From nobody Tue Jul 25 21:14:25 2023 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 4R9VCQ05fTz4nw0Q for ; Tue, 25 Jul 2023 21:14:26 +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 4R9VCP4mfmz3y5G for ; Tue, 25 Jul 2023 21:14:25 +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=1690319665; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=5vfkwbx1Hb+A2GEj7MmkOxgayqjx0uFjNHko9OthyW8=; b=tgirz0ipC61Fqz4YN3Wg3DczqpzyqxITks/BS+muaz1N09pjB03Cj9fQn9euAAqtd99I/N dcYbh31vHqGhKT8HNjJ9EmsrBdbbAvCKcSbscFePzIsQV9TcvMhyYNUXK85nRGqN4+lVvE h/N+JeEth6NF+JvlrMNSjBCMMKidHLyxlbzn7vKxvSdH0UuqfSJujrzn8EN+j/3AIx/1pj zkq1JynMbEGmxyRciK8e0io3zd3hL5rS0toL2Bb5w1SlPDMj9j46G05lLrdsUeAxnyXGzS ND8QhRJlfMOm1K8JRA4JUvMC9H0yW8qMXPUYko4GkV3JelTOzzpR1OMG9xGbMw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1690319665; a=rsa-sha256; cv=none; b=gX/UGPzlZJ3DNo0suvAM6Bphn0sArplfX5j4ZlYZ1RVrvu2bCGK2/0Oia2BhMLE6Q8LOwB 0Sq+3d3CGNrXl1M0BWdrLLjc+c1/h1QXj46UGvWvUeEhCsJpHG2ZkW4UZhoSHcqMXHRnmi EKPqus4PF8sP3ZGYbqZVBZOykFMzq0EdrZb41ebhIAhYXh0fecHDQBaIzbBc9F/xrm4kff bcJOigDVC7NRLLQQQXP/v1Rp9qgDO1MBpCAJ1Uy08jWpJGQSpVhjmapF/7iNVKMX2PfsLu ckou3RvK6od5//WoAMT/kibEXb0TbWRE0jGdNqwkbePklY1SOfS5BwjgDCCCZw== Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:21]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4R9VCP0Q7rzGVy for ; Tue, 25 Jul 2023 21:14:25 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 1b45 by beefy18.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy18.nyi.freebsd.org); Tue, 25 Jul 2023 21:14:25 +0000 To: yuri@FreeBSD.org Subject: [package - main-amd64-default][science/py-openbabel] Failed for py39-openbabel-3.1.1.1 in build Cc: pkg-fallout@FreeBSD.org Date: Tue, 25 Jul 2023 21:14:25 +0000 Message-Id: <64c03b31.1b45.37cb0c01@beefy18.nyi.freebsd.org> From: 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/beefy18/data/main-amd64-default/p629834653cee_s789df254cc/logs/py39-openbabel-3.1.1.1.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p629834653cee_s789df254cc Log: =>> Building science/py-openbabel build started at Tue Jul 25 21:13:50 UTC 2023 port directory: /usr/ports/science/py-openbabel package name: py39-openbabel-3.1.1.1 building for: FreeBSD main-amd64-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 amd64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1400093 Job Id: 10 !!! Jail is newer than host. (Jail: 1400093, Host: 1400089) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400093 UNAME_v=FreeBSD 14.0-CURRENT 1400093 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-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-amd64-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-- PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/science/py-openbabel/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-openbabel/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-openbabel/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-openbabel/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-openbabel/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-openbabel/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/science/py-openbabel/work-py39 XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/py-openbabel/work-py39 XDG_CACHE_HOME=/wrkdirs/usr/ports/science/py-openbabel/work-py39/.cache HOME=/wrkdirs/usr/ports/science/py-openbabel/work-py39 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/py-openbabel/work-py39/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/py-openbabel/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 -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_INSTA LL_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/openbabel" EXAMPLESDIR="share/examples/openbabel" DATADIR="share/openbabel" WWWDIR="www/openbabel" ETCDIR="etc/openbabel" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/openbabel DOCSDIR=/usr/local/share/doc/openbabel EXAMPLESDIR=/usr/local/share/examples/openbabel WWWDIR=/usr/local/www/openbabel ETCDIR=/usr/local/etc/openbabel --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 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd14.0 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 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400093 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES 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) 33554432 stack size (kbytes, -s) 524288 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 GPLv2+ accepted by the user =========================================================================== =================================================== ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [main-amd64-default-job-10] Installing pkg-1.20.4... [main-amd64-default-job-10] Extracting pkg-1.20.4: .......... done ===> py39-openbabel-3.1.1.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py39-openbabel-3.1.1.1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building =========================================================================== =================================================== ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building => SHA256 Checksum OK for openbabel-3.1.1.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building ===> Extracting for py39-openbabel-3.1.1.1 => SHA256 Checksum OK for openbabel-3.1.1.