From nobody Tue Jul 19 01:18:40 2022 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4Ln1Dw4fXBz4WWTC for ; Tue, 19 Jul 2022 01:18:40 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Ln1Dw2xVPz3GWk; Tue, 19 Jul 2022 01:18:40 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere1.nyi.freebsd.org (ampere1.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:23]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4Ln1Dw1zHsz10yD; Tue, 19 Jul 2022 01:18:40 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere1.nyi.freebsd.org (localhost [127.0.0.1]) by ampere1.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 26J1IeNi035123; Tue, 19 Jul 2022 01:18:40 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere1.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 26J1Ie8J035115; Tue, 19 Jul 2022 01:18:40 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 19 Jul 2022 01:18:40 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202207190118.26J1Ie8J035115@ampere1.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - 130arm64-quarterly][biology/py-pysam] Failed for py39-pysam-0.19.1 in build Cc: pkg-fallout@FreeBSD.org ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1658193520; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=coDcAEs4/PQRJUKDzLp37+plPBw61vWG2djhAOzWpoc=; b=O5qfpXeI21/mIJrrAbSM/CGs+2WQyaVZ5dGxOGreSj836+q6dyObA2+12So9cYE47mjC3M G8xQW34LObGUVR9ENc/q6n/YAMKcQcfSJeTShSkiAuqJiWRcjl3eg631UeyFe1SgpgXJ90 O4xLJRzLSdb6qjiCfz2aTNfKJoDQ2d6WXexLNA3dPmeVwU3DXmDAmZHS4f1mCNby/rqqPK /PURXtgs1rOchuNFzL7UAy0MW1bsmWjU+wHFfpm7P5KuYmPgOCxijP1I9FXbdSsOD2sPMX m8Q6IWCtyjfqLQUTYXErAxf4k7mSrSA5g19fT+lZ9rVbRZTYJUGXt2rv/+eyow== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1658193520; a=rsa-sha256; cv=none; b=dEjh9vUiDVzSRytzleX1XYiABRvWCVUxDQBQ6ZKKR8qdPJTYV5KqiNRpkAqlGKNrtERz2p wUxI//zxCMxx54Y7S+/IrrUszvLv1YQTadgivtWilQesC/pccpv0Hvd86MEutbshLqdDxD Kyh36MaGcY8bt7A+4eb5osutjrzfyI2jEwyOnK9T68Sm8ppOwuvd9i1T6JVhy69ewilpJf Kq/K1twCEz2dgU5qkM7jsIv8mbdMvEaufk6j8oeUp4pIrlrnPXAWGyB2BkpvnENHZr10v+ 1cMDvLQ6anWruXgaM5rcWV6tHomvnfjT1LjyipFhJlM4h683pjUNMFBS2WI3tg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: http://ampere1.nyi.freebsd.org/data/130arm64-quarterly/339f635d7900/logs/py39-pysam-0.19.1.log Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=130arm64-quarterly&build=339f635d7900 Log: =>> Building biology/py-pysam build started at Tue Jul 19 01:13:25 UTC 2022 port directory: /usr/ports/biology/py-pysam package name: py39-pysam-0.19.1 building for: FreeBSD 130arm64-quarterly-job-01 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 arm64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400063 Jail OSVERSION: 1300139 Job Id: 01 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300139 UNAME_v=FreeBSD 13.0-RELEASE-p11 UNAME_r=13.0-RELEASE-p11 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/130arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/130arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=130arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/130arm64-quarterly/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR=py39 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py39 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pysam/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pysam/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py39/.cache HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pysam/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pysam/work-py39/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/libdata/pkgconfig NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd13 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=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/pysam" EXAMPLESDIR="share/examples/pysam" DATADIR="share/pysam" WWWDIR="www/pysam" ETCDIR="etc/pysam" --End PLIST_SUB-- --SUB_LIST-- 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 --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=13.0-RELEASE-p11 OSREL=13.0 OSVERSION=1300139 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License MIT accepted by the user =========================================================================== =================================================== ===> py39-pysam-0.19.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.18.3.pkg [130arm64-quarterly-job-01] Installing pkg-1.18.3... [130arm64-quarterly-job-01] Extracting pkg-1.18.3: .......... done ===> py39-pysam-0.19.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-pysam-0.19.1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by py39-pysam-0.19.1 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by py39-pysam-0.19.1 for building => SHA256 Checksum OK for pysam-0.19.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by py39-pysam-0.19.1 for building ===> Extracting for py39-pysam-0.19.1 => SHA256 Checksum OK for pysam-0.19.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for py39-pysam-0.19.1 ===> Applying FreeBSD patches for py39-pysam-0.19.1 from /usr/ports/biology/py-pysam/files =========================================================================== =================================================== ===> py39-pysam-0.19.1 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [130arm64-quarterly-job-01] Installing gmake-4.3_2... [130arm64-quarterly-job-01] `-- Installing gettext-runtime-0.21... [130arm64-quarterly-job-01] | `-- Installing indexinfo-0.3.1... [130arm64-quarterly-job-01] | `-- Extracting indexinfo-0.3.1: .... done [130arm64-quarterly-job-01] `-- Extracting gettext-runtime-0.21: .......... done [130arm64-quarterly-job-01] Extracting gmake-4.3_2: .......... done ===> py39-pysam-0.19.1 depends on package: gmake>=4.3 - found ===> Returning to build of py39-pysam-0.19.1 ===> py39-pysam-0.19.1 depends on executable: cython-3.9 - not found ===> Installing existing package /packages/All/py39-cython-0.29.30_1.pkg [130arm64-quarterly-job-01] Installing py39-cython-0.29.30_1... [130arm64-quarterly-job-01] `-- Installing py39-setuptools-62.1.0_1... [130arm64-quarterly-job-01] | `-- Installing python39-3.9.13... [130arm64-quarterly-job-01] | | `-- Installing libffi-3.4.2... [130arm64-quarterly-job-01] | | `-- Extracting libffi-3.4.2: .......... done [130arm64-quarterly-job-01] | | `-- Installing mpdecimal-2.5.1... [130arm64-quarterly-job-01] | | `-- Extracting mpdecimal-2.5.1: .......... done cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/kfunc.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/kstring.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/md5.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/multipart.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/probaln.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/realn.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/regidx.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/region.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/region.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/sam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/synced_bcf_reader.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/tbx.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/textutils.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/thread_pool.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement htslib/thread_pool.c:699:9: warning: code will never be executed [-Wunreachable-code] printf("%d waiting, %d running, %d output, %d, arun %d => %d\t", p->njobs, ^~~~~~ htslib/thread_pool.c:698:9: note: silence by adding parentheses to mark code as explicitly dead if (0) { ^ /* DISABLES CODE */ ( ) 1 warning generated. cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/vcf.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/vcf_sweep.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c htslib/vcfutils.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/htslib_util.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libchtslib.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/bcf_sr_sort.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/bgzf.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/cram_codecs.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/cram_decode.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/cram_encode.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/cram_external.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/cram_index.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/cram_io.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/cram_stats.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/mFILE.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/open_trace_file.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/ cram/pooled_alloc.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/cram/string_alloc.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/errmod.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/faidx.