_state.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/cols.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/cols.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/cols.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/consensus.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/consensus.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/convert.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/convert.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/convert.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/csq.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/csq.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/dbuf.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/dist.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/dist.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/dist.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/em.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/em.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/extsort.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/extsort.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/extsort.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/filter.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/filter.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/filter.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/gvcf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/gvcf.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/gvcf.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/hclust.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/hclust.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/hclust.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/hex.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/khash_str2str.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/kheap.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/kmin.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/kmin.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/kmin.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/main.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/main.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/mcall.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/mcall.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/mpileup.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/mpileup.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/mw.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/ploidy.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/ploidy.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/ploidy.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/prob1.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/prob1.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/prob1.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/rbuf.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/read_consensus.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/read_consensus.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/read_consensus.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/regidx.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/regidx.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/regidx.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/reheader.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/reheader.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/smpl_ilist.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/smpl_ilist.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/smpl_ilist.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/str_finder.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/str_finder.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/str_finder.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/tabix.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/tabix.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/tsv2vcf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/tsv2vcf.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/tsv2vcf.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/utlist.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/variantkey.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfannotate.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfannotate.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfbuf.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfbuf.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfbuf.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfcall.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfcall.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfcnv.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfcnv.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfconcat.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfconcat.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfconvert.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfconvert.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcffilter.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcffilter.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfgtcheck.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfgtcheck.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfhead.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfhead.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfindex.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfindex.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfisec.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfisec.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfmerge.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfmerge.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfnorm.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfnorm.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfplugin.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfplugin.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfquery.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfquery.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfroh.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfroh.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfsom.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfsom.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfsort.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfsort.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfstats.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfstats.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfview.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcfview.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcmp.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcmp.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/vcmp.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/version.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/version.c.pysam.c -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/version.sh -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools copying bcftools/config.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) building 'pysam.libchtslib' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39 creating build/temp.dragonfly-6.5-x86_64-cpython-39/pysam cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/htslib_util.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libchtslib.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/htslib_util.o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libchtslib.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libchtslib.cpython-39.so -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/samtools creating build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/lz4 cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcsamtools.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/amplicon_stats.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/amplicon_stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam2depth.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_ampliconclip.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_aux.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_cat.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_color.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_consensus.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_flags.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_import.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_index.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_mate.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_md.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_samples.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_samples.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_sort.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_split.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bam_stat.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bamshuf.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bamtk.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bedcov.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/bedidx.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/consensus_pileup.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/coverage.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/cram_size.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/cut_target.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/dict.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/faidx.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/lz4/lz4.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/padding.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/phase.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/reference.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/reset.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/sam_opts.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/sam_utils.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/sam_view.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/sample.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/samtools.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/stats.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/stats_isize.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c samtools/tmp_file.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamtools.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/amplicon_stats.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam2depth.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_addrprg.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_ampliconclip.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_aux.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_cat.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_color.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_consensus.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_fastq.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_flags.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_import.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_index.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_lpileup.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_markdup.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_mate.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_md.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_plbuf.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_plcmd.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_quickcheck.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_reheader.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_rmdup.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_rmdupse.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_samples.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_sort.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_split.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bam_stat.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bamshuf.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bamtk.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bedcov.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/bedidx.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/consensus_pileup.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/coverage.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/cram_size.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/cut_target.