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for py39-openbabel-3.1.1.1 =========================================================================== =================================================== ===> py39-openbabel-3.1.1.1 depends on executable: swig - not found ===> Installing existing package /packages/All/swig-4.1.1.pkg [main-amd64-default-job-10] Installing swig-4.1.1... [main-amd64-default-job-10] `-- Installing pcre2-10.42... [main-amd64-default-job-10] `-- Extracting pcre2-10.42: .......... done ^ openbabel/openbabel-python_wrap.cpp:36417:77: warning: 'LineSearch' is deprecated: Current code should use LineSearch(double *, double*) instead. [-Wdeprecated-declarations] arg3 = reinterpret_cast< OpenBabel::vector3 * >(argp3); result = (arg1)->LineSearch(arg2,*arg3); ^ /usr/local/include/openbabel3/openbabel/forcefield.h:1222:5: note: 'LineSearch' has been explicitly marked deprecated here OB_DEPRECATED_MSG("Current code should use LineSearch(double *, double*) instead.") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ openbabel/openbabel-python_wrap.cpp:37025:45: warning: 'VectorLengthDerivative' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorLengthDerivative(*arg1,*arg2); ^ /usr/local/include/openbabel3/openbabel/forcefield.h:1523:5: note: 'VectorLengthDerivative' has been explicitly marked deprecated here OB_DEPRECATED ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED' #define OB_DEPRECATED [[deprecated]] ^ openbabel/openbabel-python_wrap.cpp:37071:45: warning: 'VectorAngleDerivative' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorAngleDerivative(*arg1,*arg2,*arg3); ^ /usr/local/include/openbabel3/openbabel/forcefield.h:1539:5: note: 'VectorAngleDerivative' has been explicitly marked deprecated here OB_DEPRECATED ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED' #define OB_DEPRECATED [[deprecated]] ^ openbabel/openbabel-python_wrap.cpp:37141:45: warning: 'VectorOOPDerivative' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorOOPDerivative(*arg1,*arg2,*arg3,*arg4); ^ /usr/local/include/openbabel3/openbabel/forcefield.h:1556:5: note: 'VectorOOPDerivative' has been explicitly marked deprecated here OB_DEPRECATED ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED' #define OB_DEPRECATED [[deprecated]] ^ openbabel/openbabel-python_wrap.cpp:37211:45: warning: 'VectorTorsionDerivative' is deprecated [-Wdeprecated-declarations] result = (double)OpenBabel::OBForceField::VectorTorsionDerivative(*arg1,*arg2,*arg3,*arg4); ^ /usr/local/include/openbabel3/openbabel/forcefield.h:1572:5: note: 'VectorTorsionDerivative' has been explicitly marked deprecated here OB_DEPRECATED ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED' #define OB_DEPRECATED [[deprecated]] ^ openbabel/openbabel-python_wrap.cpp:40899:47: warning: 'SetDelta' is deprecated: Has no effect. [-Wdeprecated-declarations] arg2 = static_cast< double >(val2); (arg1)->SetDelta(arg2); resultobj = SWIG_Py_Void(); return resultobj; fail: return NULL; } ^ /usr/local/include/openbabel3/openbabel/rotor.h:428:5: note: 'SetDelta' has been explicitly marked deprecated here OB_DEPRECATED_MSG("Has no effect.") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ openbabel/openbabel-python_wrap.cpp:40905:85: warning: 'GetDelta' is deprecated: Has no effect. [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (double)(arg1)->GetDelta(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:431:5: note: 'GetDelta' has been explicitly marked deprecated here OB_DEPRECATED_MSG("Has no effect.") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ openbabel/openbabel-python_wrap.cpp:40912:102: warning: 'GetFixedAtoms' is deprecated [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (OpenBabel::OBBitVec *) &(arg1)->GetFixedAtoms(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:434:5: note: 'GetFixedAtoms' has been explicitly marked deprecated here OB_DEPRECATED ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED' #define OB_DEPRECATED [[deprecated]] ^ openbabel/openbabel-python_wrap.cpp:40926:69: warning: 'SetFixedAtoms' is deprecated: See SetFixedBonds [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetFixedAtoms(*arg2); resultobj = SWIG_Py_Void(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:437:5: note: 'SetFixedAtoms' has been explicitly marked deprecated here OB_DEPRECATED_MSG("See SetFixedBonds") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ openbabel/openbabel-python_wrap.cpp:40933:102: warning: 'GetEvalAtoms' is deprecated [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (OpenBabel::OBBitVec *) &(arg1)->GetEvalAtoms(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:440:5: note: 'GetEvalAtoms' has been explicitly marked deprecated here OB_DEPRECATED ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED' #define OB_DEPRECATED [[deprecated]] ^ openbabel/openbabel-python_wrap.cpp:40947:69: warning: 'SetEvalAtoms' is deprecated [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetEvalAtoms(*arg2); resultobj = SWIG_Py_Void(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:443:5: note: 'SetEvalAtoms' has been explicitly marked deprecated here OB_DEPRECATED ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED' #define OB_DEPRECATED [[deprecated]] ^ openbabel/openbabel-python_wrap.cpp:40954:85: warning: 'GetRotAtoms' is deprecated [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (void *)(arg1)->GetRotAtoms(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:446:5: note: 'GetRotAtoms' has been explicitly marked deprecated here OB_DEPRECATED ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED' #define OB_DEPRECATED [[deprecated]] ^ openbabel/openbabel-python_wrap.cpp:40962:72: warning: 'GetResolution' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations] result = (std::vector< double,std::allocator< double > > *) &(arg1)->GetResolution(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:449:5: note: 'GetResolution' has been explicitly marked deprecated here OB_DEPRECATED_MSG("See GetTorsionValues()") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ openbabel/openbabel-python_wrap.cpp:40973:46: warning: 'SetNumCoords' is deprecated [-Wdeprecated-declarations] arg2 = static_cast< int >(val2); (arg1)->SetNumCoords(arg2); resultobj = SWIG_Py_Void(); return resultobj; fail: ^ /usr/local/include/openbabel3/openbabel/rotor.h:452:5: note: 'SetNumCoords' has been explicitly marked deprecated here OB_DEPRECATED ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED' #define OB_DEPRECATED [[deprecated]] ^ openbabel/openbabel-python_wrap.cpp:41254:81: warning: 'IdentifyEvalAtoms' is deprecated: Not declared. Use Setup() for top-level functionality [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); result = (bool)(arg1)->IdentifyEvalAtoms(*arg2); ^ /usr/local/include/openbabel3/openbabel/rotor.h:627:5: note: 'IdentifyEvalAtoms' has been explicitly marked deprecated here OB_DEPRECATED_MSG("Not declared. Use Setup() for top-level functionality") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ openbabel/openbabel-python_wrap.cpp:41267:69: warning: 'SetFixAtoms' is deprecated: See SetFixedBonds() [-Wdeprecated-declarations] arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetFixAtoms(*arg2); resultobj = SWIG_Py_Void(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:633:5: note: 'SetFixAtoms' has been explicitly marked deprecated here OB_DEPRECATED_MSG("See SetFixedBonds()") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ openbabel/openbabel-python_wrap.cpp:41274:87: warning: 'HasFixedAtoms' is deprecated: See HasFixedBonds() [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotorList * >(argp1); result = (bool)(arg1)->HasFixedAtoms(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:643:5: note: 'HasFixedAtoms' has been explicitly marked deprecated here OB_DEPRECATED_MSG("See HasFixedBonds()") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ openbabel/openbabel-python_wrap.cpp:41281:72: warning: 'IgnoreSymmetryRemoval' is deprecated: Currently has no effect [-Wdeprecated-declarations] arg1 = reinterpret_cast< OpenBabel::OBRotorList * >(argp1); (arg1)->IgnoreSymmetryRemoval(); resultobj = SWIG_Py_Void(); ^ /usr/local/include/openbabel3/openbabel/rotor.h:650:5: note: 'IgnoreSymmetryRemoval' has been explicitly marked deprecated here OB_DEPRECATED_MSG("Currently has no effect") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ In file included from openbabel/openbabel-python_wrap.cpp:3415: /usr/local/include/openbabel3/openbabel/bond.h:58:15: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations] class OBAPI OBBond: public OBBase ^ openbabel/openbabel-python_wrap.cpp:4075:46: note: in implicit copy constructor for 'OpenBabel::OBBond' first required here return traits_from_ptr::from(new Type(val), 1); ^ openbabel/openbabel-python_wrap.cpp:4094:31: note: in instantiation of member function 'swig::traits_from::from' requested here return traits_from::from(val); ^ openbabel/openbabel-python_wrap.cpp:4662:20: note: in instantiation of function template specialization 'swig::from' requested here return swig::from(v); ^ openbabel/openbabel-python_wrap.cpp:4749:9: note: in instantiation of member function 'swig::from_oper::operator()' requested here return from(static_cast(*(base::current))); ^ openbabel/openbabel-python_wrap.cpp:4788:5: note: in instantiation of member function 'swig::SwigPyForwardIteratorClosed_T, OpenBabel::OBBond>::value' requested here SwigPyIteratorClosed_T(out_iterator curr, out_iterator first, out_iterator last, PyObject *seq) ^ openbabel/openbabel-python_wrap.cpp:4818:16: note: in instantiation of member function 'swig::SwigPyIteratorClosed_T, OpenBabel::OBBond>::SwigPyIteratorClosed_T' requested here return new SwigPyIteratorClosed_T(current, begin, end, seq); ^ openbabel/openbabel-python_wrap.cpp:6408:20: note: in instantiation of function template specialization 'swig::make_output_iterator>' requested here return swig::make_output_iterator(self->begin(), self->begin(), self->end(), *PYTHON_SELF); ^ /usr/local/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.") ^ /usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG' #define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]] ^ 36 warnings and 6 errors generated. error: command '/usr/bin/cc' failed with exit code 1 *** Error code 1 Stop. make: stopped in /usr/ports/science/py-openbabel