From nobody Sat Nov 26 04:57:53 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 4NJzxs6LGVz4hPMT for ; Sat, 26 Nov 2022 04:57:53 +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 4NJzxs4SCNz470Y for ; Sat, 26 Nov 2022 04:57:53 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1669438673; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=YbtuIUEEHn6/0/3Hr8iJWE94Ddt6aecNDoM54213jiM=; b=a2XYJ6Z4lHemLwh6SmMLDOBGCH+sVVXkQtkPO38wFBHKyNW4JfaeeVrzpvr+Z2FWxLbHAT kig8uzGKI8EgY8IhrlvD49ggufJIzMI8t5+ealttppxJr0eXN4bZ2IDIq2VnbxlOZFgYUI 2uXT4XgLNL/jgqANqXO2QVfhB23UHcDonsepkHcrP8mGkyNi8WVkO19CImDnKfa3doQRSf JcL4gUMs8yV77RtrYUA1BMsa4SifCCdiL2tUBc0hSRAPFOvx9EHVn44diw0AaETJSpdShl PGkzAMvb2s+zQBjUvKD90soGMGZS9JGrMwkig8cg9OOTKu05nyp3lgAw8Cy2AA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1669438673; a=rsa-sha256; cv=none; b=DumtXXoff7FW2+1bHHNwyD41Fh3Nvh3LEhAg2+F6QahdSFNR+jHfMX9eZ5Qo+TzEPi+utI ptZB+XB40LPLrA4f1hQmKthJr3KIaxotNahWLSIqzBWYSh+KkYpZko88suiErVJrFe8cXS /pE+KYe71S8XBLBXCH6pFLvfTe+zda+CLs08Y44ID5mQlR0AiKzJFrXDtn1McJKS5nzIrF Ycq53pVF+oTtJv43/FAr4zmxYr/F8D3d7g6Upnk0LAvgfD2Hc03GqtQEC3I50kFjScqmCf wt5k0dTYbIahu+fR3QSy0SbFLOemgDIJ6bsl6AATHzqUsGPDC5PYBaB4Woiing== Received: from ampere2.nyi.freebsd.org (ampere2.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:24]) (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 4NJzxs3V94z16xf for ; Sat, 26 Nov 2022 04:57:53 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere2.nyi.freebsd.org (localhost [127.0.0.1]) by ampere2.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 2AQ4vrU4045822 for ; Sat, 26 Nov 2022 04:57:53 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere2.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 2AQ4vrfT045821; Sat, 26 Nov 2022 04:57:53 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 26 Nov 2022 04:57:53 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202211260457.2AQ4vrfT045821@ampere2.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - main-armv7-default][biology/py-pysam] Failed for py39-pysam-0.20.0 in build 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: https://pkg-status.freebsd.org/ampere2/data/main-armv7-default/pf323e9d40f68_s41be508d31/logs/py39-pysam-0.20.0.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=pf323e9d40f68_s41be508d31 Log: =>> Building biology/py-pysam build started at Sat Nov 26 04:55:37 UTC 2022 port directory: /usr/ports/biology/py-pysam package name: py39-pysam-0.20.0 building for: FreeBSD main-armv7-default-job-01 14.0-CURRENT FreeBSD 14.0-CURRENT 1400073 arm maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1400073 Job Id: 01 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400073 UNAME_v=FreeBSD 14.0-CURRENT 1400073 UNAME_r=14.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/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/local/share/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/local/share/pkgconfig:/usr/libdata/pkgconfig 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 -fPIC -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fPIC -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=freebsd14 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=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/pysam" EXAMPLESDIR="share/examples/pysam" DATADIR="share/pysam" WWWDIR="www/pysam" ETCDIR="etc/pysam" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pysam DOCSDIR=/usr/local/share/doc/pysam EXAMPLESDIR=/usr/local/share/examples/pysam WWWDIR=/usr/local/www/pysam ETCDIR=/usr/local/etc/pysam --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv7-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv7-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--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_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv7-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400073 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-0.20.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.18.4.pkg [main-armv7-default-job-01] Installing pkg-1.18.4... [main-armv7-default-job-01] Extracting pkg-1.18.4: .......... done ===> py39-pysam-0.20.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-pysam-0.20.