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/dict.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/faidx.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/lz4/lz4.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/padding.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/phase.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/reference.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/reset.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/sam_opts.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/sam_utils.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/sam_view.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/sample.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/samtools.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/stats.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/stats_isize.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/samtools/tmp_file.c.pysam.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamtools.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/HMM.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/abuf.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/bcftools.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/bin.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/ccall.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/cols.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/consensus.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/convert.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/csq.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/dist.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/em.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/extsort.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/filter.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/gvcf.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/hclust.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/kmin.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/main.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/mcall.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/mpileup.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/ploidy.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/prob1.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/read_consensus.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/regidx.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/reheader.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/str_finder.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/tabix.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement In function 'init_data', inlined from 'main_vcfcall' at bcftools/vcfcall.c.pysam.c:1114:5: bcftools/vcfcall.c.pysam.c:664:39: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] args->aux.ploidy = (uint8_t*) malloc(args->nsamples); ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/local/include/htslib/kstring.h:30, from /usr/local/include/htslib/hts.h:37, from /usr/local/include/htslib/vcf.h:39, from bcftools/vcfcall.c.pysam.c:35: bcftools/vcfcall.c.pysam.c: In function 'main_vcfcall': /usr/include/stdlib.h:108:7: note: in a call to allocation function 'malloc' declared here void *malloc(size_t) __malloclike __heedresult __alloc_size(1); ^~~~~~ cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfhead.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcfview.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/vcmp.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c bcftools/version.c.pysam.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcbcftools.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/HMM.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/abuf.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bam2bcf.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bam2bcf_iaux.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bam2bcf_indel.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bam_sample.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bcftools.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/bin.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/ccall.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/cols.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/consensus.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/convert.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/csq.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/dist.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/em.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/extsort.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/filter.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/gvcf.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/hclust.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/kmin.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/main.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/mcall.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/mpileup.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/ploidy.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/prob1.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/read_consensus.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/regidx.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/reheader.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/smpl_ilist.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/str_finder.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/tabix.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/tsv2vcf.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfannotate.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfbuf.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfcall.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfcnv.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfconcat.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfconvert.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcffilter.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfgtcheck.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfhead.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfindex.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfisec.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfmerge.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfnorm.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfplugin.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfquery.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfroh.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfsom.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfsort.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfstats.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcfview.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/vcmp.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/bcftools/version.c.pysam.o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcftools.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcftools.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcutils.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/pysam_util.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcutils.o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/pysam_util.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcsamtools.cpython-39 -lcbcftools.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcutils.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcalignmentfile.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignmentfile.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignmentfile.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcsamfile.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamfile.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamfile.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcalignedsegment.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignedsegment.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignedsegment.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libctabix.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libctabix.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabix.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcfaidx.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcfaidx.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcfaidx.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcbcf.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcf.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcf.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcbgzf.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcbgzf.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbgzf.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libctabixproxies.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libctabixproxies.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabixproxies.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.21.0/pysam -I/usr/local/include -I/construction/biology/py-pysam/pysam-0.21.0/samtools -I/construction/biology/py-pysam/pysam-0.21.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.21.0/bcftools -I/construction/biology/py-pysam/pysam-0.21.0 -I/usr/local/include/python3.9 -c pysam/libcvcf.c -o build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-6.5-x86_64-cpython-39/pysam/libcvcf.o -L/construction/biology/py-pysam/pysam-0.21.0/pysam -L/usr/local/lib -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -Lbuild/lib.dragonfly-6.5-x86_64-cpython-39/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcvcf.cpython-39.so -Wl,-rpath,$ORIGIN SUCCEEDED 00:11:17 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> py39-pysam-0.21.0 depends on executable: cython-3.9 - found ===> py39-pysam-0.21.0 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pysam-0.21.0 depends on file: /usr/local/bin/python3.9 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for py39-pysam-0.21.0 ===> py39-pysam-0.21.0 depends on executable: cython-3.9 - found ===> py39-pysam-0.21.0 depends on package: py39-setuptools>=63.1.0 - found ===> py39-pysam-0.21.0 depends on file: /usr/local/bin/python3.9 - found ===> Generating temporary packing list # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is external # pysam: HTSLIB_CONFIGURE_OPTIONS=None running install /usr/local/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py copying pysam/config.py -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam running 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 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' no previously-included directories found matching 'tests/' warning: no previously-included files found matching 'htslib/*config*.h' warning: no previously-included files found matching 'htslib/config.mk' warning: no previously-included files found matching 'htslib/htscodecs.mk' adding license file 'AUTHORS' writing manifest file 'pysam.egg-info/SOURCES.txt' /usr/local/lib/python3.9/site-packages/setuptools/command/build_py.py:153: 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 samtools/samtools_config_vars.h -> build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools running build_ext skipping 'pysam/libchtslib.c' Cython extension (up-to-date) skipping 'pysam/libcsamtools.c' Cython extension (up-to-date) skipping 'pysam/libcbcftools.c' Cython extension (up-to-date) skipping 'pysam/libcutils.c' Cython extension (up-to-date) skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date) skipping 'pysam/libcsamfile.c' Cython extension (up-to-date) skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date) skipping 'pysam/libctabix.c' Cython extension (up-to-date) skipping 'pysam/libcfaidx.c' Cython extension (up-to-date) skipping 'pysam/libcbcf.c' Cython extension (up-to-date) skipping 'pysam/libcbgzf.c' Cython extension (up-to-date) skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date) skipping 'pysam/libcvcf.c' Cython extension (up-to-date) creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension running install_lib creating /construction/biology/py-pysam/stage/usr/local/lib/python3.9 creating /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages creating /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcutils.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabixproxies.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/config.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcftools.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignmentfile.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabix.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcfaidx.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcf.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libchtslib.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/cbcftools_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/csamtools_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/htslib_util.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/htslib_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignedsegment.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignedsegment.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignedsegment.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignedsegment.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignmentfile.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignmentfile.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignmentfile.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignmentfile.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcf.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcf.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcf.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcftools.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcftools.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcftools.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbcftools.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbgzf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbgzf.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbgzf.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcfaidx.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcfaidx.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcfaidx.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcfaidx.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libchtslib.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libchtslib.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libchtslib.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libchtslib.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamfile.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamfile.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamfile.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamfile.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamtools.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamtools.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamtools.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamtools.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabix.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabix.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabix.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabix.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabixproxies.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabixproxies.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabixproxies.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libctabixproxies.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcutils.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcutils.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcutils.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcutils.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcvcf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcvcf.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcvcf.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcvcf.pyx -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/py.typed -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/pysam_stream.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/pysam_util.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/pysam_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/version.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/version.pyi -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamtools.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcalignedsegment.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcbgzf.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcvcf.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/Pileup.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/__init__.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/bcftools.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/samtools.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/utils.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/version.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam creating /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include creating /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/samtools_config_vars.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/LICENSE -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/README -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/amplicon_stats.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/amplicon_stats.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam2depth.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam2depth.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_addrprg.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_addrprg.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_ampliconclip.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_ampliconclip.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_ampliconclip.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_aux.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_aux.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_cat.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_cat.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_color.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_color.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_consensus.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_consensus.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_fastq.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_fastq.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_flags.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_flags.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_import.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_import.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_index.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_index.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_lpileup.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_lpileup.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_lpileup.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_markdup.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_markdup.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_mate.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_mate.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_md.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_md.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_plbuf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_plbuf.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_plbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_plcmd.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_plcmd.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_quickcheck.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_quickcheck.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_reheader.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_reheader.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_rmdup.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_rmdup.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_rmdupse.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_rmdupse.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_samples.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_samples.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_sort.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_sort.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_split.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_split.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_stat.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bam_stat.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bamshuf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bamshuf.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bamtk.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bamtk.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bedcov.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bedcov.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bedidx.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bedidx.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/bedidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/consensus_pileup.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/consensus_pileup.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/consensus_pileup.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/coverage.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/coverage.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/cram_size.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/cram_size.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/cut_target.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/cut_target.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/dict.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/dict.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/faidx.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/faidx.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/padding.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/padding.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/phase.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/phase.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/reference.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/reference.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/reset.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/reset.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sam_opts.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sam_opts.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sam_opts.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sam_utils.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sam_utils.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sam_utils.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sam_view.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sam_view.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sample.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sample.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/sample.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/samtools.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/samtools.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/samtools.pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/splaysort.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/stats.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/stats.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/stats_isize.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/stats_isize.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/stats_isize.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/tmp_file.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/tmp_file.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/tmp_file.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/version.sh -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools creating /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools/lz4 copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/lz4/LICENSE -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools/lz4 copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/lz4/lz4.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools/lz4 copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/lz4/lz4.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools/lz4 copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/lz4/lz4.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools/lz4 copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/samtools/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/samtools creating /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/HMM.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/HMM.