[package - 130i386-default][science/rdkit] Failed for rdkit-2021.09.4 in build
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Date: Tue, 18 Jan 2022 02:19:21 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: http://beefy15.nyi.freebsd.org/data/130i386-default/7201e24c4c91/logs/rdkit-2021.09.4.log
Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=130i386-default&build=7201e24c4c91
Log:
=>> Building science/rdkit
build started at Tue Jan 18 01:56:42 UTC 2022
port directory: /usr/ports/science/rdkit
package name: rdkit-2021.09.4
building for: FreeBSD 130i386-default-job-03 13.0-RELEASE-p6 FreeBSD 13.0-RELEASE-p6 i386
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> rdkit-2021.09.4 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.17.5.pkg
[130i386-default-job-03] Installing pkg-1.17.5...
[130i386-default-job-03] Extracting pkg-1.17.5: .......... done
===> rdkit-2021.09.4 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of rdkit-2021.09.4
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by rdkit-2021.09.4 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by rdkit-2021.09.4 for building
=> SHA256 Checksum OK for rdkit-2021.09.4/Comic_Neue.zip.
=> SHA256 Checksum OK for rdkit-2021.09.4/rdkit-rdkit-Release_2021_09_4_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2021.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by rdkit-2021.09.4 for building
===> Extracting for rdkit-2021.09.4
=> SHA256 Checksum OK for rdkit-2021.09.4/Comic_Neue.zip.
=> SHA256 Checksum OK for rdkit-2021.09.4/rdkit-rdkit-Release_2021_09_4_GH0.tar.gz.
=> SHA256 Checksum OK for rdkit-2021.09.4/rareylab-RingDecomposerLib-v1.1.3_rdkit_GH0.tar.gz.
Archive: /portdistfiles/rdkit-2021.09.4/Comic_Neue.zip
extracting: OFL.txt
extracting: ComicNeue-Light.ttf
extracting: ComicNeue-LightItalic.ttf
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===========================================================================
=======================<phase: patch-depends >============================
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=======================<phase: patch >============================
<snip>
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MACCS.cpp:13:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
1 warning generated.
[ 49% 297/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -
fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MHFP.cpp
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MHFP.cpp:26:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/MolOps.h:23:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/SanitException.h:16:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/GraphMol.h:19:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/ROMol.h:37:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
1 warning generated.
[ 49% 298/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -
fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:18:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/AtomPairGenerator.h:16:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintUtil.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
1 warning generated.
[ 50% 299/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -
fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:11:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
1 warning generated.
[ 50% 300/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -
fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MorganGenerator.cpp
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/MorganGenerator.cpp:11:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
1 warning generated.
[ 50% 301/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -
fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:12:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
1 warning generated.
[ 50% 302/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -
fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintUtil.cpp
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintUtil.cpp:11:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
1 warning generated.
[ 50% 303/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/usr/local/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -
fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:11:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:16:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/FingerprintUtil.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/RDKitBase.h:25:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Conformer.h:14:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Geometry/point.h:24:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/Numerics/Vector.h:15:
In file included from /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/RDGeneral/utils.h:18:
In file included from /usr/local/include/boost/random.hpp:36:
In file included from /usr/local/include/boost/random/additive_combine.hpp:27:
/usr/local/include/boost/random/linear_congruential.hpp:140:20: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if(_x <= 0 && _x != 0) {
~~~~~~~~^~~~~~~~~~
/usr/local/include/boost/random/linear_congruential.hpp:393:11: note: in instantiation of member function 'boost::random::linear_congruential_engine<unsigned long long, 25214903917, 11, 281474976710656>::seed' requested here
{ lcf.seed(cnv(x0)); }
^
1 warning generated.
