From nobody Tue May 03 07:09:24 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 92AD41AA83ED for ; Tue, 3 May 2022 07:09:24 +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 4Ksrg81TZjz3R0Z; Tue, 3 May 2022 07:09:24 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere3.nyi.freebsd.org (ampere3.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:26]) (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 115CD19DD4; Tue, 3 May 2022 07:09:24 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere3.nyi.freebsd.org (localhost [127.0.0.1]) by ampere3.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 24379O52011316; Tue, 3 May 2022 07:09:24 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere3.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 24379OgJ011315; Tue, 3 May 2022 07:09:24 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 3 May 2022 07:09:24 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202205030709.24379OgJ011315@ampere3.nyi.freebsd.org> To: yuri@FreeBSD.org Subject: [package - 130arm64-default][biology/py-pysam] Failed for py38-pysam-0.19.0 in build Cc: pkg-fallout@FreeBSD.org ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1651561764; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=sObYdyBF8ofBcjXHqvXVSkSgY7ROTJcVpqMTpddPDUQ=; b=pOZTaaezVJ4fIQJQtluEwal62yTpaORCbYAUUk89RQJQtlevuFzoqGG3Dl09M7qBfj1/XK eWXdoV5P1nQXZfXdYmvQ7N22vdYjUYRT6KQ+hJBImHVKiE+Njd3ZhcLjWjG0+zQlGVMpzm SmF45JIkKBsLxsG7J1TaJ0XhTgXO4nP4+DlYnho3P4Y2Kelqv6QKKFb5wYqQMYMWrIPUyg WWWtoRu0dr2Iavwb8p94A3DrqL7mvVwKG+5Mjv2yaaoOt3BTz1WbOW4WMikYSCo1nGUfvQ zb3U3o05/pV1XxY6Q02wmP8Wv26K+0usPE5MIY53pP8Hd4fDF8OpInYIwlbe0Q== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1651561764; a=rsa-sha256; cv=none; b=GZJH1RMTSL40AakupdvF2JVBr+1BQpsVbmsJS97KUN3yU7r1BPU5SWYnQJdgALgcGfeIYH DakR30ZD9q7K9pRp11VSLNnO2qLyA+2MrmVsq7Xi12cTKEsBec1NuuHkCGeWL4GzS7Api4 JOLcMGGh3gVXiuUNiFzDcHuBQ5qzY7v5nBenEWyesPoQHVWYlY8TDusUnuM0BcVnigBZ4D C/fnaD3nrvrwb+vz2I9sHcbvbGDBOrjtrMVDvuwA3xCeM0f+HyaZJsofkMb6avSw5js9Rx G2UVSqdFxLSWoZUvLhalghgRpqVA+f+aMf+5zAzqPc6fsgLwrif73b5y01Z+Qw== 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://ampere3.nyi.freebsd.org/data/130arm64-default/b1ba4eb5d03e/logs/py38-pysam-0.19.0.log Build URL: http://ampere3.nyi.freebsd.org/build.html?mastername=130arm64-default&build=b1ba4eb5d03e Log: =>> Building biology/py-pysam build started at Tue May 3 07:03:43 UTC 2022 port directory: /usr/ports/biology/py-pysam package name: py38-pysam-0.19.0 building for: FreeBSD 130arm64-default-job-11 13.0-RELEASE-p11 FreeBSD 13.0-RELEASE-p11 arm64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400050 Jail OSVERSION: 1300139 Job Id: 11 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300139 UNAME_v=FreeBSD 13.0-RELEASE-p11 UNAME_r=13.0-RELEASE-p11 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/130arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/130arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=130arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/130arm64-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=py38 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py38 ---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/python3.8" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py38 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py38 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py38/.cache HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py38 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pysam/work-py38/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py38 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py38 XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py38/.cache HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py38 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pysam/work-py38/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin 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/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/pysam" EXAMPLESDIR="share/examples/pysam" DATADIR="share/pysam" WWWDIR="www/pysam" ETCDIR="etc/pysam" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pysam DOCSDIR=/usr/local/share/doc/pysam EXAMPLESDIR=/usr/local/share/examples/pysam WWWDIR=/usr/local/www/pysam ETCDIR=/usr/local/etc/pysam --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: aarch64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=13.0-RELEASE-p11 OSREL=13.0 OSVERSION=1300139 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License MIT accepted by the user =========================================================================== =================================================== ===> py38-pysam-0.19.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5_1.pkg [130arm64-default-job-11] Installing pkg-1.17.5_1... [130arm64-default-job-11] Extracting pkg-1.17.5_1: .......... done ===> py38-pysam-0.19.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py38-pysam-0.19.