[package - main-amd64-default][science/py-openbabel] Failed for py39-openbabel-3.1.1.1 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Tue, 25 Jul 2023 21:14:25 UTC
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--
=======================<phase: check-sanity >============================
===> License GPLv2+ accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> 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
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2+ accepted by the user
===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building
===========================================================================
=======================<phase: checksum >============================
===> 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.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> 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.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py39-openbabel-3.1.1.1
===========================================================================
=======================<phase: build-depends >============================
===> 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
<snip>
^
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<Type>::from(new Type(val), 1);
^
openbabel/openbabel-python_wrap.cpp:4094:31: note: in instantiation of member function 'swig::traits_from<OpenBabel::OBBond>::from' requested here
return traits_from<Type>::from(val);
^
openbabel/openbabel-python_wrap.cpp:4662:20: note: in instantiation of function template specialization 'swig::from<OpenBabel::OBBond>' requested here
return swig::from(v);
^
openbabel/openbabel-python_wrap.cpp:4749:9: note: in instantiation of member function 'swig::from_oper<OpenBabel::OBBond>::operator()' requested here
return from(static_cast<const value_type&>(*(base::current)));
^
openbabel/openbabel-python_wrap.cpp:4788:5: note: in instantiation of member function 'swig::SwigPyForwardIteratorClosed_T<std::__wrap_iter<OpenBabel::OBBond *>, 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<std::__wrap_iter<OpenBabel::OBBond *>, OpenBabel::OBBond>::SwigPyIteratorClosed_T' requested here
return new SwigPyIteratorClosed_T<OutIter>(current, begin, end, seq);
^
openbabel/openbabel-python_wrap.cpp:6408:20: note: in instantiation of function template specialization 'swig::make_output_iterator<std::__wrap_iter<OpenBabel::OBBond *>>' 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