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/header.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/hfile.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/hts.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/hts_expr.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/hts_os.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/htscodecs/htscodecs/arith_dynamic.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/htscodecs/htscodecs/fqzcomp_qual.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/htscodecs/htscodecs/htscodecs.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/htscodecs/htscodecs/pack.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpyth on-39/htslib/htscodecs/htscodecs/rANS_static! .o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/htscodecs/htscodecs/rANS_static4x16pr.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/htscodecs/htscodecs/rle.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/htscodecs/htscodecs/tokenise_name3.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/kfunc.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/kstring.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/md5.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/multipart.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/probaln.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/realn.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/regidx.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/region.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/sam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/synced_bcf_reader.o build/temp.fr eebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/tbx.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/textutils.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/thread_pool.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/vcf.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/vcf_sweep.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/htslib/vcfutils.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/htslib_util.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libchtslib.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -o build/lib.freebsd-13.0-RELEASE-p 11-arm64-cpython-39/pysam/libchtslib.cpython! -39.so -W! l,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools creating build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/lz4 cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcsamtools.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/amplicon_stats.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam2depth.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_ampliconclip.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_aux.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_cat.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_color.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_consensus.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_flags.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_import.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_index.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_mate.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_md.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_samples.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_sort.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_split.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bam_stat.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bamshuf.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bamtk.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bedcov.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/bedidx.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/consensus_pileup.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/coverage.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/cut_target.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/dict.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/faidx.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/lz4/lz4.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/padding.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/phase.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/sam_opts.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/sam_utils.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/sam_view.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/sample.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/samtools.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/stats.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/stats_isize.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c samtools/tmp_file.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcsamtools.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/amplicon_stats.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam2depth.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_addrprg.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_ampliconclip.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_aux.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_cat.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_color.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_consensus.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_fastq.c.pysam.o buil d/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_flags.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_import.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_index.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_lpileup.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_markdup.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_mate.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_md.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_plbuf.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_plcmd.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_quickcheck.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_reheader.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_rmdup.c.pysam.o build/te mp.freebsd-13.0-RELEASE-p11-arm64-cpython-39! /samtools/bam_rmdupse.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_samples.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_sort.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_split.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bam_stat.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bamshuf.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bamtk.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bedcov.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/bedidx.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/consensus_pileup.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/coverage.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/cut_target.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/dict.c .pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/faidx.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/lz4/lz4.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/padding.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/phase.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/sam_opts.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/sam_utils.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/sam_view.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/sample.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/samtools.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/stats.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/stats_isize.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/samtools/tmp_file.c.pysam.o -L/wrkdirs/usr/ports/biology/py-pys am/work-py39/pysam-0.19.1/pysam -L/wrkdirs/u! sr/ports/! biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcsamtools.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/HMM.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/abuf.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bcftools.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/bin.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/ccall.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/cols.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/consensus.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/convert.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/convert.c.pysam.c:534:66: warning: code will never be executed [-Wunreachable-code] default: error("Unexpected type: %d\n", fmt->fmt->type); bcftools_exit(1); break; ^~~~~~~~~~~~~ 1 warning generated. cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/csq.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/dist.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/em.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/extsort.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/filter.