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by py38-pysam-0.19.0 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by py38-pysam-0.19.0 for building => SHA256 Checksum OK for pysam-0.19.0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by py38-pysam-0.19.0 for building ===> Extracting for py38-pysam-0.19.0 => SHA256 Checksum OK for pysam-0.19.0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for py38-pysam-0.19.0 ===> Applying FreeBSD patches for py38-pysam-0.19.0 from /usr/ports/biology/py-pysam/files =========================================================================== =================================================== ===> py38-pysam-0.19.0 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [130arm64-default-job-11] Installing gmake-4.3_2... [130arm64-default-job-11] `-- Installing gettext-runtime-0.21... [130arm64-default-job-11] | `-- Installing indexinfo-0.3.1... [130arm64-default-job-11] | `-- Extracting indexinfo-0.3.1: .... done [130arm64-default-job-11] `-- Extracting gettext-runtime-0.21: .......... done [130arm64-default-job-11] Extracting gmake-4.3_2: .......... done ===> py38-pysam-0.19.0 depends on package: gmake>=4.3 - found ===> Returning to build of py38-pysam-0.19.0 ===> py38-pysam-0.19.0 depends on executable: cython-3.8 - not found ===> Installing existing package /packages/All/py38-cython-0.29.28.pkg [130arm64-default-job-11] Installing py38-cython-0.29.28... [130arm64-default-job-11] `-- Installing py38-setuptools-57.0.0... [130arm64-default-job-11] | `-- Installing python38-3.8.13_1... [130arm64-default-job-11] | | `-- Installing libffi-3.3_1... [130arm64-default-job-11] | | `-- Extracting libffi-3.3_1: .......... done [130arm64-default-job-11] | | `-- Installing mpdecimal-2.5.1... [130arm64-default-job-11] | | `-- Extracting mpdecimal-2.5.1: .......... done cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0 -I/usr/local/include/python3.8 -c pysam/libctabixproxies.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libctabixproxies.c:17429:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:17554:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:17671:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:17869:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:17971:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:18076:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:18219:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:18364:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:18497:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:18614:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:18710:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:18806:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:18902:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:23405:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libctabixproxies.c:25736:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 15 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam/libctabixproxies.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0 -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysa m -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-38 -lcutils.cpython-38 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam/libctabixproxies.cpython-38.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-py38/pysam-0.19.0/htslib -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -I/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0 -I/usr/local/include/python3.8 -c pysam/libcvcf.c -o build/temp.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libcvcf.c:31888:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libcvcf.c:32010:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libcvcf.c:32135:3: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, /*tp_print*/ ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libcvcf.c:38536:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ pysam/libcvcf.c:40465:5: warning: 'tp_print' is deprecated [-Wdeprecated-declarations] 0, ^ /usr/local/include/python3.8/cpython/object.h:260:5: note: 'tp_print' has been explicitly marked deprecated here Py_DEPRECATED(3.8) int (*tp_print)(PyObject *, FILE *, int); ^ /usr/local/include/python3.8/pyport.h:515:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 5 warnings generated. cc -shared -fstack-protector-strong -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam/libcvcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/pysam -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0 -L/wrkdirs/usr/ports/biology/py-pysam/work-py38/pysam-0.19.0/build/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild /lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -Lbuild/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-38 -lcutils.cpython-38 -o build/lib.freebsd-13.0-RELEASE-p11-arm64-3.8/pysam/libcvcf.cpython-38.so -Wl,-rpath,$ORIGIN 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.10 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.9 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.2 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.7 conflicting symbol (libchtslib libcsamtools libcbcftools libcutils libcalignmentfile libcsamfile libcalignedsegment libctabix libcfaidx libcbcf libcbgzf libctabixproxies libcvcf): $d.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.4 error: symbols defined in multiple extensions *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-pysam