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/HMM.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/LICENSE -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/README -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/abuf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/abuf.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/abuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam2bcf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam2bcf.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam2bcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam2bcf_iaux.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam2bcf_iaux.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam2bcf_indel.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam2bcf_indel.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam_sample.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam_sample.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bam_sample.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bcftools.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bcftools.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bcftools.pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bin.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bin.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/bin.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/call.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/ccall.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/ccall.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/cigar_state.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/cols.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/cols.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/cols.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/consensus.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/consensus.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/convert.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/convert.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/convert.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/csq.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/csq.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/dbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/dist.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/dist.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/dist.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/em.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/em.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/extsort.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/extsort.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/extsort.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/filter.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/filter.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/filter.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/gvcf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/gvcf.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/gvcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/hclust.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/hclust.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/hclust.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/hex.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/khash_str2str.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/kheap.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/kmin.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/kmin.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/kmin.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/main.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/main.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/mcall.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/mcall.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/mpileup.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/mpileup.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/mw.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/ploidy.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/ploidy.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/ploidy.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/prob1.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/prob1.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/prob1.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/rbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/read_consensus.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/read_consensus.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/read_consensus.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/regidx.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/regidx.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/regidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/reheader.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/reheader.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/smpl_ilist.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/smpl_ilist.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/smpl_ilist.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/str_finder.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/str_finder.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/str_finder.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/tabix.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/tabix.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/tsv2vcf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/tsv2vcf.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/tsv2vcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/utlist.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/variantkey.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfannotate.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfannotate.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfbuf.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfbuf.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfcall.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfcall.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfcnv.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfcnv.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfconcat.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfconcat.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfconvert.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfconvert.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcffilter.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcffilter.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfgtcheck.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfgtcheck.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfhead.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfhead.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfindex.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfindex.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfisec.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfisec.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfmerge.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfmerge.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfnorm.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfnorm.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfplugin.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfplugin.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfquery.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfquery.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfroh.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfroh.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfsom.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfsom.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfsort.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfsort.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfstats.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfstats.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfview.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcfview.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcmp.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcmp.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/vcmp.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/version.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/version.c.pysam.c -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/version.sh -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/bcftools/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/bcftools copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/include/__init__.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include copying build/lib.dragonfly-6.5-x86_64-cpython-39/pysam/libcsamfile.cpython-39.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/config.py to config.cpython-39.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/Pileup.py to Pileup.cpython-39.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/__init__.py to __init__.cpython-39.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/bcftools.py to bcftools.cpython-39.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/samtools.py to samtools.cpython-39.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/utils.py to utils.cpython-39.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/version.py to version.cpython-39.pyc byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam/include/__init__.py to __init__.cpython-39.pyc writing byte-compilation script '/tmp/tmpd5gaef0g.py' /usr/local/bin/python3.9 /tmp/tmpd5gaef0g.py removing /tmp/tmpd5gaef0g.py running install_egg_info Copying pysam.egg-info to /construction/biology/py-pysam/stage/usr/local/lib/python3.9/site-packages/pysam-0.21.0-py3.9.egg-info running install_scripts writing list of installed files to '/construction/biology/py-pysam/.PLIST.pymodtmp' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Error: /usr/local/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39.so is linked to /usr/local/lib/libdeflate.so.0 from archivers/libdeflate but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libdeflate.so:archivers/libdeflate Error: /usr/local/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39.so is linked to /usr/local/lib/libcurl.so.4 from ftp/curl but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libcurl.so:ftp/curl Error: /usr/local/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39.so is linked to /usr/local/lib/libcrypto.so.11 from security/openssl but it is not declared as a dependency Warning: you need USES=ssl Error: /usr/local/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39.so is linked to /usr/local/lib/libnghttp2.so.14 from www/libnghttp2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libnghttp2.so:www/libnghttp2 Error: /usr/local/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39.so is linked to /usr/local/lib/libssh2.so.1 from security/libssh2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libssh2.so:security/libssh2 Error: /usr/local/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39.so is linked to /usr/local/lib/libpsl.so.5 from dns/libpsl but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libpsl.so:dns/libpsl Error: /usr/local/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39.so is linked to /usr/local/lib/libssl.so.11 from security/openssl but it is not declared as a dependency Warning: you need USES=ssl Error: /usr/local/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39.so is linked to /usr/local/lib/libidn2.so.0 from dns/libidn2 but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libidn2.so:dns/libidn2 Error: /usr/local/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39.so is linked to /usr/local/lib/libunistring.so.5 from devel/libunistring but it is not declared as a dependency Warning: you need LIB_DEPENDS+=libunistring.so:devel/libunistring Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:33 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for py39-pysam-0.21.0 file sizes/checksums [369]: 0% file sizes/checksums [369]: 27% file sizes/checksums [369]: 54% file sizes/checksums [369]: 81% file sizes/checksums [369]: 100% Service unavailablepacking files [369]: 0% packing files [369]: 27% packing files [369]: 54% packing files [369]: 81% packing files [369]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:08 TOTAL TIME 00:12:13