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/filter.c.pysam.c:3422:12: warning: code will never be executed [-Wunreachable-code] if (0) filter_debug_print(out, NULL, nout); ^~~~~~~~~~~~~~~~~~ bcftools/filter.c.pysam.c:3422:9: note: silence by adding parentheses to mark code as explicitly dead if (0) filter_debug_print(out, NULL, nout); ^ /* DISABLES CODE */ ( ) 1 warning generated. cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/gvcf.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/hclust.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/kmin.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/main.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/mcall.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/mpileup.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/ploidy.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/prob1.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/regidx.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/reheader.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/str_finder.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/tabix.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/tabix.c.pysam.c:58:22: warning: code will never be executed [-Wunreachable-code] detect = 0; ^ 1 warning generated. cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement bcftools/vcfgtcheck.c.pysam.c:1189:39: warning: code will never be executed [-Wunreachable-code] args->min_inter_err = strtod(optarg,&tmp); ^~~~~~ 1 warning generated. cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfhead.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcfview.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/vcmp.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c bcftools/version.c.pysam.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-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 -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcbcftools.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/HMM.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/abuf.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/bam2bcf.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/bam2bcf_indel.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/bam_sample.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/bcftools.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/bin.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/ccall.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/cols.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/consensus.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/convert.c.pysam.o build/temp.freebsd-13.0-RELEASE- p11-arm64-cpython-39/bcftools/csq.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/dist.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/em.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/extsort.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/filter.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/gvcf.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/hclust.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/kmin.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/main.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/mcall.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/mpileup.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/ploidy.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/prob1.c.pysam.o build/temp.freebs d-13.0-RELEASE-p11-arm64-cpython-39/bcftools! /regidx.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/reheader.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/smpl_ilist.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/str_finder.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/tabix.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/tsv2vcf.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfannotate.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfbuf.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfcall.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfcnv.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfconcat.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfconvert.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcffilter.c.pysam.o build /temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfgtcheck.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfhead.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfindex.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfisec.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfmerge.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfnorm.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfplugin.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfquery.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfroh.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfsom.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfsort.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcfstats.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11 -arm64-cpython-39/bcftools/vcfview.c.pysam.o! build/te! mp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/vcmp.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/bcftools/version.c.pysam.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcbcftools.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcbcftools.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcutils' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcutils.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/pysam_util.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcutils.o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/pysam_util.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcsamtools.cpython-39 -lcbcftools.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcutils.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcalignmentfile' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcalignmentfile.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcalignmentfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcalignmentfile.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcsamfile.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcsamfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcsamfile.cpython-39 .so -Wl,-rpath,$ORIGIN building 'pysam.libcalignedsegment' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcalignedsegment.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcalignedsegment.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.fre ebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcalignedsegment.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libctabix.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libctabix.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchts lib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libctabix.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcfaidx' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcfaidx.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcfaidx.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpyth on-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcfaidx.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcf' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcbcf.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcbcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython -39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcbcf.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcbgzf' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcbgzf.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcbgzf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpytho n-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcbgzf.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libctabixproxies' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libctabixproxies.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libctabixproxies.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm6 4-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libctabixproxies.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcvcf' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcvcf.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcvcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.9/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython -39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-cpython-39/pysam/libcvcf.cpython-39.so -Wl,-rpath,$ORIGIN conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.3 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.10 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.4 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.2 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.7 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.6 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.9 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.5 error: symbols defined in multiple extensions *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-pysam