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by py39-pysam-0.20.0 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by py39-pysam-0.20.0 for building => SHA256 Checksum OK for pysam-0.20.0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by py39-pysam-0.20.0 for building ===> Extracting for py39-pysam-0.20.0 => SHA256 Checksum OK for pysam-0.20.0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for py39-pysam-0.20.0 ===> Applying FreeBSD patches for py39-pysam-0.20.0 from /usr/ports/biology/py-pysam/files =========================================================================== =================================================== ===> py39-pysam-0.20.0 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-armv7-default-job-01] Installing gmake-4.3_2... [main-armv7-default-job-01] `-- Installing gettext-runtime-0.21... [main-armv7-default-job-01] | `-- Installing indexinfo-0.3.1... [main-armv7-default-job-01] | `-- Extracting indexinfo-0.3.1: .... done [main-armv7-default-job-01] `-- Extracting gettext-runtime-0.21: .......... done [main-armv7-default-job-01] Extracting gmake-4.3_2: .......... done ===> py39-pysam-0.20.0 depends on package: gmake>=4.3 - found ===> Returning to build of py39-pysam-0.20.0 ===> py39-pysam-0.20.0 depends on executable: cython-3.9 - not found ===> Installing existing package /packages/All/py39-cython-0.29.32.pkg [main-armv7-default-job-01] Installing py39-cython-0.29.32... [main-armv7-default-job-01] `-- Installing py39-setuptools-63.1.0... [main-armv7-default-job-01] | `-- Installing python39-3.9.15_1... cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o textutils.o textutils.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o thread_pool.o thread_pool.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcf.o vcf.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o vcfutils.o vcfutils.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_codecs.o cram/cram_codecs.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_decode.o cram/cram_decode.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_encode.o cram/cram_encode.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_external.o cram/cram_external.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_index.o cram/cram_index.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_io.o cram/cram_io.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/cram_stats.o cram/cram_stats.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/mFILE.o cram/mFILE.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/open_trace_file.o cram/open_trace_file.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/pooled_alloc.o cram/pooled_alloc.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o cram/string_alloc.o cram/string_alloc.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c cc -Wall -O2 -pipe -fPIC -fstack-protector-strong -fno-strict-aliasing -fvisibility=hidden -I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement -c -o htscodecs/htscodecs/rANS_static32x16pr_neon.o htscodecs/htscodecs/rANS_static32x16pr_neon.c htscodecs/htscodecs/rANS_static32x16pr_neon.c:199:31: warning: implicit declaration of function 'vtrn1q_u32' is invalid in C99 [-Wimplicit-function-declaration] uint32x4_t A1_1 = vtrn1q_u32(A_1, B_1); ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:199:24: error: initializing 'uint32x4_t' (vector of 4 'uint32_t' values) with an expression of incompatible type 'int' uint32x4_t A1_1 = vtrn1q_u32(A_1, B_1); ^ ~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:200:24: error: initializing 'uint32x4_t' (vector of 4 'uint32_t' values) with an expression of incompatible type 'int' uint32x4_t C1_1 = vtrn1q_u32(C_1, D_1); ^ ~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:201:31: warning: implicit declaration of function 'vtrn2q_u32' is invalid in C99 [-Wimplicit-function-declaration] uint32x4_t A2_1 = vtrn2q_u32(A_1, B_1); ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:201:24: error: initializing 'uint32x4_t' (vector of 4 'uint32_t' values) with an expression of incompatible type 'int' uint32x4_t A2_1 = vtrn2q_u32(A_1, B_1); ^ ~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:202:24: error: initializing 'uint32x4_t' (vector of 4 'uint32_t' values) with an expression of incompatible type 'int' uint32x4_t C2_1 = vtrn2q_u32(C_1, D_1); ^ ~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:206:39: warning: implicit declaration of function 'vtrn1q_u64' is invalid in C99 [-Wimplicit-function-declaration] uint32x4_t Xmaxv1=u32_u64(vtrn1q_u64(u64_u32(A1_1),u64_u32(C1_1))); ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:206:31: error: passing 'int' to parameter of incompatible type 'uint64x2_t' (vector of 2 'uint64_t' values) uint32x4_t Xmaxv1=u32_u64(vtrn1q_u64(u64_u32(A1_1),u64_u32(C1_1))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:204:42: note: expanded from macro 'u32_u64' #define u32_u64(x) vreinterpretq_u32_u64((x)) ^~~ /usr/lib/clang/14.0.5/include/arm_neon.h:32801:50: note: passing argument to parameter '__p0' here __ai uint32x4_t vreinterpretq_u32_u64(uint64x2_t __p0) { ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:207:39: warning: implicit declaration of function 'vtrn2q_u64' is invalid in C99 [-Wimplicit-function-declaration] uint32x4_t Biasv1=u32_u64(vtrn2q_u64(u64_u32(A1_1),u64_u32(C1_1))); ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:207:31: error: passing 'int' to parameter of incompatible type 'uint64x2_t' (vector of 2 'uint64_t' values) uint32x4_t Biasv1=u32_u64(vtrn2q_u64(u64_u32(A1_1),u64_u32(C1_1))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:204:42: note: expanded from macro 'u32_u64' #define u32_u64(x) vreinterpretq_u32_u64((x)) ^~~ /usr/lib/clang/14.0.5/include/arm_neon.h:32801:50: note: passing argument to parameter '__p0' here __ai uint32x4_t vreinterpretq_u32_u64(uint64x2_t __p0) { ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:208:31: error: passing 'int' to parameter of incompatible type 'uint64x2_t' (vector of 2 'uint64_t' values) uint32x4_t RFv1 =u32_u64(vtrn1q_u64(u64_u32(A2_1),u64_u32(C2_1))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:204:42: note: expanded from macro 'u32_u64' #define u32_u64(x) vreinterpretq_u32_u64((x)) ^~~ /usr/lib/clang/14.0.5/include/arm_neon.h:32801:50: note: passing argument to parameter '__p0' here __ai uint32x4_t vreinterpretq_u32_u64(uint64x2_t __p0) { ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:209:31: error: passing 'int' to parameter of incompatible type 'uint64x2_t' (vector of 2 'uint64_t' values) uint32x4_t FSv1 =u32_u64(vtrn2q_u64(u64_u32(A2_1),u64_u32(C2_1))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:204:42: note: expanded from macro 'u32_u64' #define u32_u64(x) vreinterpretq_u32_u64((x)) ^~~ /usr/lib/clang/14.0.5/include/arm_neon.h:32801:50: note: passing argument to parameter '__p0' here __ai uint32x4_t vreinterpretq_u32_u64(uint64x2_t __p0) { ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:216:24: error: initializing 'uint32x4_t' (vector of 4 'uint32_t' values) with an expression of incompatible type 'int' uint32x4_t A1_2 = vtrn1q_u32(A_2, B_2); ^ ~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:217:24: error: initializing 'uint32x4_t' (vector of 4 'uint32_t' values) with an expression of incompatible type 'int' uint32x4_t C1_2 = vtrn1q_u32(C_2, D_2); ^ ~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:218:24: error: initializing 'uint32x4_t' (vector of 4 'uint32_t' values) with an expression of incompatible type 'int' uint32x4_t A2_2 = vtrn2q_u32(A_2, B_2); ^ ~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:219:24: error: initializing 'uint32x4_t' (vector of 4 'uint32_t' values) with an expression of incompatible type 'int' uint32x4_t C2_2 = vtrn2q_u32(C_2, D_2); ^ ~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:221:31: error: passing 'int' to parameter of incompatible type 'uint64x2_t' (vector of 2 'uint64_t' values) uint32x4_t Xmaxv2=u32_u64(vtrn1q_u64(u64_u32(A1_2),u64_u32(C1_2))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:204:42: note: expanded from macro 'u32_u64' #define u32_u64(x) vreinterpretq_u32_u64((x)) ^~~ /usr/lib/clang/14.0.5/include/arm_neon.h:32801:50: note: passing argument to parameter '__p0' here __ai uint32x4_t vreinterpretq_u32_u64(uint64x2_t __p0) { ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:222:31: error: passing 'int' to parameter of incompatible type 'uint64x2_t' (vector of 2 'uint64_t' values) uint32x4_t Biasv2=u32_u64(vtrn2q_u64(u64_u32(A1_2),u64_u32(C1_2))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:204:42: note: expanded from macro 'u32_u64' #define u32_u64(x) vreinterpretq_u32_u64((x)) ^~~ /usr/lib/clang/14.0.5/include/arm_neon.h:32801:50: note: passing argument to parameter '__p0' here __ai uint32x4_t vreinterpretq_u32_u64(uint64x2_t __p0) { ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:223:31: error: passing 'int' to parameter of incompatible type 'uint64x2_t' (vector of 2 'uint64_t' values) uint32x4_t RFv2 =u32_u64(vtrn1q_u64(u64_u32(A2_2),u64_u32(C2_2))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:204:42: note: expanded from macro 'u32_u64' #define u32_u64(x) vreinterpretq_u32_u64((x)) ^~~ /usr/lib/clang/14.0.5/include/arm_neon.h:32801:50: note: passing argument to parameter '__p0' here __ai uint32x4_t vreinterpretq_u32_u64(uint64x2_t __p0) { ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:224:31: error: passing 'int' to parameter of incompatible type 'uint64x2_t' (vector of 2 