[ 50% 304/598] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -shared -Wl,-soname,libRDKitFingerprints.so.1 -o lib/libRDKitFingerprints.so.1.2021.09.4 Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o Code/
GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib: lib/libRDKitSubgraphs.so.1.2021.09.4 lib/libRDKitSubstructMatch.so.1.2021.09.4 lib/libRDKitSmilesParse.so.1.2021.09.4 lib/libRDKitGraphMol.so.1.2021.09.4 lib/libRDKitRDGeometryLib.so.1.2021.09.4 lib/libRDKitDataStructs.so.1.2021.09.4 lib/libRDKitRingDecomposerLib.so.1.2021.09.4 lib/libRDKitRDGeneral.so.1.2021.09.4 -pthread -ldl && :
[ 51% 305/598] /usr/local/bin/cmake -E cmake_symlink_library lib/libRDKitFingerprints.so.1.2021.09.4 lib/libRDKitFingerprints.so.1 lib/libRDKitFingerprints.so && :
[ 51% 306/598] : && /usr/bin/c++ -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -pthread -shared -L/usr/local/lib -fstack-protector-strong -shared -o rdkit/Chem/rdMHFPFingerprint.so Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -Wl,-rpath,/wrkdirs/usr/ports/science/rdkit/work/.build/lib:/usr/local/lib: lib/libRDKitFingerprints.so.1.2021.09.4 lib/libRDKitRDBoost.so.1.2021.09.4 lib/libRDKitSubgraphs.so.1.2021.09.4 lib/libRDKitSubstructMatch.so.1.2021.09.4 lib/libRDKitSmilesParse.so.1.2021.09.4 lib/libRDKitGraphMol.so.1.2021.09.4 lib/libRDKitRDGeometryLib.so.1.2021.09.4 lib/libRDKitDataStructs.so.1.2021.09.4 lib/libRDKitRingDecomposerLib.so.1.2021.09.4 /usr/local/lib/libpython3.8.so /usr/local/lib/libboost_python38.
so lib/libRDKitRDGeneral.so.1.2021.09.4 -pthread -ldl && :
[ 51% 307/598] /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdFingerprintGenerator_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict
-aliasing -Wno-format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp
FAILED: Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o
/usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDK_USE_URF -DrdFingerprintGenerator_EXPORTS -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/RingFamilies/RingDecomposerLib/src/RingDecomposerLib -I/usr/local/include/python3.8 -I/usr/local/lib/python3.8/site-packages/numpy/core/include -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code -I/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/External/boost-numeric-bindings -isystem /usr/local/include -isystem /usr/local/include/eigen3 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -mpopcnt -Wall -Wextra -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wno-
format -Wno-logical-op-parentheses -fPIC -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -pthread -std=gnu++14 -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing]
npy_intp size[1] = {ebv->size()};
^~~~~~~~~~~
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: note: insert an explicit cast to silence this issue
npy_intp size[1] = {ebv->size()};
^~~~~~~~~~~
static_cast<npy_intp>( )
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing]
npy_intp size[1] = {fp->size()};
^~~~~~~~~~
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: note: insert an explicit cast to silence this issue
npy_intp size[1] = {fp->size()};
^~~~~~~~~~
static_cast<npy_intp>( )
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing]
npy_intp size[1] = {fp->size()};
^~~~~~~~~~
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:479:12: note: in instantiation of function template specialization 'RDKit::FingerprintWrapper::getNumPyCountFingerprint<unsigned int>' requested here
getNumPyCountFingerprint<std::uint32_t>,
^
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: note: insert an explicit cast to silence this issue
npy_intp size[1] = {fp->size()};
^~~~~~~~~~
static_cast<npy_intp>( )
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing]
npy_intp size[1] = {ebv->size()};
^~~~~~~~~~~
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:526:37: note: in instantiation of function template specialization 'RDKit::FingerprintWrapper::getNumPyFingerprint<unsigned int>' requested here
.def("GetFingerprintAsNumPy", getNumPyFingerprint<std::uint32_t>,
^
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: note: insert an explicit cast to silence this issue
npy_intp size[1] = {ebv->size()};
^~~~~~~~~~~
static_cast<npy_intp>( )
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing]
npy_intp size[1] = {fp->size()};
^~~~~~~~~~
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:630:12: note: in instantiation of function template specialization 'RDKit::FingerprintWrapper::getNumPyCountFingerprint<unsigned long long>' requested here
getNumPyCountFingerprint<std::uint64_t>,
^
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:237:23: note: insert an explicit cast to silence this issue
npy_intp size[1] = {fp->size()};
^~~~~~~~~~
static_cast<npy_intp>( )
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: error: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list [-Wc++11-narrowing]
npy_intp size[1] = {ebv->size()};
^~~~~~~~~~~
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:677:37: note: in instantiation of function template specialization 'RDKit::FingerprintWrapper::getNumPyFingerprint<unsigned long long>' requested here
.def("GetFingerprintAsNumPy", getNumPyFingerprint<std::uint64_t>,
^
/wrkdirs/usr/ports/science/rdkit/work/rdkit-Release_2021_09_4/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:212:23: note: insert an explicit cast to silence this issue
npy_intp size[1] = {ebv->size()};
^~~~~~~~~~~
static_cast<npy_intp>( )
6 errors generated.
ninja: build stopped: subcommand failed.
*** Error code 1
Stop.
make: stopped in /usr/ports/science/rdkit