From nobody Wed Jul 20 14:49:19 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 4Lnz9r0mLgz4XBsy for ; Wed, 20 Jul 2022 14:49:20 +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 4Lnz9q5t0pz3mR0; Wed, 20 Jul 2022 14:49:19 +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 4Lnz9q4xbKz12Qm; Wed, 20 Jul 2022 14:49:19 +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 26KEnJS3052333; Wed, 20 Jul 2022 14:49:19 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere1.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 26KEnJpn052328; Wed, 20 Jul 2022 14:49:19 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 20 Jul 2022 14:49:19 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202207201449.26KEnJpn052328@ampere1.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - 123arm64-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=1658328559; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=j2AaLXwJ5+CShDUObx699zaseyD/R1Vaz30lVb2yxpk=; b=ksQ+1Sy6nr6jTnPifIhDP8zY18cdSdc07hRQ9mRDFZx7o0cd7iJptpVizFj0STug5+dVo/ h/JSMqPBulsCekSudcZ6+Q4z8yA/kLw4yh4q2+xQHsTS4K/IIImFsV1xtjBmexqDymxpU2 VnLPSoaKRivdQso9Jc3Tst2BnHU+/dW6egcG2W3ON3MpWv9Bf5tx4iZ5hXSmruDRQYkE5y imOF+LPSyWFPdDuxTPJMYZlzr9b+MXCoN90uJy9tNNRyy12iKgRqp/G98D8FOslgrfPyiA NQhtzfIMl3aIKfypKeN7zebd/dHdbjLtqh96hd73goFQApNHALYUP9EbgHvt2A== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1658328559; a=rsa-sha256; cv=none; b=PBmWWY4HSqo6BQK3aaO8lmJAYHZh399a2jUVy0Wf7OZWqPcnVOOU1u60x6u8O26XK/kQqd GMVbfklkIvIzwfU+xZligb1FHUpRbC4emEOvoLa7K3Z7O/cLTlY/VtvmM1x8N16qQPsZyu ZChFG4RLzoCTozBCXIEpmbLhtq3mF22BnqBcR5qmN5tP3jTes/V0TEpVo87c3iB3ZKubbo C/4ecCOma3lXouQ1pKx9JkB004VtcF3wRMTGUPdQVQTMt18a3G7aWGOZaTH3KLvbOJ3hU4 hl69IBESGQm08SjeuZuKf1l3uHQerpaC8IaGbeFD9wVAhb9r5IHAb5NYzsdNKg== 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/123arm64-quarterly/339f635d7900/logs/py39-pysam-0.19.1.log Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=123arm64-quarterly&build=339f635d7900 Log: =>> Building biology/py-pysam build started at Wed Jul 20 14:43:55 UTC 2022 port directory: /usr/ports/biology/py-pysam package name: py39-pysam-0.19.1 building for: FreeBSD 123arm64-quarterly-job-09 12.3-RELEASE-p5 FreeBSD 12.3-RELEASE-p5 arm64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400063 Jail OSVERSION: 1203000 Job Id: 09 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1203000 UNAME_v=FreeBSD 12.3-RELEASE-p5 UNAME_r=12.3-RELEASE-p5 BLOCKSIZE=K MAIL=/var/mail/root 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/123arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/123arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=123arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/123arm64-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=freebsd12 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=12.3 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 10.0.1 (git@github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: aarch64-unknown-freebsd12.3 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.1 (git@github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: aarch64-unknown-freebsd12.3 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 10.0.1 (git@github.com:llvm/llvm-project.git llvmorg-10.0.1-0-gef32c611aa2) Target: aarch64-unknown-freebsd12.3 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.3-RELEASE-p5 OSREL=12.3 OSVERSION=1203000 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 [123arm64-quarterly-job-09] Installing pkg-1.18.3... [123arm64-quarterly-job-09] 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 [123arm64-quarterly-job-09] Installing gmake-4.3_2... [123arm64-quarterly-job-09] `-- Installing gettext-runtime-0.21... [123arm64-quarterly-job-09] | `-- Installing indexinfo-0.3.1... [123arm64-quarterly-job-09] | `-- Extracting indexinfo-0.3.1: .... done [123arm64-quarterly-job-09] `-- Extracting gettext-runtime-0.21: .......... done [123arm64-quarterly-job-09] 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 [123arm64-quarterly-job-09] Installing py39-cython-0.29.30_1... [123arm64-quarterly-job-09] `-- Installing py39-setuptools-62.1.0_1... [123arm64-quarterly-job-09] | `-- Installing python39-3.9.13... [123arm64-quarterly-job-09] | | `-- Installing libffi-3.4.2... [123arm64-quarterly-job-09] | | `-- Extracting libffi-3.4.2: .......... done [123arm64-quarterly-job-09] | | `-- Installing mpdecimal-2.5.1... [123arm64-quarterly-job-09] | | `-- Extracting mpdecimal-2.5.1: .......... done [123arm64-quarterly-job-09] | | `-- Installing readline-8.1.2... [123arm64-quarterly-job-09] | | `-- Extracting readline-8.1.2: .......... 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/htscodecs/htscodecs/rANS_static4x16pr.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/rANS_static4x16pr.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/htscodecs/htscodecs/rle.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/rle.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/htscodecs/htscodecs/tokenise_name3.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/tokenise_name3.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/kfunc.c -o build/temp.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-cpython-39/htslib/bcf_sr_sort.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/bgzf.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_codecs.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_decode.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_encode.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_external.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_index.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_io.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/cram_stats.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/mFILE.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/open_trace_file.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/pooled_ alloc.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/cram/string_alloc.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/errmod.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/faidx.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/header.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/hfile.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/hts.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/hts_expr.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/hts_os.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/arith_dynamic.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/fqzcomp_qual.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/htscodecs.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/pack.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/ht scodecs/rANS_static.o build/temp.freebsd-12.! 3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/rANS_static4x16pr.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/rle.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/htscodecs/htscodecs/tokenise_name3.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/kfunc.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/kstring.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/md5.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/multipart.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/probaln.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/realn.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/regidx.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/region.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/sam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/synced_bcf_reader.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39 /htslib/tbx.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/textutils.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/thread_pool.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/vcf.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/vcf_sweep.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/htslib/vcfutils.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/htslib_util.o build/temp.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libchtslib.cpython-39.s o -Wl,-rpath,$ORIGIN creating samtools/samtools_config_vars.h for 'pysam.libcsamtools' extension building 'pysam.libcsamtools' extension creating build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools creating build/temp.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamtools.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/amplicon_stats.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam2depth.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_addrprg.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_ampliconclip.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_aux.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_cat.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_color.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_consensus.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_fastq.c.pysam.o build/temp.free bsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_flags.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_import.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_index.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_lpileup.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_markdup.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_mate.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_md.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_plbuf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_plcmd.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_quickcheck.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_reheader.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_rmdup.c.pysam.o build/temp.freebsd-12.3-RELEASE -p5-arm64-cpython-39/samtools/bam_rmdupse.c.! pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_samples.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_sort.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_split.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bam_stat.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bamshuf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bamtk.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bedcov.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/bedidx.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/consensus_pileup.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/coverage.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/cut_target.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/dict.c.pysam.o build/temp.freebsd-12.3-REL EASE-p5-arm64-cpython-39/samtools/faidx.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/lz4/lz4.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/padding.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/phase.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sam_opts.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sam_utils.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sam_view.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/sample.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/samtools.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/stats.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/stats_isize.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/samtools/tmp_file.c.pysam.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/p orts/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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamtools.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcbcftools' extension creating build/temp.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-cpython-39/bcftools/HMM.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/abuf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bam2bcf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bam2bcf_indel.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bam_sample.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bcftools.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/bin.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/ccall.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/cols.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/consensus.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/convert.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cp ython-39/bcftools/csq.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/dist.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/em.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/extsort.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/filter.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/gvcf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/hclust.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/kmin.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/main.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/mcall.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/mpileup.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/ploidy.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/prob1.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64- cpython-39/bcftools/regidx.c.pysam.o build/t! emp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/reheader.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/smpl_ilist.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/str_finder.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/tabix.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/tsv2vcf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfannotate.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfbuf.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfcall.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfcnv.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfconcat.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfconvert.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcffilter.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-c python-39/bcftools/vcfgtcheck.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfhead.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfindex.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfisec.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfmerge.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfnorm.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfplugin.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfquery.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfroh.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfsom.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfsort.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfstats.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/vcfview.c.pysam.o build /temp.freebsd-12.3-RELEASE-p5-arm64-cpython-! 39/bcftoo! ls/vcmp.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/bcftools/version.c.pysam.o build/temp.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcutils.o build/temp.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcalignmentfile.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libcsamfile' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libcsamfile.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libcsamfile.cpython-39.so -Wl,- rpath,$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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3 -RELEASE-p5-arm64-cpython-39/pysam/libcalignedsegment.cpython-39.so -Wl,-rpath,$ORIGIN building 'pysam.libctabix' extension cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -I/usr/local/include/python3.9 -c pysam/libctabix.c -o build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libctabix.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1 -L/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.19.1/build/lib.freebsd-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpytho n-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam/libctabix.cpython-39.so -Wl,-rpath,$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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam - Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-3 9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-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-12.3-RELEASE-p5-arm64-3.9/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam - Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -Lbuild/lib.freebsd-12.3-RELEASE-p5-arm64-cpython-39/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-39 -lcutils.cpython-39 -o build/lib.freebsd-12.3-RELEASE-p5-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.7 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.5 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.4 error: symbols defined in multiple extensions *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-pysam