'uint64_t' values) uint32x4_t FSv2 =u32_u64(vtrn2q_u64(u64_u32(A2_2),u64_u32(C2_2))); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:204:42: note: expanded from macro 'u32_u64' #define u32_u64(x) vreinterpretq_u32_u64((x)) ^~~ /usr/lib/clang/14.0.5/include/arm_neon.h:32801:50: note: passing argument to parameter '__p0' here __ai uint32x4_t vreinterpretq_u32_u64(uint64x2_t __p0) { ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:231:31: warning: implicit declaration of function 'vaddvq_u32' is invalid in C99 [-Wimplicit-function-declaration] uint32_t imask1 = vaddvq_u32(vandq_u32(Cv1, bit)); ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:236:21: warning: implicit declaration of function 'vqtbl1_u8' is invalid in C99 [-Wimplicit-function-declaration] norm1 = vqtbl1_u8(vreinterpretq_u8_u32(Rv1),vtab[imask1]); ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:236:19: error: assigning to 'uint8x8_t' (vector of 8 'uint8_t' values) from incompatible type 'int' norm1 = vqtbl1_u8(vreinterpretq_u8_u32(Rv1),vtab[imask1]); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:237:19: error: assigning to 'uint8x8_t' (vector of 8 'uint8_t' values) from incompatible type 'int' norm2 = vqtbl1_u8(vreinterpretq_u8_u32(Rv2),vtab[imask2]); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ htscodecs/htscodecs/rANS_static32x16pr_neon.c:263:31: warning: implicit declaration of function 'vmull_high_u32' is invalid in C99 [-Wimplicit-function-declaration] uint64x2_t qvh1 = vmull_high_u32(Rv1, RFv1); ^ htscodecs/htscodecs/rANS_static32x16pr_neon.c:263:24: error: initializing 'uint64x2_t' (vector of 2 'uint64_t' values) with an expression of incompatible type 'int' uint64x2_t qvh1 = vmull_high_u32(Rv1, RFv1); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ fatal error: too many errors emitted, stopping now [-ferror-limit=] 7 warnings and 20 errors generated. make[1]: *** [Makefile:173: htscodecs/htscodecs/rANS_static32x16pr_neon.o] Error 1 make[1]: Leaving directory '/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.20.0/htslib' Traceback (most recent call last): File "", line 1, in File "setup.py", line 631, in dist = setup(**metadata) File "/usr/local/lib/python3.9/site-packages/setuptools/__init__.py", line 87, in setup return distutils.core.setup(**attrs) File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 177, in setup return run_commands(dist) File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 193, in run_commands dist.run_commands() File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 968, in run_commands self.run_command(cmd) File "/usr/local/lib/python3.9/site-packages/setuptools/dist.py", line 1217, in run_command super().run_command(command) File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 987, in run_command cmd_obj.run() File "setup.py", line 258, in run build.run(self) File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 131, in run self.run_command(cmd_name) File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 317, in run_command self.distribution.run_command(command) File "/usr/local/lib/python3.9/site-packages/setuptools/dist.py", line 1217, in run_command super().run_command(command) File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 987, in run_command cmd_obj.run() File "/usr/local/lib/python3.9/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run _build_ext.build_ext.run(self) File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 339, in run self.build_extensions() File "/usr/local/lib/python3.9/site-packages/Cython/Distutils/old_build_ext.py", line 195, in build_extensions _build_ext.build_ext.build_extensions(self) File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 459, in build_extensions self._build_extensions_serial() File "/usr/local/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 485, in _build_extensions_serial self.build_extension(ext) File "/wrkdirs/usr/ports/biology/py-pysam/work-py39/pysam-0.20.0/cy_build.py", line 88, in build_extension ext._prebuild_func(ext, self.force) File "setup.py", line 516, in prebuild_libchtslib run_make(["ALL_CPPFLAGS=-I. " + args + " $(CPPFLAGS)", "lib-static"]) File "setup.py", line 75, in run_make subprocess.check_call([os.environ.get("MAKE", "make")] + targets) File "/usr/local/lib/python3.9/subprocess.py", line 373, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['make', 'ALL_CPPFLAGS=-I. -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement $(CPPFLAGS)', 'lib-static']' returned non-zero exit status 2. *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-pysam